TY - JOUR TI - Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions for the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S.soli and S. suarezii. AU - Pikuta, E.V. AU - Lyu, Z. AU - Williams, M.D. AU - Patel, N.B. AU - Liu, Y. AU - Hoover, R.B. AU - Busse, H.J. AU - Lawson, P.A. AU - Whitman, W.B. T2 - International journal of systematic and evolutionary microbiology AB - A novel psychrotolerant bacterium, strain ISLP-3T, was isolated from a sample of naturally formed ice sculpture on the shore of Lake Podprudnoye in Antarctica. Cells were motile, stained Gram-positive, non-spore-forming, straight or slightly curved rods with the shape of a baseball bat. The new isolate was facultatively anaerobic and catalase-positive. Growth occurred at 3-35 °C with an optimum at 22-24 °C, 0-2 % (w/v) NaCl with an optimum at 0.3 % and pH 6.2-9.5 with an optimum at pH 7.5. Strain ISLP-3T grew on several carbon sources, with the best growth on cellobiose. The isolate possessed ureolytic activity but growth was inhibited by urea. The strain was sensitive to: ampicillin, gentamycin, kanamycin rifampicin, tetracycline and chloramphenicol. Major fatty acids were: anteiso-C15 : 0, iso-C16 : 0, C16 : 0, C14 : 0 and iso-C15 : 0. The predominant menaquinone was MK-9(H4). The genomic G+C content was 69.5 mol%. The 16S rRNA gene showed 99 % sequence similarity to that of Sanguibacter suarezii ST-26T, but their recA genes shared ≤91 % sequence similarity, suggesting that this new isolate represents a novel species within the genus Sanguibacter. This conclusion was supported by average nucleotide identity, which was ≤91 % to the most closely related strain. The name Sanguibacter gelidistatuariae sp. nov. is proposed for the novel species with the type strain ISLP-3T=ATCC TSD-17T=DSM 100501T=JCM 30887T). The complete genome draft sequence of ISLP-3T was deposited under IMG OID 2657245272. Emendments to the descriptions of related taxa have been made based on experimental data from our comparative analysis. DA - 2017/2// PY - 2017/2// DO - 10.1099/ijsem.0.001838 UR - http://europepmc.org/abstract/med/28150571 ER - TY - JOUR TI - Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase AU - Lyu, Zhe AU - Chou, Chau-wen AU - Shi, Hao AU - Patel, Ricky AU - Duin, Evert C. AU - Whitman, William B. AB - Abstract Catalyzing the key step for anaerobic methane production and oxidation, methyl-coenzyme M reductase or Mcr plays a key role in the global methane cycle. The McrA subunit possesses up to five post-translational modifications (PTM) at its active site. Bioinformatic analyses had previously suggested that methanogenesis marker protein 10 (Mmp10) could play an important role in methanogenesis. To examine its role, MMP1554, the gene encoding Mmp10 in Methanococcus maripaludis , was deleted with a new genetic tool, resulting in the specific loss of the 5-(S)-methylarginine PTM of residue 275 in the McrA subunit and a 40~60 % reduction in the maximal rates of methane formation by whole cells. Methylation was restored by complementations with the wild-type gene. However, the rates of methane formation of the complemented strains were not always restored to the wild type level. This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity. DA - 2017/10/30/ PY - 2017/10/30/ DO - 10.1101/211441 VL - 10 UR - https://doi.org/10.1101/211441 ER - TY - JOUR TI - An Important Role for Purifying Selection in Archaeal Genome Evolution AU - Lyu, Zhe AU - Li, Zhi-Gang AU - He, Fei AU - Zhang, Ziding T2 - mSystems AB - The evolution of genome complexities is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis of genetic drift, which showed relaxed purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes. DA - 2017/10// PY - 2017/10// DO - 10.1128/msystems.00112-17 VL - 2 IS - 5 SP - e00112-17 UR - https://doi.org/10.1128/mSystems.00112-17 ER - TY - JOUR TI - Williamwhitmania taraxaci gen. nov., sp. nov., a proteolytic anaerobe with a novel type of cytology from Lake Untersee in Antarctica, description of Williamwhitmaniaceae fam. nov., and emendation of the order Bacteroidales Krieg 2012. T2 - International journal of systematic and evolutionary microbiology AB - The proteolytic bacterium strain A7P-90mT was isolated from Lake Untersee, Antarctica. The anoxic water was collected from a perennially sealed (~100 millennia) glacial ice lake. Gram-stain-negative cells were 0.18-0.3×8.0-25.0 µm in size, straight, slender rods with unusual gliding motility by external, not previously reported, organelles named here as antiae. At the end of stationary phase of growth, spheroplasts were terminally formed and the cells resembled dandelions. After death, cells were helical. The isolate was an athalassic, strictly anaerobic and catalase-negative proteolytic chemoorganotroph. It was moderately psychrophilic with a temperature range for growth of 3-26 °C and an optimum at 22-23 °C. The pH range for growth was 5.5-7.8 with an optimum at 6.9. Major cellular fatty acids were branched pentadecanoic and tridecanoic acids, and saturated tetradecanoic acids. The quinone system comprised menaquinone MK-7. The strain was sensitive to all checked antibiotics and ascorbic acid. The G+C content of the genomic DNA was 42.6 mol%. Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order Bacteroidales and formed a novel family with the proposed name Williamwhitmaniaceae fam. nov. The description of the order Bacteroidales was emended accordingly. The name Williamwhitmania taraxaci gen. nov., sp. nov. is proposed for the new genus and novel species with the type strain A7P-90mT (=DSM 100563T=JCM 30888T). The complete draft genome sequence was deposited at the Joint Genomes Institute (JGI) under number IMG OID 2654588148 and in SRA listed as SRP088197. DA - 2017/9// PY - 2017/9// DO - 10.1099/ijsem.0.002266 VL - 9 UR - http://europepmc.org/abstract/med/28905708 ER - TY - JOUR TI - Developing Career Self Efficacy through Biotechnology Industry Practicum Projects AU - Nappo, M.K. AU - Hamilton, P.T. T2 - The Innovator DA - 2017/// PY - 2017/// VL - 10 IS - 3 SP - 19–23 ER - TY - JOUR TI - Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought. T2 - Plant, cell & environment AB - Abstract Drought stress is a major problem for agriculture worldwide, causing significant yield losses. Plants have developed highly flexible mechanisms to deal with drought, including organ‐ and developmental stage‐specific responses. In young leaves, growth is repressed as an active mechanism to save water and energy, increasing the chances of survival but decreasing yield. Despite its importance, the molecular basis for this growth inhibition is largely unknown. Here, we present a novel approach to explore early molecular mechanisms controlling Arabidopsis leaf growth inhibition following mild drought. We found that growth and transcriptome responses to drought are highly dynamic. Growth was only repressed by drought during the day, and our evidence suggests that this may be due to gating by the circadian clock. Similarly, time of day strongly affected the extent, specificity, and in certain cases even direction of drought‐induced changes in gene expression. These findings underscore the importance of taking into account diurnal patterns to understand stress responses, as only a small core of drought‐responsive genes are affected by drought at all times of the day. Finally, we leveraged our high‐resolution data to demonstrate that phenotypic and transcriptome responses can be matched to identify putative novel regulators of growth under mild drought. DA - 2017/2// PY - 2017/2// DO - 10.1111/pce.12809 VL - 2 UR - http://europepmc.org/abstract/med/27479938 KW - leaf growth regulation KW - mild drought response KW - time-course transcriptomics ER - TY - DATA TI - E-MTAB-6209 - The expression profiles of 30 transcription factors in 17 inducible gain-of-function lines after activation of overexpression, including 5 time points DA - 2017/// PY - 2017/// UR - https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6209 ER - TY - DATA TI - E-MTAB-6205 - The expression profiles of 31 transcription factors in wild-type Col-0 plants upon mild osmotic stress, including 10 time points and different leaf tissues DA - 2017/// PY - 2017/// UR - https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6205 ER - TY - JOUR TI - From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress AU - Broeck, Lisa Van AU - Dubois, Marieke AU - Vermeersch, Mattias AU - Storme, Veronique AU - Matsui, Minami AU - Inzé, Dirk T2 - Molecular Systems Biology AB - Article21 December 2017Open Access Source DataTransparent process From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress Lisa Van den Broeck Lisa Van den Broeck orcid.org/0000-0003-0226-0757 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Marieke Dubois Marieke Dubois orcid.org/0000-0002-5190-2130 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Mattias Vermeersch Mattias Vermeersch Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Veronique Storme Veronique Storme Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Minami Matsui Minami Matsui RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Search for more papers by this author Dirk Inzé Corresponding Author Dirk Inzé [email protected] orcid.org/0000-0002-3217-8407 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Lisa Van den Broeck Lisa Van den Broeck orcid.org/0000-0003-0226-0757 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Marieke Dubois Marieke Dubois orcid.org/0000-0002-5190-2130 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Mattias Vermeersch Mattias Vermeersch Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Veronique Storme Veronique Storme Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Minami Matsui Minami Matsui RIKEN Center for Sustainable Resource Science, Kanagawa, Japan Search for more papers by this author Dirk Inzé Corresponding Author Dirk Inzé [email protected] orcid.org/0000-0002-3217-8407 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium VIB Center for Plant Systems Biology, Ghent, Belgium Search for more papers by this author Author Information Lisa Van den Broeck1,2,‡, Marieke Dubois1,2,4,‡, Mattias Vermeersch1,2, Veronique Storme1,2, Minami Matsui3 and Dirk Inzé *,1,2 1Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium 2VIB Center for Plant Systems Biology, Ghent, Belgium 3RIKEN Center for Sustainable Resource Science, Kanagawa, Japan 4Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Strasbourg, France ‡These authors contributed equally to this work *Corresponding author. Tel: +32 9 331 38 06; E-mail: [email protected] Molecular Systems Biology (2017)13:961https://doi.org/10.15252/msb.20177840 PDFDownload PDF of article text and main figures. Peer ReviewDownload a summary of the editorial decision process including editorial decision letters, reviewer comments and author responses to feedback. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract Plants have established different mechanisms to cope with environmental fluctuations and accordingly fine-tune their growth and development through the regulation of complex molecular networks. It is largely unknown how the network architectures change and what the key regulators in stress responses and plant growth are. Here, we investigated a complex, highly interconnected network of 20 Arabidopsis transcription factors (TFs) at the basis of leaf growth inhibition upon mild osmotic stress. We tracked the dynamic behavior of the stress-responsive TFs over time, showing the rapid induction following stress treatment, specifically in growing leaves. The connections between the TFs were uncovered using inducible overexpression lines and were validated with transient expression assays. This study resulted in the identification of a core network, composed of ERF6, ERF8, ERF9, ERF59, and ERF98, which is responsible for most transcriptional connections. The analyses highlight the biological function of this core network in environmental adaptation and its redundancy. Finally, a phenotypic analysis of loss-of-function and gain-of-function lines of the transcription factors established multiple connections between the stress-responsive network and leaf growth. Synopsis This study unravels a transcriptional network controlling Arabidopsis leaf growth inhibition in response to osmotic stress. The network consists of 20 transcription factors, whose complex and redundant patterns of interconnections enable robust adaptation to environmental changes. Linear pathways are a simplification. Multiple transcription factors can regulate the same target genes and, in some cases more than one transcription factor is necessary to induce the expression of a target gene. The network is robust because regulatory redundancy is built in, making the network less susceptible to mutations. ERF6 and ERF98 are both induced in the first induction group and can transcriptionally activate a large part of the network. They have an overlap of 6 target genes. ERF8 and ERF9 are both induced in the third induction group and can transcriptionally repress a large part of the network, showing an overlap of 9 target genes. The network is efficient for environmental adaption to a stress signal. The repressing activities in the network after 2 h of stress enables the network to return to its prestimulus state. The network is highly responsive to a range of input signals and might be part of a general stress response. However, the need for two transcription factors to transactivate target genes prevents stochastic activation of the network. The random induction of the network would lead to a needless stress response which is disadvantageous for the plant. Introduction Plant growth is a very complex quantitative trait and depends on both the genetic background and environmental conditions that can stimulate or adversely affect growth (Doust et al, 2014; Saïdou et al, 2014). Each environmental stimulus causes a specific response established by multiple regulatory components forming an interconnected network rather than a linear pathway (Vermeirssen et al, 2014; Miao et al, 2015; Luo et al, 2016). In addition, environmental changes are often multifactorial, such as heat and drought often occurring simultaneously. The combination of different environmental signals thus leads to complex responses, which are integrated by gene regulatory networks (GRNs) that enable the regulation of complex traits such as growth. It is therefore necessary to study these genetic networks as one entity in addition to studying the role of their individual components in order to get insights into the arising phenotype. A GRN can be defined as a combination of regulatory proteins such as transcription factors (TFs) that function together to regulate a specific set of output genes. A very well-known example of a GRN is the circadian clock regulatory network (Nagel & Kay, 2012; Pokhilko et al, 2012; Seaton et al, 2015; Hernando et al, 2017). This network consists of a core oscillator module of three TFs (CIRCADIAN CLOCK ASSOCIATED1 (CCA1), LATE HYPOCOTYL (LHY) and TIMING OF CAB1 (TOC1)) that forms the base of a larger interconnected network regulating circadian rhythms, hypocotyl growth, and flowering of Arabidopsis plants through transcriptional but also post-translational regulation, chromatin remodeling, and alternative splicing (Nakamichi, 2011; Malapeira et al, 2012; Perez-Santángelo et al, 2013; Wang & Ma, 2013). The core circadian clock network in Arabidopsis has even been extrapolated to crops such as rice, maize, soybean, and Brassica rapa (Murakami et al, 2007; Liu et al, 2009; Xu et al, 2010; Wang et al, 2011). A more specific example of a smaller GRN is the BRASSINAZOLE RESISTANT(BZR)—PHYTOCHROME INTERACTING FACTOR 4 (PIF4)—DELLA module that integrates brassinosteroid, light, and gibberellin signals to regulate cell elongation (Bai et al, 2012; Claeys et al, 2014a; Zhiponova et al, 2014). Environmental signals disturb the molecular steady state of GRNs by changing the gene expression levels or by post-translational modifications triggering the (de)activation of a protein. Under such changing conditions, networks dynamically evolve to reach a new steady state in which the components are in balance. At the phenotypic level, the modifications in the GRN ultimately lead to a particular output, for example, growth stimulation or inhibition. The existence of such complex networks facilitates the fine-tuning of the response to a continuously varying input, such as heat or drought stress. The compound mannitol is used in plant research as a molecule to induce osmotic stress and interfere with plant growth (Claeys et al, 2014b). Low concentrations of mannitol (25 mM) induce mild stress, triggering a decrease in Arabidopsis rosette size of approximately 50% without affecting the development or survival. Therefore, this setup can be used to investigate the molecular mechanisms underlying leaf growth inhibition (Skirycz et al, 2011; Claeys et al, 2014b). During Arabidopsis leaf development, the growth of an emerging leaf primordium is first solely driven by cell proliferation, resulting in an increased cell number. After a few days, cells at the distal end of the leaf exit the mitotic cell cycle and start to expand and subsequently differentiate (Donnelly et al, 1999; Andriankaja et al, 2012). At this point, growth is merely driven by cell expansion and, in the epidermis, by the division activity of meristemoid cells (White, 2006; Andriankaja et al, 2012; Gonzalez et al, 2015). Both cell proliferation and cell expansion can be adversely affected by mild osmotic stress conditions (Skirycz et al, 2011; Huber et al, 2014). Mannitol-induced stress inhibits the cell cycle by a two-step process called the “pause-and-stop” mechanism (Skirycz et al, 2011). In the first phase, the “pause” phase, the cells are kept in a latent state allowing rapid resumption of the cell cycle when conditions are again favorable. When the osmotic stress persists, the cells permanently exit the cell cycle and differentiate, called the “stop” phase. Previously, a transcriptome analysis on microdissected, actively growing leaf tissue exposed to low concentrations of mannitol was performed to identify putative molecular players orchestrating the observed growth arrest (Skirycz et al, 2011). Upon short-term exposure to mannitol, a gradually increasing number of genes encoding TFs is significantly upregulated, suggesting that a transcriptional cascade initiates the early response to mannitol. Few members of this transcriptional cascade have been studied previously, such as the rapidly induced ETHYLENE RESPONSE FACTOR 6 (ERF6), which activates the expression of GIBBERELLIN2-OXIDASE6 (GA2-OX6), a gene encoding a gibberellin-inactivating enzyme (Rieu et al, 2008; Dubois et al, 2013). Because of the resulting lower levels of gibberellin, DELLA proteins are stabilized, which ensures that cells permanently exit the cell division phase and are pushed to cell differentiation (Claeys et al, 2012). The transcriptional repressor ERF11 also has been characterized and could counteract the effect of ERF6 both on molecular and phenotypic level (Dubois et al, 2015). In this study, we investigated a subset of mannitol-responsive TFs and show that they form a dense GRN that is very rapidly induced upon mannitol treatment. We demonstrate the transcriptional connections between these individual components and give new insights into their regulatory capacities on the expression of target genes. Using this systems biology approach, we identified a hub of five TFs (ERF6, ERF8, ERF9, ERF59, and ERF98) that drives most regulatory connections. Finally, we studied the role of the 20 TFs in the regulation of leaf growth under standard conditions and when exposed to mild osmotic stress, leading to the identification of multiple growth-regulating TFs. Results A GRN of 20 TFs is specifically activated in growing leaves exposed to mannitol A previous transcriptome analysis upon short-term exposure of Arabidopsis seedlings to mannitol has identified genes that are rapidly induced upon osmotic stress in young proliferating leaves (Skirycz et al, 2011). Among them, ERF6 appeared to play a key role in this early stress response, enabling the inhibition of leaf growth and the simultaneous activation of stress-inducible genes. Based on the identified mannitol-responsive genes (Skirycz et al, 2011) and the ERF6 target genes (Dubois et al, 2013), we selected 28 genes encoding TFs with a putative role in the mannitol-mediated growth retardation. To measure the transcriptional induction of these 28 genes by mannitol, 15-day-old plants grown on half-strength Murashige and Skoog (1/2 MS) medium covered with a nylon mesh were transferred to medium containing 25 mM mannitol or control medium (Skirycz et al, 2011). After 4 h, the third leaf was harvested for transcript profiling. At this stage, the third leaf is actively growing and mostly contains expanding cells. Because the transcriptional induction was confirmed for 20 genes (Appendix Fig S1), we hypothesized that these 20 TFs could act together in a transcriptional network to regulate growth upon stress. Half of the TFs of the putative mannitol-responsive GRN belong to the ERF family (Appendix Table S1) (Nakano et al, 2006; Skirycz et al, 2011; Phukan et al, 2017), containing a single AP2/ERF domain that is responsible for the specific binding to GCC boxes in the promoter of their target genes (Fujimoto et al, 2000; Yang et al, 2009). Three ERF proteins, ERF8, ERF9, and ERF11, belong to group VIII and are putative transcriptional repressors, because they contain an ERF-associated amphiphilic repression (EAR) domain (Nakano et al, 2006). Six other stress-induced ERFs belong to group IX: ERF-1, ERF2, ERF5, ERF6, ERF59, and ERF98. ERF5 and ERF6 contain an additional motif, CMIX-5, which is a predicted phosphorylation site (Fujimoto et al, 2000; Nakano et al, 2006). The last ERF protein part of the putative mannitol-induced network, RAP2.6L, belongs to group X (Nakano et al, 2006). Seven members of the proposed GRN are part of the WRKY TF family: WRKY6, WRKY15, WRKY28, WRKY30, WRKY33, WRKY40, and WRKY48, which contain a conserved sequence (WRKYGQK) followed by a zinc finger motif, enabling the binding to DNA at the position of a W-box TTGAC(C/T) (Wu et al, 2005). Finally, three other TFs, ZAT6 and STZ, belonging to the Zinc Finger TF family (Englbrecht et al, 2004; Ciftci-Yilmaz & Mittler, 2008; Kiełbowicz-Matuk, 2012), and MYB51 (Stracke et al, 2001; Dubos et al, 2010), are part of the proposed mannitol-inducible network (Appendix Table S1). To investigate the developmental timing of the putative GRN into more detail, we measured the expression level of the 20 genes upon stress in the third leaf of wild-type plants during the proliferating (9 days after stratification [DAS]), expanding (15 DAS) and mature (22 DAS) developmental stage (Dataset EV1). With the exception of ERF8 and ERF9, which were most probably only transiently induced by mannitol, all other 18 TFs were significantly upregulated under stress conditions (Student's t-test, FDR < 0.05) in proliferating or expanding tissue (Fig 1). For about half of these genes, the level of induction in proliferating and expanding tissue was similar. Three genes, ERF5, ERF6, and ERF11, were induced more highly in expanding leaf tissue, whereas six genes, ERF59, ERF98, MYB51, WRKY6, WRKY30, and WRKY40, were induced more strongly in proliferating leaf tissue. Interestingly, none of the TFs were significantly upregulated in mature leaf tissue (Fig 1), suggesting that the putative stress-responsive GRN is only induced in growing leaves, because these tissues are prone to growth inhibition upon mild stress. Figure 1. Mannitol-induced transcriptional changes of the selected TFs in proliferating, expanding, and mature leaf tissue The expression of the 20 genes encoding TFs was measured 24 h after mannitol treatment during the proliferating (n = 192 plants), expanding (n = 16 plants), and mature (n = 16) leaf developmental stage. Expression levels in wild-type plants transferred to mannitol-induced stress were compared to those transferred to control conditions at the same developmental stage. Data information: Data are presented as mean ± SEM, n = 4 independent experiments. FC = fold change. *FDR < 0.05, unpaired two-sided Student's t-test. Download figure Download PowerPoint The GRN shows the sequential activation of four TF groups Because expression analysis has previously shown the early upregulation of these genes upon mannitol treatment (Skirycz et al, 2011), the young developing third leaf (15 DAS) was harvested at a high temporal resolution (20 min, 40 min, 1 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h, and 48 h) after transfer to control or 25 mM mannitol-containing medium. RNA was extracted, and a detailed expression pattern over time for each gene of the putative GRN was generated with the nCounter Nanostring® technology (Dataset EV1). This technology enables the determination of the expression level of multiple genes in parallel without losing sensitivity. Within 1 h upon stress, nine of the 20 TF-encoding genes were significantly upregulated (Table EV1; Student's t-test, FDR < 0.05) and most genes reached a maximum expression level after 2 h, demonstrating the very rapid response of this regulatory network. When considering the earliest time points in more detail, the initial upregulation was not equally fast but instead occurred in a sequential manner (Fig 2). The TFs could be classified into four different groups based on the initial time point at which their expression exceeded the threshold of log2(fold change [FC]) > 1 (Fig 2). The first group included seven genes (ERF5, ERF6, ERF11, ERF98, WRKY40, STZ and ZAT6). All genes showed a fast and strong induction, exceeding the threshold already at 40 min (Fig 2A). The second group, including ERF-1, ERF2, WRKY30, WRKY33, and MYB51, was upregulated from 1 h onward (Fig 2B). However, the induction of these genes, except for WRKY30, was not as strong as that of the first group; the genes of the second group reached a maximum of approximately log2(FC) 4 compared to a maximum of approximately log2(FC) 6 in the first group. The third group, which passed the threshold at 2 h, contained WRKY6, WRKY15, WRKY28, WRKY48, ERF59, and notably two genes encoding the repressors ERF8 and ERF9 (Fig 2C). The induction was even less strong than that of the second group; most genes reached a maximum around log2(FC) 3. In the fourth group, the expression of the activator RAP2.6L was upregulated only 4 h after mannitol treatment with a maximum of approximately log2(FC) 5 (Fig 2D). Figure 2. Four groups of transcriptional induction upon exposure to mannitol A–D. Based on a threshold of log2(FC) > 1, the 20 TFs were categorized into four groups. The first group contains TFs that reached the log2(FC) threshold 40 min after mannitol treatment (A), the second group reached the threshold after 1 h (B), the third group after 2 h (C), and the fourth group after 4 h (D). The arrow indicates the initial upregulation of every group. Data information: Data are presented as mean ± SEM. n = 4 independent experiments. FC = fold change. FDR values are available in Table EV1. Download figure Download PowerPoint During later time points (12 h, 16 h, 24 h, and 48 h), three scenarios could be observed (Appendix Fig S2). Following the initial induction, the expression of the TF either (i) gradually decreased to the expression level in control conditions and was not significantly upregulated at 48 h (Appendix Fig S2A), (ii) reached a minimum and increased again (Appendix Fig S2B), or (iii) remained induced until at least 48 h after stress (Appendix Fig S2C). In total, 11 TFs were significantly upregulated upon 48 h of stress. In conclusion, the 20 selected TFs were rapidly upregulated upon mannitol treatment and, interestingly, their induction could be divided into four groups of initial transcriptional activation. For most TFs, the maximum expression level was reached after 2 h. Remarkably, the expression of 11 genes remained higher even after 48 h of mannitol treatment, suggesting that these TFs also play a role in the long-term response to osmotic stress. The GRN is highly interconnected and dynamic To validate our hypothesis that the 20 selected TFs act as a network rather than independently, we aimed to identify and visualize the putative GRN. The putative GRN consists of 20 nodes, representing the 20 TFs, and directed edges between the nodes, indicating the transcriptional regulatory connections. To determine these regulatory connections and thus the edges, we performed a large-scale expression analysis with gain-of-function (GOF) lines. We opted for inducible constructs in which a C-terminal fusion protein of the TF of interest and a glucocorticoid receptor (GR) domain is driven by a constitutive 35S promoter. Such fusion proteins reside in the cytosol and can only translocate to the nucleus in the presence of dexamethasone (DEX), enabling the TF to regulate its downstream target genes (Corrado & Karali, 2009). Per TF, two or three independent GOF lines with intermediate or high overexpression of the TF were obtained (Appendix Figs S3–S22), with the exception of three genes (WRKY6, WRKY30, and WRKY40) for which we could not obtain a proper overexpression line. To get an indication of which genes are direct or indirect targets of the induced TF, we opted for a time-course approach rather than an inhibition of translation by cycloheximide, because the latter already induced 18 of the 20 TFs by itself (Appendix Fig S23, Hruz et al, 2008). Therefore, one independent GOF line was selected for all 17 TFs and transferred at 15 DAS to DEX-containing medium and the third leaf was harvested at 1 h, 2 h, 4 h, 8 h, and 24 h after transfer (Appendix Table S2). The expression of each of the 19 other TFs was measured with nCounter Nanostring (Source Data for Fig 3) (Geiss et al, 2008). The time-course experiment gives an indication of whether a gene is putatively a direct, and thus induced during the early time points, or an indirect target of the induced TF. The expression analysis rendered, for each time point, a network of which the edges are based on the differentially expressed genes in every GOF line (Fig 3A). For example, a directed edge from ERF6 to STZ means that STZ was significantly differentially expressed (FDR < 0.1) in the ERF6-GR line at that specific time point and could thus be directly or indirectly regulated by ERF6; STZ is then defined as a target gene of ERF6. When considering all time points, we could observe that in nine GOF lines, ERF-1-GR, ERF2-GR, ERF6-GR, ERF8-GR, ERF9-GR, ERF59-GR, ERF98-GR, WRKY15-GR, and WRKY48-GR, the expression of at least half of the other TFs was affected (log[FC] > 1) (Appendix Figs S3–S22). The large amount of observed regulatory interactions clearly demonstrates that the selected TFs form a highly interconnected GRN. Figure 3. The regulatory connections of the osmotic stress-responsive GRN The significant regulatory interactions identified by nCounter Nanostring at 1 h, 2 h, 4 h, 8 h, and 24 h after induction of overexpression of a TF. The confirmed regulatory interactions between the 20 TFs part of the GRN, according to transient expression assays (n = 4 biological repeats). Green arrows represent activation and red arrows repression. Heatmap of the significant regulations upon induction of overexpression of the five members of the core network, the activators (green) ERF6, ERF59, ERF98, and the repressors (red) ERF8 and ERF9. Color code represents FDR-corrected P-values with thresholds at FDR = 0.01, 0.05 and 0.1. Data information: In (A), data are extrapolated from estimated averages, n = 3 independent experiments, FDR-corrected P < 0.1 (mixed model analysis, user-defined Wald tests). The thickness of the arrows represents the FDR value. In (B), data are presented as averages, n = 3 independent experiments. The intensity of the color of the arrows represents the strength of the regulation according to the TEA values and the thickness the FDR value of the nCounter Nanostring experiment. In (C), data are represented as FDR-corrected P-values, n = 3 independent experiments (mixed model analysis, user-defined Wald tests). Source data are available online for this figure. Source Data for Figure 3 [msb177840-sup-0009-SDataFig3.xlsx] Download figure Download PowerPoint The inclusion of multiple time points allowed to explore dynamic changes in regulatory connections. If we assume that every TF acts directly on its target genes without being influenced by other TFs, we could expect that the continuous induction of overexpression leads to a fast induction followed by a sigmoidal expression pattern of the target genes. For example, the strong activation of WRKY15 led to the gradually increased expression of part of its target genes such as STZ, WRKY6, WRKY30, WRKY40, ERF-1, and ERF11 (Fig EV1A). However, some genes showed an oscillating pattern upon WRKY15-induced activation, such as the target genes ERF6, RAP2.6L, and ZAT6 (Fig EV1B). The oscillation of some transcripts was also visible at the network level: most interactions were formed after 1 h of induction and decreased after 2 h or 4 h, but increased again after 8 h or 24 h (Fig 3A, Source Data for Fig 3). The oscillations further strengthen the hypothesis that multiple TFs regulate the expression of the same target gene, leading to multiple indirect effects. The highly fluctuating regulations also emphasize the need for short-term analysis because the steady state of the network masks these connections. Click here to expand this figure. Figure EV1. Expression profiles of WRKY15 target genesExpanding leaf tissue (third leaf – 15 DAS) of WRKY15-GR was harvested 1 h, 2 h, 4 h, 8 h, and 24 h after transfer to dexamethasone. Expression values were normalized against the control line. WRKY15 target genes (significantly differentially expressed during one time point) that showed a gradually increasing expression pattern. WRKY15 target genes that showed an oscillating expression pattern. Data information: data are presented as mean ± SEM, n = 3 independent experiments, *FDR < 0.1 (mixed model analysis, user-defined Wald tests). Download figure Download PowerPoint To analyze the transactivation capacities of the TFs on their target genes, the edges based on the transcriptome data at 1 h, 2 h, and 4 h (in total 81 edges) were further verified with transient expression assays (TEAs). Luciferase reporter genes were used to perform TEAs in tobacco (Nicotiana tabacum) Bright Yellow-2 (BY2) protoplasts (Vanden Bossche et al, 2013). The protoplasts were co-transformed with 35S::TF and pTF::fLUC (firefly luciferase) constructs to evaluate whether a TF can activate or repress a target promoter, here defined as the region upstream of the start codon until the next gene with a maximum of 2 kb. In total, 45 out of the 81 edges were confirmed (Appendix Table S3, Appendix Figs S3–S22) and were used to build a more robust GRN (Fig 3B). Two distinct types of edges are represented in the network: red arrows represent inhibition of the expression of the target gene, whereas green arrows represent activation. All TFs were exclusive activators or repressors. For example, ERF8 and ERF9 appeared to be strong repressors, because for all tested target genes, the co-transformation with ERF8 or ERF9 led to a decreased luminescence signal (Fig 3B, Appendix Figs S3–S22). However, it should be noted that the nature of the regulation was not always consistent between the DEX-inducible in planta system and the TEA experiments. The repressing function of the literature-described repressors ERF8 and ERF9 (Ohta et al, 2001; Nakano et al, 2006) seemed to be abolished by fusion with the GR domain, as observed in planta (Appendix Figs S3–S22) and in TEAs performed with ERF8-GR or ERF9-GR (Appendix Fig S24). The discrepancy is thus most likely due to the presence of the GR domain close to the EAR motif. The TEAs performed with the TFs without GR domain are thus more likely to represent the activity of the endogenous TF. Among the 45 confirmed regulatory connections, 39 were originating from only five ERF genes, ERF6, ERF8, ERF9, ERF59, and ERF98. We further refer to these TFs as the core network (Fig 3C). In conclusion, the large-scale expression analysis revealed a dense GRN with generally a strong induction of the network genes when one member is activated. More than half of the regulatory connections could be confirmed by an independent transactivation assay and led to the identification of a core network. Most TFs are involved in DA - 2017/12// PY - 2017/12// DO - 10.15252/msb.20177840 VL - 13 IS - 12 SP - 961 UR - https://doi.org/10.15252/msb.20177840 KW - growth regulation KW - mild osmotic stress KW - short-term stress response KW - transcription factors KW - transcriptional network ER - TY - JOUR TI - Genome Surfing As Driver of Microbial Genomic Diversity AU - Choudoir, Mallory J. AU - Panke-Buisse, Kevin AU - Andam, Cheryl P. AU - Buckley, Daniel H. T2 - Trends in Microbiology AB - Microbial genomic diversity is often explained by invoking selection acting on large populations at demographic equilibrium. However, historical fluctuations in population size can produce nonadaptive changes in genomic diversity due to drift. Gene surfing can explain patterns of genomic diversity in diverse species of plants and animals as a consequence of postglacial range expansion driven by historical climate change during the Pleistocene. We propose that genome surfing can result when the demographic mechanisms which produce gene surfing act on microbial populations capable of horizontal gene transfer (HGT). Patterns of genetic diversity and gene flow within Streptomyces are indicative of postglacial demographic range expansion. Genome surfing provides a mechanism to explain ancestral patterns of horizontal gene exchange and current patterns of genomic diversity observed within Streptomyces. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. a severe reduction in a population size. the number of individuals of an idealized population needed to capture the genetic diversity of the actual population. the moving boundary of a range expansion. a reduction in genetic diversity caused when a small number of individuals founds a population. a genetic consequence of range expansion driven by neutral variations in gene frequencies that occur at an expansion edge. an evolutionary mechanism whereby allele or gene frequencies change as a result of random sampling effects. contemporaneous introgression of many horizontally acquired genes into a pan-genome as a consequence of gene surfing. the permanent incorporation of genes from one pan-genome into a second pan-genome of a divergent lineage. a mechanism that causes spatial gradients of genetic diversity when dispersal limitation allows the local accumulation of genetic variation. a radial pattern of genetic discontinuity produced during range expansions. a population characterized by unlimited gene flow. the physical co-occurrence of items in space and time. an event that occurs when a population colonizes a geographic region which it did not previously occupy, and which may or may not already be occupied by other populations, as facilitated by dispersal. an evolutionary mechanism whereby allele or gene frequencies change in response to fitness effects. a loss of genetic variation resulting from a rapid fixation of a beneficial allele or gene. DA - 2017/8// PY - 2017/8// DO - 10.1016/j.tim.2017.02.006 VL - 25 IS - 8 SP - 624-636 UR - http://dx.doi.org/10.1016/j.tim.2017.02.006 ER - TY - JOUR TI - Casein Kinase 1 Coordinates Cohesin Cleavage, Gametogenesis, and Exit from M Phase in Meiosis II AU - Argüello-Miranda, O. AU - Zagoriy, I. AU - Mengoli, V. AU - Rojas, J. AU - Jonak, K. AU - Oz, T. AU - Graf, P. AU - Zachariae, W. T2 - Developmental Cell AB - Meiosis consists of DNA replication followed by two consecutive nuclear divisions and gametogenesis or spore formation. While meiosis I has been studied extensively, less is known about the regulation of meiosis II. Here we show that Hrr25, the conserved casein kinase 1δ of budding yeast, links three mutually independent key processes of meiosis II. First, Hrr25 induces nuclear division by priming centromeric cohesin for cleavage by separase. Hrr25 simultaneously phosphorylates Rec8, the cleavable subunit of cohesin, and removes from centromeres the cohesin protector composed of shugoshin and the phosphatase PP2A. Second, Hrr25 initiates the sporulation program by inducing the synthesis of membranes that engulf the emerging nuclei at anaphase II. Third, Hrr25 mediates exit from meiosis II by activating pathways that trigger the destruction of M-phase-promoting kinases. Thus, Hrr25 synchronizes formation of the single-copy genome with gamete differentiation and termination of meiosis. DA - 2017/// PY - 2017/// DO - 10.1016/j.devcel.2016.11.021 VL - 40 IS - 1 SP - 37-52 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85008643933&partnerID=MN8TOARS ER - TY - JOUR TI - Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology AU - Jakobsson, E. AU - Argüello-Miranda, O. AU - Chiu, S.-W. AU - Fazal, Z. AU - Kruczek, J. AU - Nunez-Corrales, S. AU - Pandit, S. AU - Pritchet, L. T2 - Journal of Membrane Biology AB - Lithium has literally been everywhere forever, since it is one of the three elements created in the Big Bang. Lithium concentration in rocks, soil, and fresh water is highly variable from place to place, and has varied widely in specific regions over evolutionary and geologic time. The biological effects of lithium are many and varied. Based on experiments in which animals are deprived of lithium, lithium is an essential nutrient. At the other extreme, at lithium ingestion sufficient to raise blood concentration significantly over 1 mM/, lithium is acutely toxic. There is no consensus regarding optimum levels of lithium intake for populations or individuals—with the single exception that lithium is a generally accepted first-line therapy for bipolar disorder, and specific dosage guidelines for sufferers of that condition are generally agreed on. Epidemiological evidence correlating various markers of social dysfunction and disease vs. lithium level in drinking water suggest benefits of moderately elevated lithium compared to average levels of lithium intake. In contrast to other biologically significant ions, lithium is unusual in not having its concentration in fluids of multicellular animals closely regulated. For hydrogen ions, sodium ions, potassium ions, calcium ions, chloride ions, and magnesium ions, blood and extracellular fluid concentrations are closely and necessarily regulated by systems of highly selective channels, and primary and secondary active transporters. Lithium, while having strong biological activity, is tolerated over body fluid concentrations ranging over many orders of magnitude. The lack of biological regulation of lithium appears due to lack of lithium-specific binding sites and selectivity filters. Rather lithium exerts its myriad physiological and biochemical effects by competing for macromolecular sites that are relatively specific for other cations, most especially for sodium and magnesium. This review will consider what is known about the nature of this competition and suggest using and extending this knowledge towards the goal of a unified understanding of lithium in biology and the application of that understanding in medicine and nutrition. DA - 2017/// PY - 2017/// DO - 10.1007/s00232-017-9998-2 VL - 250 IS - 6 SP - 587-604 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85033453121&partnerID=MN8TOARS KW - Ion channels and transporters KW - Magnesium-dependent enzymes KW - Physical properties of biological membranes ER - TY - CONF TI - Effects of culture medium on growth and gene expression in the plant pathogen Mycosphaerella fijiensis AU - Green, A. AU - Thomas, E. AU - Daub, M.E. T2 - 26th Annual NC State University Spring Undergraduate Research Symposium C2 - 2017/// CY - Raleigh, NC DA - 2017/// PY - 2017/// ER - TY - CONF TI - Assessment of key genes in Cercospora nicotianae that encode resistance to cercosporin AU - Oakley, B. AU - Thomas, E. AU - Daub, M.E. T2 - 26th Annual NC State University Spring Undergraduate Research Symposium C2 - 2017/// CY - Raleigh, NC DA - 2017/// PY - 2017/// ER - TY - JOUR TI - Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations AU - Saville, Amanda AU - Charles, Melodi AU - Chavan, Suchitra AU - Muñoz, Miguel AU - Gómez-Alpizar, Luis AU - Ristaino, Jean Beagle T2 - Phytopathology® AB - Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas. DA - 2017/// PY - 2017/// DO - 10.1094/phyto-02-17-0045-r ER - TY - RPRT TI - Translation regulation of uORFs-containing genes in Arabidopsis AU - Merchante, C. AU - Yun, J. AU - Valpuesta-Fernandez, V. AU - Stepanova, A. AU - Alonso, J. DA - 2017/// PY - 2017/// ER - TY - JOUR TI - Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis AU - Ponnudurai, Ruby AU - Kleiner, Manuel AU - Sayavedra, Lizbeth AU - Petersen, Jillian M AU - Moche, Martin AU - Otto, Andreas AU - Becher, Dörte AU - Takeuchi, Takeshi AU - Satoh, Noriyuki AU - Dubilier, Nicole AU - Schweder, Thomas AU - Markert, Stephanie T2 - The ISME Journal AB - The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contributions, as well as the mechanism of carbon transfer from the symbionts to the host are poorly understood. We used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners. Our study revealed that key metabolic functions are most likely accomplished jointly by B. azoricus and its symbionts: (1) CO2 is pre-concentrated by the host for carbon fixation by the sulfur-oxidizing symbiont, and (2) the host replenishes essential biosynthetic TCA cycle intermediates for the sulfur-oxidizing symbiont. In return (3), the sulfur oxidizer may compensate for the host's putative deficiency in amino acid and cofactor biosynthesis. We also identified numerous 'symbiosis-specific' host proteins by comparing symbiont-containing and symbiont-free host tissues and symbiont fractions. These proteins included a large complement of host digestive enzymes in the gill that are likely involved in symbiont digestion and carbon transfer from the symbionts to the host. DA - 2017/2// PY - 2017/2// DO - 10.1038/ismej.2016.124 VL - 11 IS - 2 SP - 463-477 UR - https://doi.org/10.1038/ismej.2016.124 ER - TY - JOUR TI - Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance AU - Kleiner, Manuel AB - Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental microbiologists have started using metatranscriptomics and metaproteomics to look at gene expression differences between different environments or conditions. This has been mostly done by using makeshift adaptations of pure culture focused differential transcriptomics and proteomics approaches. However, since meta-omics data has many more variables attached to it as compared to pure culture derived data, such makeshift adaptations are problematic at best. One particular challenge is posed by the data normalization strategies used to account for technical and biological variables in meta-omic data. Here I discuss the most common normalization strategy for transcriptomic and proteomic data and why it is not valid by itself for meta-omic data. I provide logical proof that variation in species abundances between samples is an additional variable that must be accounted for during normalization of meta-omic data. Finally, I show how the existing normalization methods for transcriptomic and proteomic data can be augmented to be applicable to meta-omic data. DA - 2017/3/2/ PY - 2017/3/2/ DO - 10.7287/peerj.preprints.2846 VL - 3 UR - https://doi.org/10.7287/peerj.preprints.2846 ER - TY - JOUR TI - COMPUESTOS BIOACTIVOS Y ACTIVIDAD ANTIOXIDANTE DE SEMILLAS DE QUINUA PERUANA (Chenopodium quinoa W.) T2 - Revista de la Sociedad Química del Perú DA - 2017/// PY - 2017/// UR - https://www.redalyc.org/articulo.oa?id=371951877003 ER - TY - JOUR TI - Interaction Rewiring and the Rapid Turnover of Plant-Pollinator Networks AU - CaraDonna, Paul J. AU - Petry, William K. AU - Brennan, Ross M. AU - Cunningham, James L. AU - Bronstein, Judith L. AU - Waser, Nickolas M. AU - Sanders, Nathan J. T2 - Ecology Letters AB - Abstract Whether species interactions are static or change over time has wide‐reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within‐season turnover of plant–pollinator interactions from weekly censuses across 3 years in a subalpine ecosystem. Week‐to‐week turnover of interactions (1) was high, (2) followed a consistent seasonal progression in all years of study and (3) was dominated by interaction rewiring (the reassembly of interactions among species). Simulation models revealed that species’ phenologies and relative abundances constrained both total interaction turnover and rewiring. Our findings reveal the diversity of species interactions that may be missed when the temporal dynamics of networks are ignored. DA - 2017/// PY - 2017/// DO - 10.1111/ele.12740 VL - 20 IS - 3 SP - 385-394 KW - Adaptive foraging KW - beta-diversity KW - community composition KW - food webs KW - interaction turnover KW - mutualism KW - networks KW - null models KW - optimal foraging theory KW - phenology ER - TY - JOUR TI - Higher predation risk for insect prey at low latitudes and elevations AU - Roslin, Tomas AU - Hardwick, Bess AU - Novotny, Vojtech AU - Petry, William K. AU - Andrew, Nigel R. AU - Asmus, Ashley AU - Barrio, Isabel C. AU - Basset, Yves AU - Boesing, Andrea Larissa AU - Bonebrake, Timothy C. AU - Cameron, Erin K. AU - Dáttilo, Wesley AU - Donoso, David A. AU - Drozd, Pavel AU - Gray, Claudia L. AU - Hik, David S. AU - Hill, Sarah J. AU - Hopkins, Tapani AU - Huang, Shuyin AU - Koane, Bonny AU - Laird-Hopkins, Benita AU - Laukkanen, Liisa AU - Lewis, Owen T. AU - Milne, Sol AU - Mwesige, Isaiah AU - Nakamura, Akihiro AU - Nell, Colleen S. AU - Nichols, Elizabeth AU - Prokurat, Alena AU - Sam, Katerina AU - Schmidt, Niels M. AU - Slade, Alison AU - Slade, Victor AU - Suchanková, Alžběta AU - Teder, Tiit AU - Nouhuys, Saskya AU - Vandvik, Vigdis AU - Weissflog, Anita AU - Zhukovich, Vital AU - Slade, Eleanor M. T2 - Science AB - Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic trend in attack rates by birds or mammals. These matching gradients at global and regional scales suggest consistent drivers of biotic interaction strength, a finding that needs to be integrated into general theories of herbivory, community organization, and life-history evolution. DA - 2017/5/19/ PY - 2017/5/19/ DO - 10.1126/science.aaj1631 VL - 356 IS - 6339 SP - 742-744 UR - https://doi.org/10.1126/science.aaj1631 ER - TY - JOUR TI - In situ enhancement of surfactin biosynthesis in Bacillus subtilis using novel artificial inducible promoters AU - Jiao, Song AU - Li, Xu AU - Yu, Huimin AU - Yang, Huan AU - Li, Xue AU - Shen, Zhongyao T2 - Biotechnology and Bioengineering AB - ABSTRACT Surfactin‐family lipopeptides are green biosurfactants with substantial industrial potential. The major problem prohibiting surfactin use is the low titer of the wild producer, Bacillus subtilis . Using transcriptomic analysis, four strong promoters, P groE , P cdd , P rplK , and P sspE , were identified and cloned from the genome of B. subtilis THY‐7, a novel surfactin producer that has been identified from soil with a 0.55 g/L surfactin titer. An optimal promoter, P groE , was selected to replace the native THY‐7 surfactin synthase (SrfA) promoter through single‐cross homologous recombination; however, the resulting engineered strain containing the P groE substitution did not synthesize surfactin. The sucrose‐inducible promoters P sacB and P sacP were then substituted in place of P srfA , and the resulting engineered strains produced 1.09 and 0.22 g/L surfactin, respectively. An artificial, sucrose‐inducible Pg1 promoter was produced through fusion of the P groE and P sacB ribonucleic a nti t erminator (RAT), and the engineered strain containing the Pg1‐substitution produced a surfactin titer of 1.44 g/L. An artificial IPTG‐inducible promoter, Pg2, was constructed from a P groE ‐lacO fusion and then substituted for the chromosomal P srfA locus, and the surfactin titer of the resulting THY‐7/ Pg2 ‐ srfA increased to 5.98 g/L. The driving capacity of Pg2 was further improved by the inclusion of two point mutations in the −35 and −10 regions to produce the novel promoter Pg3. Pg3 exhibited super‐strong activity as measured by lacZ reporter gene overexpression (approximately 3000 U). The Pg3‐substitution strain THY‐7/ Pg3 ‐ srfA produced up to 9.74 g/L surfactin in a 5 L fermentor. The maximum productivity was 0.30 g/L/h, and the greatest yield reached 0.14 g surfactin/g sucrose. Biotechnol. Bioeng. 2017;114: 832–842. © 2016 Wiley Periodicals, Inc. DA - 2017/4// PY - 2017/4// DO - 10.1002/BIT.26197 VL - 114 IS - 4 SP - 832–842 SN - 0006-3592 UR - http://dx.doi.org/10.1002/BIT.26197 KW - biosurfactant KW - Bacillus subtilis KW - surfactin synthesis KW - artificial inducible promoter ER - TY - JOUR TI - Red and White PAP1-controlled Arabidopsis Cells Are Dependent Upon TT8 AU - Zhu, Yue AU - Xie, De-Yu T2 - In Vitro Cellular & Developmental Biology - Animal DA - 2017/// PY - 2017/// VL - 53 IS - Supplement 1 SP - S51– S51 ER - TY - JOUR TI - Regulation of Anthocyanin Biosynthesis in the WD40-bHLH-MYB Complex-Programmed Arabidopsis Cells AU - Xie, De-Yu T2 - In Vitro Cellular & Developmental Biology - Animal DA - 2017/// PY - 2017/// VL - 53 IS - Suppl 1 SP - 13– 13 ER - TY - JOUR TI - Compartmentalized Overexpression of a Synthetic Geranyl Pyrophosphate Synthase and Its Regulation on Plant Growth and Metabolism AU - Li, Gui AU - Ji, Xiaoming AU - Swantko, Sarah AU - Xie, De-Yu T2 - In Vitro Cellular & Developmental Biology - Animal DA - 2017/// PY - 2017/// VL - 53 IS - Suppl. 1 SP - 54– 55 ER - TY - JOUR TI - Overexpression of Populus×canescens isoprene synthase gene in Camelina sativa leads to alterations in its growth and metabolism AU - Rossi, Lorenzo AU - Borghi, Monica AU - Yang, Jinfen AU - Xie, De-Yu T2 - Journal of Plant Physiology AB - Isoprene (2-methyl-1,3-butadiene) is a hemiterpene molecule. It has been estimated that the plant kingdom emits 500–750 million tons of isoprene in the environment, half of which results from tropical broadleaf trees and the remainder from shrubs. Camelina (Camelina sativa (L.) Crantz) is an emerging bioenergy plant for biodiesel. In this study, we characterized isoprene formation following a diurnal/nocturnal cycle in wild-type Camelina plants. To understand the potential effects of isoprene emission on this herbaceous plant, a gray poplar Populus × canescens isoprene synthase gene (PcISPS) was overexpressed in Camelina. Transgenic plants showed increased isoprene production, and the emissions were characterized by a diurnal/nocturnal cycle. Measurements of the expression of six genes of the plastidial 2-C-methyl-d-erythriol-4-phosphate (MEP) pathway revealed that the expression patterns of three key genes were associated with isoprene formation dynamics in the three genotypic plants. Conversely, dissimilar gene expression levels existed in different genotypes, indicating that dynamics and variations occurred among plants. Moreover, transgenic plants grew shorter and developed smaller leaves than the wild-type and empty vector control transgenic plants. Photosynthetic analysis showed that the CO2 assimilation rate, intracellular CO2 concentration, mesophyll conductance and contents of chlorophylls a and b were similar among PcISPS transgenic, empty-vector control transgenic, and wild-type plants, indicating that the transgene did not negatively affect photosynthesis. Based on these results, we suggest that the reduced biomass was likely a trade-off consequence of the increased isoprene emission. DA - 2017/8// PY - 2017/8// DO - 10.1016/J.JPLPH.2017.06.005 VL - 215 SP - 122-131 J2 - Journal of Plant Physiology LA - en OP - SN - 0176-1617 UR - http://dx.doi.org/10.1016/J.JPLPH.2017.06.005 DB - Crossref KW - Camelina KW - Fast Isoprene Sensor KW - Isoprene KW - Terpenoids ER - TY - JOUR TI - Packed-bed Reactors, Dynamic Culturing, and Stress-Directed Microbiome Selection; a Case Study of Agrochemicals Soil Biodegradation T2 - In Vitro Cellular and Developmental Biology - Animal DA - 2017/// PY - 2017/// UR - https://publons.com/publon/31684349/ ER - TY - JOUR TI - Metabolic Characterization of the Anthocyanidin Reductase Pathway Involved in the Biosynthesis of Flavan-3-ols in Elite Shuchazao Tea (Camellia sinensis) Cultivar in the Field AU - Zhao, Lei AU - Jiang, Xiao-Lan AU - Qian, Yu-Mei AU - Wang, Pei-Qiang AU - Xie, De-Yu AU - Gao, Li-Ping AU - Xia, Tao T2 - Molecules AB - Anthocyanidin reductase (ANR) is a key enzyme in the ANR biosynthetic pathway of flavan-3-ols and proanthocyanidins (PAs) in plants. Herein, we report characterization of the ANR pathway of flavan-3-ols in Shuchazao tea (Camellia sinesis), which is an elite and widely grown cultivar in China and is rich in flavan-3-ols providing with high nutritional value to human health. In our study, metabolic profiling was preformed to identify two conjugates and four aglycones of flavan-3-ols: (-)-epigallocatechin-gallate [(-)-EGCG], (-)-epicatechin-gallate [(-)-ECG], (-)-epigallocatechin [(-)-EGC], (-)-epicatechin [(-)-EC], (+)-catechin [(+)-Ca], and (+)-gallocatechin [(+)-GC], of which (-)-EGCG, (-)-ECG, (-)-EGC, and (-)-EC accounted for 70-85% of total flavan-3-ols in different tissues. Crude ANR enzyme was extracted from young leaves. Enzymatic assays showed that crude ANR extracts catalyzed cyanidin and delphinidin to (-)-EC and (-)-Ca and (-)-EGC and (-)-GC, respectively, in which (-)-EC and (-)-EGC were major products. Moreover, two ANR cDNAs were cloned from leaves, namely CssANRa and CssANRb. His-Tag fused recombinant CssANRa and CssANRb converted cyanidin and delphinidin to (-)-EC and (-)-Ca and (-)-EGC and (-)-GC, respectively. In addition, (+)-EC was observed from the catalysis of recombinant CssANRa and CssANRb. Further overexpression of the two genes in tobacco led to the formation of PAs in flowers and the reduction of anthocyanins. Taken together, these data indicate that the majority of leaf flavan-3-ols in Shuchazao's leaves were produced from the ANR pathway. DA - 2017/12// PY - 2017/12// DO - 10.3390/molecules22122241 VL - 22 IS - 12 SP - 2241 UR - http://www.mdpi.com/1420-3049/22/12/2241 KW - anthocyanidin reductase KW - (+)-catechin KW - (-)-epicatechin KW - (-)-epicatechin-gallate KW - (-)-epigallocatechin KW - (-)-epigallocatechin-gallate KW - (+)-gallocatechin ER - TY - JOUR TI - Regulation of Drosophila Lifespan by bellwether Promoter Alleles AU - Garcia, Júlia Frankenberg AU - Carbone, Mary Anna AU - Mackay, Trudy F. C. AU - Anholt, Robert R. H. T2 - Scientific Reports AB - Longevity varies among individuals, but how natural genetic variation contributes to variation in lifespan is poorly understood. Drosophila melanogaster presents an advantageous model system to explore the genetic underpinnings of longevity, since its generation time is brief and both the genetic background and rearing environment can be precisely controlled. The bellwether (blw) gene encodes the α subunit of mitochondrial ATP synthase. Since metabolic rate may influence lifespan, we investigated whether alternative haplotypes in the blw promoter affect lifespan when expressed in a co-isogenic background. We amplified 521 bp upstream promoter sequences containing alternative haplotypes and assessed promoter activity both in vitro and in vivo using a luciferase reporter system. The AG haplotype showed significantly greater expression of luciferase than the GT haplotype. We then overexpressed a blw cDNA construct driven by either the AG or GT haplotype promoter in transgenic flies and showed that the AG haplotype also results in greater blw cDNA expression and a significant decrease in lifespan relative to the GT promoter haplotype, in male flies only. Thus, our results show that naturally occurring regulatory variants of blw affect lifespan in a sex-specific manner. DA - 2017/6/23/ PY - 2017/6/23/ DO - 10.1038/S41598-017-04530-X VL - 7 IS - 1 J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/S41598-017-04530-X DB - Crossref ER - TY - JOUR TI - An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning AU - Hanauer, David I. AU - Graham, Mark J. AU - Betancur, Laura AU - Bobrownicki, Aiyana AU - Cresawn, Steven G. AU - Garlena, Rebecca A. AU - Jacobs-Sera, Deborah AU - Kaufmann, Nancy AU - Pope, Welkin H. AU - Russell, Daniel A. AU - Jacobs, William R., Jr. AU - Sivanathan, Viknesh AU - Asai, David J. AU - Hatfull, Graham F. T2 - Proceedings of the National Academy of Sciences AB - Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking. DA - 2017/12/5/ PY - 2017/12/5/ DO - 10.1073/pnas.1718188115 VL - 114 IS - 51 SP - 13531-13536 J2 - Proc Natl Acad Sci USA LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1718188115 DB - Crossref KW - bacteriophage KW - genomics KW - science education KW - evolution KW - assessment ER - TY - JOUR TI - Foundational and Translational Research Opportunities to Improve Plant Health AU - Michelmore, Richard AU - Coaker, Gitta AU - Bart, Rebecca AU - Beattie, Gwyn AU - Bent, Andrew AU - Bruce, Toby AU - Cameron, Duncan AU - Dangl, Jeffery AU - Dinesh-Kumar, Savithramma AU - Edwards, Rob AU - Eves-van den Akker, Sebastian AU - Gassmann, Walter AU - Greenberg, Jean T. AU - Hanley-Bowdoin, Linda AU - Harrison, Richard J. AU - Harvey, Jagger AU - He, Ping AU - Huffaker, Alisa AU - Hulbert, Scot AU - Innes, Roger AU - Jones, Jonathan D. G. AU - Kaloshian, Isgouhi AU - Kamoun, Sophien AU - Katagiri, Fumiaki AU - Leach, Jan AU - Ma, Wenbo AU - McDowell, John AU - Medford, June AU - Meyers, Blake AU - Nelson, Rebecca AU - Oliver, Richard AU - Qi, Yiping AU - Saunders, Diane AU - Shaw, Michael AU - Smart, Christine AU - Subudhi, Prasanta AU - Torrance, Lesley AU - Tyler, Bret AU - Valent, Barbara AU - Walsh, John T2 - Molecular Plant-Microbe Interactions AB - The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture. DA - 2017/7// PY - 2017/7// DO - 10.1094/mpmi-01-17-0010-cr VL - 30 IS - 7 SP - 515-516 J2 - MPMI LA - en OP - SN - 0894-0282 UR - http://dx.doi.org/10.1094/mpmi-01-17-0010-cr DB - Crossref ER - TY - JOUR TI - Quantitation of Tolyporphins, Diverse Tetrapyrrole Secondary Metabolites with Chlorophyll-Like Absorption, from a Filamentous Cyanobacterium-Microbial Community AU - Zhang, Yunlong AU - Zhang, Ran AU - Hughes, Rebecca-Ayme AU - Dai, Jingqiu AU - Gurr, Joshua R. AU - Williams, Philip G. AU - Miller, Eric S. AU - Lindsey, Jonathan S. T2 - Phytochemical Analysis AB - Abstract Introduction Tolyporphins are unusual tetrapyrrole macrocycles produced by a non‐axenic filamentous cyanobacterium (HT‐58‐2). Tolyporphins A–J, L, and M share a common dioxobacteriochlorin core, differ in peripheral substituents, and exhibit absorption spectra that overlap that of the dominant cyanobacterial pigment, chlorophyll a . Identification and accurate quantitation of the various tolyporphins in these chlorophyll‐rich samples presents challenges. Objective To develop methods for the quantitative determination of tolyporphins produced under various growth conditions relative to that of chlorophyll a . Methodology Chromatographic fractionation of large‐scale (440 L) cultures afforded isolated individual tolyporphins. Lipophilic extraction of small‐scale (25 mL) cultures, HPLC separation with an internal standard, and absorption detection enabled quantitation of tolyporphin A and chlorophyll a , and by inference the amounts of tolyporphins A–M. Absorption spectroscopy with multicomponent analysis of lipophilic extracts (2 mL cultures) afforded the ratio of all tolyporphins to chlorophyll a . The reported absorption spectral data for the various tolyporphins required re‐evaluation for quantitative purposes. Results and Discussion The amount of tolyporphin A after 50 days of illumination ranged from 0.13 nmol/mg dry cells (media containing nitrate) to 1.12 nmol/mg (without nitrate), with maximum 0.23 times that of chlorophyll a . Under soluble‐nitrogen deprivation after 35–50 days, tolyporphin A represents 1/3–1/2 of the total tolyporphins, and the total amount of tolyporphins is up to 1.8‐fold that of chlorophyll a . Conclusions The quantitative methods developed herein should facilitate investigation of the biosynthesis of tolyporphins (and other tetrapyrroles) as well as examination of other strains for production of tolyporphins. Copyright © 2017 John Wiley & Sons, Ltd. DA - 2017/11/6/ PY - 2017/11/6/ DO - 10.1002/pca.2735 VL - 29 IS - 2 SP - 205-216 J2 - Phytochem. Anal. LA - en OP - SN - 0958-0344 UR - http://dx.doi.org/10.1002/pca.2735 DB - Crossref KW - HPLC KW - mass spectrometry KW - absorption spectroscopy with multicomponent analysis KW - nitrogen deprivation KW - growth curve ER - TY - CHAP TI - The triple response assay and its use to characterize ethylene mutants in arabidopsis AU - Merchante, C. AU - Stepanova, A.N. T2 - Methods in Molecular Biology AB - Exposure of plants to ethylene results in drastic morphological changes. Seedlings germinated in the dark in the presence of saturating concentrations of ethylene display a characteristic phenotype known as the triple response. This phenotype is robust and easy to score. In Arabidopsis the triple response is usually evaluated at 3 days post germination in seedlings grown in the dark in rich media supplemented with 10 μM of the ethylene precursor ACC in air or in unsupplemented media in the presence of 10 ppm ethylene. The triple response in Arabidopsis consists of shortening and thickening of hypocotyls and roots and exaggeration of the curvature of apical hooks. The search for Arabidopsis mutants that fail to show this phenotype in ethylene or, vice versa, display the triple response in the absence of exogenously supplied hormone has allowed the identification of the key components of the ethylene biosynthesis and signaling pathways. Herein, we describe a simple protocol for assaying the triple response in Arabidopsis. The method can also be employed in many other dicot species, with minor modifications to account for species-specific differences in germination. We also compiled a comprehensive table of ethylene-related mutants of Arabidopsis, including many lines with auxin-related defects, as wild-type levels of auxin biosynthesis, transport, signaling, and response are necessary for the normal response of plants to ethylene. PY - 2017/// DO - 10.1007/978-1-4939-6854-1_13 VL - 1573 SP - 163-209 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85015705453&partnerID=MN8TOARS KW - Phytohormone KW - Ethylene KW - ACC KW - Triple response KW - Arabidopsis KW - Seedlings KW - Germination KW - Hypocotyl KW - Root KW - Apical hook KW - Mutants ER - TY - JOUR TI - Editorial: Relevance of translational regulation on plant growth and environmental responses AU - Ferrando, A. AU - Castellano, M.M. AU - Lisón, P. AU - Leister, D. AU - Stepanova, A.N. AU - Hanson, J. T2 - Frontiers in Plant Science AB - EDITORIAL article Front. Plant Sci., 19 December 2017Sec. Plant Physiology Volume 8 - 2017 | https://doi.org/10.3389/fpls.2017.02170 DA - 2017/// PY - 2017/// DO - 10.3389/fpls.2017.02170 VL - 8 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85040509996&partnerID=MN8TOARS KW - mRNA translation KW - translation factors KW - post-transcriptional regulation KW - translatome KW - organellar gene expression ER - TY - CHAP TI - The Predictive Power of Ecological Niche Modeling for Global Arbuscular Mycorrhizal Fungal Biogeography T2 - Biogeography of Mycorrhizal Symbiosis AB - The distributions of arbuscular mycorrhizal (AM) fungal communities are driven by climate, soil nutrients, and plant community composition. However, these distributions are estimated at the community level and AM fungal taxa will respond to selection pressure of global change at the species level. Thus, ecological niche models of individual AM fungal taxa may be an informative approach to predict AM fungal composition and function under future climates at the global scale. Here we present the first attempt to model AM fungal distributions with ecological niche models for the widespread AM fungal taxon Rhizophagus irregularis (formerly Glomus intraradices). We show that despite varying the definition of the operational taxonomic unit (OTU) for R. irregularis, the predicted distributions of this species complex are consistently affected by a positive association with soil moisture. The spatial extent of ecological niche models affected the predicted distribution of R. irregularis, with climatic drivers and resources affecting its distribution more strongly in the northern and southern hemispheres, respectively. Given that AM fungi are not dispersal limited and coexist at the landscape scale relevant for ecological niche model predictions, this widely distributed fungal clade provides a robust case study to apply hypothesis-driven distributional models to predict the biogeography of microorganisms. PY - 2017/// DO - 10.1007/978-3-319-56363-3_7 UR - http://dx.doi.org/10.1007/978-3-319-56363-3_7 ER - TY - JOUR TI - Brave new world T2 - Biogeochemistry DA - 2017/3// PY - 2017/3// DO - 10.1007/s10533-017-0316-y UR - http://dx.doi.org/10.1007/s10533-017-0316-y ER - TY - JOUR TI - Regardless of N-substrate, multiple fungal root endophytes isolated from pastures outgrow and outcompete those isolated from undisturbed sites T2 - Pedobiologia AB - Edaphic properties such as soil nutrients structure belowground fungal communities and alter their intimate interactions with plants. Yet little work has compared the traits of fungal root endophytes and tested if specific soil nutrients determine their growth and competition. We hypothesized that fungi isolated from particular resource environments should grow and compete better when resources matched their “home” environment. We conducted experiments to compare growth rate and competitive ability of eight fungal root endophytes, cultured from either low nutrient undisturbed sites or from sites converted to high nutrient pastures, varying the nutrient environments to match the different sites. In isolation, biomass depended on nutrient limitation and fungal identity. Pasture endophytes all had high biomass in high nitrogen environments while endophytes from undisturbed sites showed greater variation among isolates. In competition, growth differences quantitatively depended on the fungus’s identity, its competitor’s identity and nutrients, yet pasture fungi out-competed “undisturbed” fungi in nearly every case. Rapid growth and competitive ability appears to be a trait of these fungal endophytes isolated from pastures and not solely a product of high nutrients, which may inhibit successful reintroduction of fungi from undisturbed sites. DA - 2017/7// PY - 2017/7// DO - 10.1016/j.pedobi.2017.05.006 UR - http://dx.doi.org/10.1016/j.pedobi.2017.05.006 KW - Endophytes KW - Fungal traits KW - Competition KW - FL rosemary scrub KW - Pasture KW - Land use KW - Restoration ER - TY - JOUR TI - Microbial Tools in Agriculture Require an Ecological Context: Stress-Dependent Non-Additive Symbiont Interactions T2 - Agronomy Journal AB - Core Ideas Leaf fungal symbionts represent a potential new tool in agriculture. Effective fungal application requires an understanding of their interactions. Fungal interactions resulted in non‐additive plant growth and wilt responses. Fungal metabolites indicated qualitative additive, synergistic, or antagonistic plant responses. Fungal trait dissimilarity predicted the size of plant response deviations. Fungal symbionts are increasingly targeted as tools for crop management, but their use in the field requires an understanding of how fungi interact in a community context. Fungal interactions may result in additive effects on the host plant, which could be predicted simply based on individual fungal behavior. Alternatively, interactions among fungi may result in non‐additive synergistic or antagonistic effects on plant performance that are more challenging to predict. Here, we hypothesized that the effects of fungal interactions on the plant host could be predicted from their niche overlap. To test this idea, we used foliar fungal endophytes with a range of niche overlap based on trait dissimilarities to examine the effects of six fungal species pairs compared to the corresponding individual fungal species on switchgrass ( Panicum virgatum L.) in water‐stressed and well‐watered conditions. Mixtures of endophytes had either no effect or predictable, additive effects on plant tiller number, but effects on plant growth rate and wilting were largely non‐additive. Moisture level, fungal stress, and metabolic trait dissimilarity predicted 51 to 92% of the deviation of fungal effects from additive, with less similar fungi likely to have more synergistic effects on the plant host. Furthermore, we identified indicator metabolites for fungal interaction outcomes. However, the effects of endophyte interactions on the plant host were environment dependent making single community applications more challenging. Overall, future development of microbial tools for use in agriculture must consider their interactions to optimize application. DA - 2017/// PY - 2017/// DO - 10.2134/agronj2016.10.0568 UR - http://dx.doi.org/10.2134/agronj2016.10.0568 ER - TY - JOUR TI - Translating Phytobiomes from Theory to Practice: Ecological and Evolutionary Considerations AU - Hawkes, Christine V. AU - Connor, Elise W. T2 - Phytobiomes Journal AB - The tremendous potential of the plant microbiome to improve plant growth and production means that microbes are in the process of becoming an everyday tool in agronomic practices. However, historically field applications of microbes have had low success. We propose that development and optimization of microbiome treatments will benefit from the integration of ecological and evolutionary niche theory into plant microbiome studies. Thus, we review several niche-based processes that can aid in the development and implementation of microbiome treatments. Current predictive approaches include evolutionary history, habitat origin, ecological traits, resource trade, and gene signatures, none of which are mutually exclusive. A robust predictive framework must further account for observed plasticity and context dependence in microbial function. Development of microbiome treatments that will successfully establish in the field can also benefit from a better understanding of niche-based processes such as niche partitioning to limit competitive interactions and maximize persistence, priority effects to allow establishment before resident taxa, storage effects that take advantage of temporal variation in niche availability, and local adaptation to specific environments. Using endophytic fungi as examples, we illustrate current knowledge and gaps in these areas. Finally, we address existing limitations to the broad-scale development of successful microbiome tools. DA - 2017/1// PY - 2017/1// DO - 10.1094/PBIOMES-05-17-0019-RVW VL - 1 IS - 2 SP - 57-69 UR - https://doi.org/10.1094/PBIOMES-05-17-0019-RVW KW - agriculture KW - ecology ER - TY - JOUR TI - Historical climate controls soil respiration responses to current soil moisture AU - Hawkes, Christine V. AU - Waring, Bonnie G. AU - Rocca, Jennifer D. AU - Kivlin, Stephanie N. T2 - Proceedings of the National Academy of Sciences AB - Ecosystem carbon losses from soil microbial respiration are a key component of global carbon cycling, resulting in the transfer of 40-70 Pg carbon from soil to the atmosphere each year. Because these microbial processes can feed back to climate change, understanding respiration responses to environmental factors is necessary for improved projections. We focus on respiration responses to soil moisture, which remain unresolved in ecosystem models. A common assumption of large-scale models is that soil microorganisms respond to moisture in the same way, regardless of location or climate. Here, we show that soil respiration is constrained by historical climate. We find that historical rainfall controls both the moisture dependence and sensitivity of respiration. Moisture sensitivity, defined as the slope of respiration vs. moisture, increased fourfold across a 480-mm rainfall gradient, resulting in twofold greater carbon loss on average in historically wetter soils compared with historically drier soils. The respiration-moisture relationship was resistant to environmental change in field common gardens and field rainfall manipulations, supporting a persistent effect of historical climate on microbial respiration. Based on these results, predicting future carbon cycling with climate change will require an understanding of the spatial variation and temporal lags in microbial responses created by historical rainfall. DA - 2017/6/13/ PY - 2017/6/13/ DO - 10.1073/pnas.1620811114 UR - https://doi.org/10.1073/pnas.1620811114 KW - microbial KW - climate change KW - precipitation KW - legacies ER - TY - JOUR TI - Hydrocotyle bowlesioides (Araliaceae): New to the Flora of North Carolina AU - Krings, Alexander AU - Newton, Shannon AU - Liles, Nelson P., Jr. T2 - Castanea DA - 2017/3// PY - 2017/3// DO - 10.2179/16-109 VL - 82 IS - 1 SP - 47-47 J2 - Castanea LA - en OP - SN - 0008-7475 1938-4386 UR - http://dx.doi.org/10.2179/16-109 DB - Crossref ER - TY - JOUR TI - The proteome of higher plant mitochondria AU - Rao, R.S.P. AU - Salvato, F. AU - Thal, B. AU - Eubel, H. AU - Thelen, J.J. AU - M?ller, I.M. T2 - Mitochondrion AB - Plant mitochondria perform a wide range of functions in the plant cell ranging from providing energy and metabolic intermediates, via coenzyme biosynthesis and their own biogenesis to retrograde signaling and programmed cell death. To perform these functions, they contain a proteome of > 2000 different proteins expressed in some cells under some conditions. The vast majority of these proteins are imported, in many cases by a dedicated protein import machinery. Recent proteomic studies have identified about 1000 different proteins in both Arabidopsis and potato mitochondria, but even for energy-related proteins, the most well-studied functional protein group in mitochondria, < 75% of the proteins are recognized as mitochondrial by even one of six of the most widely used prediction algorithms. The mitochondrial proteomes contain proteins representing a wide range of different functions. Some protein groups, like energy-related proteins, membrane transporters, and de novo fatty acid synthesis, appear to be well covered by the proteome, while others like RNA metabolism appear to be poorly covered possibly because of low abundance. The proteomic studies have improved our understanding of basic mitochondrial functions, have led to the discovery of new mitochondrial metabolic pathways and are helping us towards appreciating the dynamic role of the mitochondria in the responses of the plant cell to biotic and abiotic stress. DA - 2017/// PY - 2017/// DO - 10.1016/j.mito.2016.07.002 VL - 33 SP - 22-37 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84996551851&partnerID=MN8TOARS KW - (Plant) mitochondria KW - Proteomics KW - Localization prediction programs ER - TY - JOUR TI - Proteomics for Bioenergy Production T2 - Plant-Based Genetic Tools for Biofuels Production DA - 2017/6/11/ PY - 2017/6/11/ DO - 10.2174/9781681084619117010008 SP - 103-121 ER - TY - JOUR TI - Luxurious Nitrogen Fertilization of Two Sugar Cane Genotypes Contrasting for Lignin Composition Causes Changes in the Stem Proteome Related to Carbon, Nitrogen, and Oxidant Metabolism but Does Not Alter Lignin Content AU - Salvato, Fernanda AU - Wilson, Rashaun AU - Llerena, Juan Pablo Portilla AU - Kiyota, Eduardo AU - Reis, Karina Lima AU - Boaretto, Luis Felipe AU - Balbuena, Tiago S. AU - Azevedo, Ricardo A. AU - Thelen, Jay J. AU - Mazzafera, Paulo T2 - Journal of Proteome Research AB - Sugar cane is an important crop for sugar and biofuel production. Its lignocellulosic biomass represents a promising option as feedstock for second-generation ethanol production. Nitrogen fertilization can affect differently tissues and its biopolymers, including the cell-wall polysaccharides and lignin. Lignin content and composition are the most important factors associated with biomass recalcitrance to convert cell-wall polysaccharides into fermentable sugars. Thus it is important to understand the metabolic relationship between nitrogen fertilization and lignin in this feedstock. In this study, a large-scale proteomics approach based on GeLC–MS/MS was employed to identify and relatively quantify proteins differently accumulated in two contrasting genotypes for lignin composition after excessive nitrogen fertilization. From the ∼1000 nonredundant proteins identified, 28 and 177 were differentially accumulated in response to nitrogen from IACSP04-065 and IACSP04-627 lines, respectively. These proteins were associated with several functional categories, including carbon metabolism, amino acid metabolism, protein turnover, and oxidative stress. Although nitrogen fertilization has not changed lignin content, phenolic acids and lignin composition were changed in both species but not in the same way. Sucrose and reducing sugars increased in plants of the genotype IACSP04-065 receiving nitrogen. DA - 2017/10/6/ PY - 2017/10/6/ DO - 10.1021/acs.jproteome.7b00397 VL - 16 IS - 10 SP - 3688-3703 UR - https://doi.org/10.1021/acs.jproteome.7b00397 KW - Saccharum officinarum KW - cell wall KW - lignocellulosic ethanol KW - lignin KW - proteomics ER - TY - JOUR TI - Comparative proteomic analysis provides insight into the biological role of protein phosphatase inhibitor-2 from Arabidopsis AU - Ahsan, Nagib AU - Chen, Mingjie AU - Salvato, Fernanda AU - Wilson, Rashaun S. AU - Rao, R. Shyama Prasad AU - Thelen, Jay J. T2 - Journal of Proteomics AB - Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes. Decreased abundance of several ribosomal proteins, a DEAD box RNA helicase family protein (AtRH3), Clp protease (ClpP3) and proteins associated with cell division suggests a bottleneck in chloroplast ribosomal biogenesis and cell cycle regulation in AtPPI-2 mutant plants. In contrast, eight out of nine Arabidopsis TOPP isoforms were increased at the transcript level in AtPPI-2 leaves compared to WT. A protein-protein interaction network revealed that > 75% of the differentially accumulated proteins have at least secondary and/or tertiary connections with AtPPI-2. Collectively, these data reveal a potential basis for the growth defects of AtPPI-2 and support the presumed role of AtPPI-2 as a master regulator for TOPPs, which regulate diverse growth and developmental processes. Comparative label-free proteomics was used to characterize an AtPPI-2 T-DNA knockdown mutant. The complex, reduced growth phenotype supports the notion that AtPPI-2 is a global regulator of TOPPs, and possibly other proteins. Comparative proteomics revealed a range of differences in protein abundance from various cellular processes such as chloroplast development, ribosome biogenesis, and transporter activity in the AtPPI-2 mutant relative to WT Arabidopsis. Collectively the results of proteomic analysis and the protein-protein network suggest that AtPPI-2 is involved in a wide range of biological processes either directly or indirectly including plastid biogenesis, translational mechanisms, and cell cycle regulation. The proposed protein interaction network comprises a testable model underlying changes in protein abundance in the AtPPI-2 mutant, and provides a better framework for future studies. DA - 2017/8// PY - 2017/8// DO - 10.1016/j.jprot.2017.06.006 VL - 165 SP - 51-60 KW - Type one phosphatase KW - Phosphatase inhibitor KW - Comparative proteomics KW - Ribosome biogenesis KW - Protein-protein interaction ER - TY - CHAP TI - Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS) AU - Clark, Natalie M. AU - Sozzani, Rosangela T2 - Plant Genomics A2 - Busch, Wolfgang T3 - Methods in Molecular Biology AB - Scanning fluorescence correlation spectroscopy (scanning FCS) can be used to determine protein movement, oligomerization state, and protein–protein interaction. Here, we describe how to use the scanning FCS techniques of raster image correlation spectroscopy (RICS) and pair correlation function (pCF) to determine the rate and direction of protein movement. In addition, we detail how number and brightness (N&B) and cross-correlation analyses can be used to determine oligomerization state and binding ratios of protein complexes. We specifically describe how to acquire suitable images for scanning FCS analysis using the model plant Arabidopsis and how to perform the various analyses using the SimFCS software. PY - 2017/// DO - 10.1007/978-1-4939-7003-2_16 VL - 1610 SP - 251-266 PB - Springer New York SN - 978-1-4939-7001-8 978-1-4939-7003-2 UR - http://link.springer.com/10.1007/978-1-4939-7003-2_16 DB - Crossref Y2 - 2019/1/30/ KW - Scanning fluorescence correlation spectroscopy KW - Diffusion coefficient KW - Protein movement KW - Oligomerization state KW - Protein stoichiometry ER - TY - CHAP TI - Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach AU - Luis Balaguer, Maria Angels AU - Sozzani, Rosangela T2 - Plant Gene Regulatory Networks A2 - Kaufmann, Kerstin A2 - Mueller-Roeber, Bernd T3 - Methods in Molecular Biology AB - Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN. PY - 2017/// DO - 10.1007/978-1-4939-7125-1_21 VL - 1629 SP - 331-348 PB - Springer New York SN - 978-1-4939-7124-4 978-1-4939-7125-1 UR - http://link.springer.com/10.1007/978-1-4939-7125-1_21 DB - Crossref Y2 - 2019/1/30/ KW - Gene regulatory network KW - Dynamic Bayesian network KW - Ordinary differential equation KW - Arabidopsis root ER - TY - JOUR TI - Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance AU - Kleiner, M. T2 - PeerJ Preprints AB - Metatranscriptomics and metaproteomics make it possible to measure gene expression in microbial communities. So far these approaches were mostly used to get a general overview of the dominant metabolism and physiologies of community members. Recently, environmental microbiologists have started using metatranscriptomics and metaproteomics to look at gene expression differences between different environments or conditions. This has been mostly done by using makeshift adaptations of pure culture focused differential transcriptomics and proteomics approaches. However, since meta-omics data has many more variables attached to it as compared to pure culture derived data, such makeshift adaptations are problematic at best. One particular challenge is posed by the data normalization strategies used to account for technical and biological variables in meta-omic data. Here I discuss the most common normalization strategy for transcriptomic and proteomic data and why it is not valid by itself for meta-omic data. I provide logical proof that variation in species abundances between samples is an additional variable that must be accounted for during normalization of meta-omic data. Finally, I show how the existing normalization methods for transcriptomic and proteomic data can be augmented to be applicable to meta-omic data. DA - 2017/// PY - 2017/// DO - 10.7287/peerj.preprints.2846v1 VL - 5 SP - e2846v1 UR - https://doi.org/10.7287/peerj.preprints.2846v1 ER - TY - DATA TI - Re-analysis of an ultra-deep and quantitative saliva proteome DA - 2017/// PY - 2017/// UR - http://www.ebi.ac.uk/pride/archive/projects/PXD006366 ER - TY - DATA TI - Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics DA - 2017/// PY - 2017/// UR - http://www.ebi.ac.uk/pride/archive/projects/PXD006118 ER - TY - DATA TI - Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains DA - 2017/// PY - 2017/// UR - http://www.ebi.ac.uk/pride/archive/projects/PXD006343 ER - TY - JOUR TI - Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont. T2 - Standards in Genomic Sciences AB - Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics. In this study, we report the first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus, here tentatively named Candidatus Thioglobus thermophilus. The draft genome (3.1 Mb) harbors 3045 protein-coding genes. It revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation. Enzymes required for the synthesis of the tricarboxylic acid cycle intermediates oxaloacetate and succinate were absent, suggesting that these intermediates may be substituted by metabolites from external sources. We also detected a repertoire of genes associated with cell surface adhesion, bacteriotoxicity and phage immunity, which may perform symbiosis-specific roles in the B. thermophilus symbiosis. DA - 2017/// PY - 2017/// DO - 10.1186/s40793-017-0266-y UR - http://europepmc.org/abstract/med/28878861 KW - Uncultured endosymbiont KW - Hydrothermal vents KW - Marine invertebrate symbiosis KW - Thiotrophy KW - Autotrophy ER - TY - JOUR TI - Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps AU - Rubin-Blum, Maxim AU - Antony, Chakkiath Paul AU - Borowski, Christian AU - Sayavedra, Lizbeth AU - Pape, Thomas AU - Sahling, Heiko AU - Bohrmann, Gerhard AU - Kleiner, Manuel AU - Redmond, Molly C. AU - Valentine, David L. AU - Dubilier, Nicole T2 - Nature Microbiology AB - Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knolls in the southern Gulf of Mexico. Genomic and transcriptomic analyses revealed that, in contrast to all previously known Cycloclasticus, the symbiotic Cycloclasticus appears to lack the genes needed for PAH degradation. Instead, these symbionts use propane and other short-chain alkanes such as ethane and butane as carbon and energy sources, thus expanding the limited range of substrates known to power chemosynthetic symbioses. Analyses of short-chain alkanes in the environment of the Campeche Knolls symbioses revealed that these are present at high concentrations (in the μM to mM range). Comparative genomic analyses revealed high similarities between the genes used by the symbiotic Cycloclasticus to degrade short-chain alkanes and those of free-living Cycloclasticus that bloomed during the Deepwater Horizon oil spill. Our results indicate that the metabolic versatility of bacteria within the Cycloclasticus clade is higher than previously assumed, and highlight the expanded role of these keystone species in the degradation of marine hydrocarbons. Cycloclasticus bacterial symbionts of mussels and sponges that live in deep-sea gas and oil seeps are capable of using short-chain alkanes as their primary energy source, providing further insight into chemosynthetic symbioses. DA - 2017/// PY - 2017/// DO - 10.1038/nmicrobiol.2017.93 VL - 2 SP - 17093 UR - https://doi.org/10.1038/nmicrobiol.2017.93 ER - TY - JOUR TI - Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp AU - Dong, Xiaoli AU - Kleiner, Manuel AU - Sharp, Christine E. AU - Thorson, Erin AU - Li, Carmen AU - Liu, Dan AU - Strous, Marc AB - Abstract Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp . Since its launch two years ago, MetaAmp has been used >2,800 times, by many users worldwide. DA - 2017/4// PY - 2017/4// DO - 10.1101/131631 VL - 4 ER - TY - JOUR TI - Assessing species biomass contributions in microbial communities via metaproteomics AU - Kleiner, Manuel AU - Thorson, Erin AU - Sharp, Christine E. AU - Dong, Xiaoli AU - Liu, Dan AU - Li, Carmen AU - Strous, Marc AB - Abstract Assessment of microbial community composition is the cornerstone of microbial ecology. Microbial community composition can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. However, as cell volumes can differ by orders of magnitude, these two approaches yield vastly different results. Methods for quantifying cell numbers are already available (e.g. fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing), yet methods for assessing community composition in terms of biomass are lacking. We developed metaproteomics based methods for assessing microbial community composition using protein abundance as a measure for biomass contributions of individual populations. We optimized the accuracy and sensitivity of the method using artificially assembled microbial communities and found that it is less prone to some of the biases found in sequencing-based methods. We applied the method using communities from two different environments, microbial mats from two alkaline soda lakes and saliva from multiple individuals. DA - 2017/4// PY - 2017/4// DO - 10.1101/130575 VL - 4 UR - https://doi.org/10.1101/130575 ER - TY - JOUR TI - Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp AU - Dong, Xiaoli AU - Kleiner, Manuel AU - Sharp, Christine E. AU - Thorson, Erin AU - Li, Carmen AU - Liu, Dan AU - Strous, Marc T2 - Frontiers in Microbiology AB - Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel sequencing of multiplexed samples, combined with the relative ease of data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present the MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures. It accepts single-end or paired-end sequences in fasta or fastq format from various sequencing platforms. It includes read quality control, and merging of forward and reverse reads of paired-end reads. It makes use of UPARSE, Mothur, and the SILVA database for clustering, removal of chimeric reads, taxonomic classification, and generation of diversity metrics. The pipeline has been validated with a mock community of known composition. MetaAmp provides a convenient web interface as well as command line interface. It is freely available at: http://ebg.ucalgary.ca/metaamp. Since its launch 2 years ago, MetaAmp has been used >2,800 times, by many users worldwide. DA - 2017/8/3/ PY - 2017/8/3/ DO - 10.3389/fmicb.2017.01461 VL - 8 KW - metagenomics KW - amplicon sequencing KW - bioinformatics KW - microbial ecology KW - microbiome ER - TY - JOUR TI - Demographic compensation does not rescue populations at a trailing range edge AU - Sheth, Seema Nayan AU - Angert, Amy Lauren T2 - Proceedings of the National Academy of Sciences of the United States of America AB - ABSTRACT As climate change shifts species' climatic envelopes across the landscape, equilibrium between geographic ranges and niches is likely diminishing due to time lags in demography and dispersal. If a species' range and niche are out of equilibrium, then population performance should decrease from cool, “leading” range edges, where populations are expanding into recently ameliorated habitats, to warm, “trailing” range edges, where populations are contracting from newly unsuitable areas. Population contraction signals that compensatory changes in vital rates are insufficient to buffer population growth from deteriorating environments. Life history theory predicts tradeoffs between fast development, high reproduction, and short longevity at low latitudes and slow development, less frequent but multiple bouts of reproduction, and long lifespan at high latitudes. If demographic compensation is driven by life history evolution, compensatory negative correlations in vital rates may be associated with this fast-slow continuum. An outstanding question is whether range limits and range contractions reflect inadequate compensatory life history shifts along environmental gradients, causing population growth rates to fall below replacement levels at range edges. We surveyed demography of 32 populations of the scarlet monkeyflower ( Erythranthe cardinalis ) spanning 11° latitude in western North America and used integral projection models to infer population dynamics and assess demographic compensation. Population growth rates decreased from north to south, consistent with leading-trailing dynamics. Southern populations are declining due to reduced survival, growth, and recruitment, despite compensatory increases in reproduction and faster life history characteristics, suggesting that demographic compensation will not rescue populations at the trailing range edge. SIGNIFICANCE STATEMENT While climate change is causing poleward shifts in many species' geographic distributions, some species' ranges have remained stable, particularly at low-latitude limits. One explanation for why some species' ranges have not shifted is demographic compensation, whereby declines in some demographic processes are offset by increases in others, potentially buffering populations from extinction. However, we have limited understanding of whether demographic compensation can prevent collapse of populations facing climate change. We examined the demography of natural populations of a perennial herb spanning a broad latitudinal gradient. Despite increases in reproduction, low-latitude populations declined due to diminished survival, growth, and recruitment. Thus, demographic compensation may not be sufficient to rescue low-latitude, warm-edge populations from extinction. DA - 2017/3/17/ PY - 2017/3/17/ DO - 10.1101/117606 VL - 3 IS - 10 SP - 2413–2418 UR - https://doi.org/10.1101/117606 ER - TY - JOUR TI - An Internship May Not Be Enough: Enhancing Bioscience Industry Job Readiness through Practicum Experiences. AU - Cramer, JM AU - Hamilton, PT T2 - Journal of microbiology & biology education AB - In contrast to the narrowing of options in academic careers, the bioscience industry offers robust employment opportunities for STEM-trained workers, especially those who display both scientific and business talent. Unfortunately, traditional science programs typically lack curricular features that develop this type of worker. The North Carolina State University Master of Microbial Biotechnology (MMB) program facilitates industry-specific experiential learning to fill this training gap. Similar programs often rely on a single industry internship to provide students relevant work experience, but completion of one internship might not suffice to position students for employment in a highly competitive job market. The MMB program requires students to complete an internship and three practicum projects in an industry setting, to promote development of key skills in a variety of areas, to build confidence in the ability to perform initial job duties, and to establish a more extensive work history in industry. In this Perspective we discuss an unmet need in undergraduate and graduate STEM education that can be filled by incorporating a similar set of industry-specific work experiences for students who desire to transition from academe into the life science industry. DA - 2017/4// PY - 2017/4// DO - 10.1128/jmbe.v18i1.1248 VL - 18 IS - 1 UR - http://europepmc.org/abstract/med/28512519 ER - TY - JOUR TI - Modifications to a LATE MERISTEM IDENTITY gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.) AU - Andres, R.J. AU - Coneva, V. AU - Frank, M.H. AU - Tuttle, J.R. AU - Samayoa, L.F. AU - Han, S.-W. AU - Kaur, B. AU - Zhu, L. AU - Fang, H. AU - Bowman, D.T. AU - Rojas-Pierce, M. AU - Haigler, C.H. AU - Jones, D.C. AU - Holland, J.B. AU - Chitwood, D.H. AU - Kuraparthy, V. T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D1), which is responsible for the major leaf shapes in cotton. The l-D1 locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D1 locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype. DA - 2017/// PY - 2017/// DO - 10.1073/pnas.1613593114 VL - 114 IS - 1 SP - E57-E66 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85007524047&partnerID=MN8TOARS KW - cotton KW - leaf shape KW - okra KW - gene cloning ER - TY - JOUR TI - Assessing, water-related plant traits to explain slow-wilting in soybean PI 471938 AU - Bagherzadi, Laleh AU - Sinclair, Thomas R. AU - Zwieniecki, Maciej AU - Secchi, Francesca AU - Hoffmann, William AU - Carter, Thomas E. AU - Rufty, Thomas W. T2 - JOURNAL OF CROP IMPROVEMENT AB - Soybean [Glycine max (L.) Merr.] genotype PI 471938 expresses a slow-wilting phenotype in the field, and the progeny of this genotype have shown to have high yield under water deficit conditions. However, the physiological basis for the slow-wilting trait in PI 471938 remains unclear, and failure to understand the causal mechanism may limit future breeding efforts. This study investigated three primary hypotheses for trait expression that could explain slow-wilting trait in PI 471938: (1) a low osmotic potential in the leaves allowing greater water retention, (2) high elastic modulus of leaves resulting in delayed development of wilting, and (3) high hydraulic conductance allowing rapid water redistribution in the plants. Experiments included three other soybean genotypes as references for the results obtained with PI 471938. Surprisingly, the results for PI 471938 did not prove to be unique as compared to the other three tested genotypes for any of the three hypotheses. These negative results indicate that a hypothesis outside the usual candidates describing plant water transport, possibly anatomical features related to specific water transport properties, is required to explain slow-wilting in PI 471938. DA - 2017/// PY - 2017/// DO - 10.1080/15427528.2017.1309609 VL - 31 IS - 3 SP - 400-417 SN - 1542-7536 KW - Drought tolerance KW - elastic modulus KW - hydraulic conductance KW - osmotic potential KW - soybean KW - transpiration ER - TY - CHAP TI - Epigenetic Reprogramming During Plant Reproduction AU - Lin, Jer-Young AU - Hsieh, Tzung-Fu T2 - Plant Epigenetics AB - Epigenetics is the study of heritable change in gene expression state that is independent of DNA sequence variation. Such change can occur through DNA methylation or posttranscriptional modifications of histones. Epigenetic mechanisms play critical roles in regulating gene expression during development and in response to environmental stimulation. Such epigenetic information represents the transcriptional memory associated with cell fate decisions, developmental switches, or stress responses; memory that often needs to be erased and reset during reproduction. By contrast, transgenerational epigenetic information refers to more indelible marks that can be stably transmitted through meiosis and inherited in the subsequent generation. Epigenetic reprogramming, a global change in DNA and/or histone methylation, has been reported during reproduction in mammals and in flowering plants. Such reprogramming is thought to be essential for ensuring meiosis competence, establishing genomic imprinting, and silencing transposons. In Arabidopsis, gene imprinting is a consequence of a large-scale epigenetic reprogramming via DEMETER-mediated active DNA demethylation during gametogenesis. Such reprogramming is believed to be critical for the maintenance of trans-generational epigenome integrity. PY - 2017/// DO - 10.1007/978-3-319-55520-1_20 SP - 405-425 OP - PB - Springer International Publishing SN - 9783319555195 9783319555201 UR - http://dx.doi.org/10.1007/978-3-319-55520-1_20 DB - Crossref KW - Epigenetics KW - Reprogramming KW - Gametogenesis KW - Reproduction KW - DNA Methylation KW - Active DNA Demethylation KW - Chromatin Remodeling KW - Transgenerational Inheritance KW - siRNAs ER - TY - JOUR TI - Revisiting Graduate Student Training to Address Agricultural and Environmental Societal Challenges AU - Duckworth, Owen W. AU - Andrews, Megan Y. AU - Cubeta, Marc A. AU - Grunden, Amy M. AU - Ojiambo, Peter S. T2 - AGRICULTURAL & ENVIRONMENTAL LETTERS AB - Core Ideas Society is faced with daunting environmental and agricultural challenges. There is a pressing need for multidisciplinary teams of collaborative scientists. Novel graduate educational models may be needed to train students to address grand challenges. An example of illustrating the model through microbiome science of plants and soil is presented. Society and the higher education system are faced with daunting challenges associated with supplying food, energy, and water to a growing population while maintaining environmental quality and preserving natural resources. Too often, the higher education system does not facilitate collaborative immersion required to foster concerted multidisciplinary efforts needed to address societal grand challenges. In this commentary, we present an innovative model of cohort education, which equips graduate students with core skills and enables collaborative dissertation research among students. In addition, we provide an example of a program aimed at understanding the plant–soil microbiome, a critical research area that may yield significant advances in plant health and productivity. DA - 2017/12// PY - 2017/12// DO - 10.2134/ael2017.06.0019 VL - 2 IS - 1 SP - SN - 2471-9625 ER - TY - JOUR TI - Metabolic characterization of the anthocyanidin reductase pathway involved in the biosynthesis of flavan-3-ols in Elite Shuchazao Tea (Camellia sinensis) cultivar in the field AU - Zhao, L. AU - Jiang, X. L. AU - Qian, Y. M. AU - Wang, P. Q. AU - Xie, D. Y. AU - Gao, L. P. AU - Xia, T. T2 - Molecules DA - 2017/// PY - 2017/// VL - 22 IS - 12 ER - TY - JOUR TI - Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling AU - Liao, Kang-Ling AU - Melvin, Charles E. AU - Sozzani, Rosangela AU - Jones, Roger D. AU - Elston, Timothy C. AU - Jones, Alan M. T2 - PLOS ONE AB - In animal cells, activation of heterotrimeric G protein signaling generally occurs when the system’s cognate signal exceeds a threshold, whereas in plant cells, both the amount and the exposure time of at least one signal, D-glucose, are used toward activation. This unusual signaling property called Dose-Duration Reciprocity, first elucidated in the genetic model Arabidopsis thaliana, is achieved by a complex that is comprised of a 7-transmembrane REGULATOR OF G SIGNALING (RGS) protein (AtRGS1), a Gα subunit that binds and hydrolyzes nucleotide, a Gβγ dimer, and three WITH NO LYSINE (WNK) kinases. D-glucose is one of several signals such as salt and pathogen-derived molecular patterns that operates through this protein complex to activate G protein signaling by WNK kinase transphosphorylation of AtRGS1. Because WNK kinases compete for the same substrate, AtRGS1, we hypothesize that activation is sensitive to the AtRGS1 amount and that modulation of the AtRGS1 pool affects the response to the stimulant. Mathematical simulation revealed that the ratio of AtRGS1 to the kinase affects system sensitivity to D-glucose, and therefore illustrates how modulation of the cellular AtRGS1 level is a means to change signal-induced activation. AtRGS1 levels change under tested conditions that mimic physiological conditions therefore, we propose a previously-unknown mechanism by which plants react to changes in their environment. DA - 2017/12/29/ PY - 2017/12/29/ DO - 10.1371/journal.pone.0190000 VL - 12 IS - 12 SP - SN - 1932-6203 ER - TY - JOUR TI - Evolution, development, and genetics of floral display-form, size, and arrangement AU - Zhang, Wenheng AU - Xiang, Qiu-Yun AU - Wen, Jun T2 - JOURNAL OF SYSTEMATICS AND EVOLUTION AB - The flower, frequently arranged in clusters known as inflorescences, is one of the most fascinating outcomes through evolution (Endress, 2010). The dimensions of floral diversity in angiosperms are enormous through variations, such as, in floral size, color, shape, scent, and flowering time. The diverse ways of the flower arrangement on inflorescences add another layer to this complexity of the floral display. The origin and evolution of the flower have been a key piece of puzzles toward understanding the origin and diversification of angiosperms. Charles Darwin, in a letter to Joseph Hooker, famously called the origin of flowers and the early evolution of flowering plants as an “abominable mystery” (Darwin & Seward, 1903), which remains to be resolved. Floral display is essential to the success of angiosperm reproduction. Alteration in floral display strategies regarding variation in form, size, and arrangement can result in evolutionary innovation leading to new ecological adaptation and speciation. Despite its importance to angiosperm diversification, our knowledge of the evolutionary patterns and the underlying developmental and genetic basis of the floral display is still limited. In the modern times, with the advent of integrating approaches among phylogenetics, ecology, molecular genetics, and development, plant biologists have begun to shed lights on the evolutionary patterns, the underlying driving forces, and the developmental and molecular basis of the floral diversity in some angiosperm lineages (e.g., Gerrath et al., 2017; Kulbaba et al., 2017; Liu et al., 2017; Nikolov & Davis, 2017; Schrager-Lavelle et al., 2017; Zhang et al., 2017; see review by Ma et al., 2017, this issue). A symposium with the same title of this issue was organized at the 2016 Botanical Society of America Annual Meetings in Savannah, Georgia to bring plant biologists from diverse fields to discuss the advances and future directions in understanding the evolution, development, and genetics of the diversity in floral display (http://2016.botanyconference.org/engine/search/?func=AbstractTitle§ion=479). Most works presented at the symposium were included in this special issue of Journal of Systematics and Evolution. This issue includes both reviews and research papers reporting works on diverse angiosperm lineages, from dicots (Gerrath et al., 2017; Kulbaba et al., 2017; Liu et al., 2017; Nikolov & Davis, 2017; Zhang et al., 2017) to monocots (Schrager-Lavelle et al., 2017), from autotrophs (Gerrath et al., 2017; Kulbaba et al., 2017; Liu et al., 2017; Schrager-Lavelle et al., 2017; Zhang et al., 2017) to heterotrophs (Nikolov & Davis, 2017), and from ecological (Kulbaba et al., 2017) to morphological and molecular aspects (Gerrath et al., 2017; Liu et al., 2017; Nikolov & Davis, 2017; Schrager-Lavelle et al., 2017; Zhang et al., 2017). Four review articles included in this issue discussed diverse methodologies and study systems for understanding the floral display. Ma et al. (2017) systematically reviewed the recent advances in understanding the developmental and genetic basis of floral and inflorescence diversity. They also summarized the experimental approaches applied to plant developmental genetic studies of the model, emerging model, and non-model species. These authors highlighted the importance of carrying out the comparative analysis under a well-established phylogenetic framework to uncover the evolutionary changes at the molecular level in evo-devo studies. Nikolov & Davis (2017) reviewed their works on understanding the evo-devo of the world's largest flower in Rafflesiaceae. The body plan of species in Rafflesiaceae is substantially modified to adapt to its life style as holoparasites. These authors reviewed their discoveries of the pattern and scale of horizontal gene transfer based on a reliable phylogenetic placement of Rafflesiaceae and the morphology of the rare and unique vegetative and floral features of the group. Together, the review tackled the mystery of the evolution of this world's largest flower, which evolved from autotrophic plants with tiny flowers. Gerrath et al. (2017) reviewed the inflorescence characteristics of various lineages of the grape order Vitales. They compared these characteristics on a phylogenetic framework and concluded that each major clade of the Vitales had evolved a unique set of inflorescence morphology, including the homologous tendril characters (also see Zhang et al., 2015). Schrager-Lavelle et al. (2017) argued that the grass flowers can be an excellent model for studying floral evo-devo although the natures of the flowers are specialized for wind pollination (see Soreng et al., 2015). These authors illustrated the many floral variations found in the family and conveyed that grass flowers can also be a powerful tool to understand the molecular genetics of floral evolution. Three research articles included in this issue reported the patterns on floral display in Cornaceae, Solanaceae, and Ranunculaceae through molecular genetic, phylogenetic, and ecological studies. Liu et al. (2017) explored the function and role of the AP3 gene homolog in the evolution of explosive pollen release in Cornus canadensis (Cornaceae). Using a stable Agrobacterium-mediated transformation technique and comparative gene expression methods, they found that a proper level of expression of the AP3 gene during floral development plays important roles in the formation of a special floral structure that is essential to the catapult pollen release unique to the herbaceous lineage of Cornus. They proposed that a shift in the expression pattern of the AP3-like gene during the evolution of Cornus have contributed to the evolution of the explosive mechanism of pollen release in the genus. Zhang et al. (2017) studied the evolution of floral symmetry in Solanaceae using a phylogeny. Based on the evidence from morphology, ontogeny, and ancestral state reconstructions, these authors proposed that the floral symmetry evolution in the androecium and corolla was along different evolutionary trajectories. They emphasized the importance for proper delimitation of characters and character states for understanding floral symmetry evolution since the evolution of floral symmetry can be complicated for particular angiosperm clades. From an ecological aspect, Kulbaba et al. (2017) tested the hypothesis that the trait that flowers with variations systematically arranging along inflorescences could be heritable and under selection due to resource competition among flowers. They assessed the various existing techniques of functional data analysis in comparison to their new method using Delphinium glaucum (Ranunculaceae) as a model and demonstrated that their methods are more robust to test the adaptive nature of the systematic trait variation, which was often thought to be due to aspects of development. In this issue, the contributing authors have celebrated the diversity of views on how to better understand the diverse patterns of the floral display through the utility of novel methodologies, emerging model systems as well as a phylogenetic framework. There is no doubt that our knowledge about the evolution, development, and genetics of floral display will continue to advance while these research lines bloom. We dedicate this special issue to the late Professor Yancheng Tang (1926–2016) of the Institute of Botany, Chinese Academy of Sciences, for his efforts to introduce modern theories and methods of plant systematics into China and for his mentoring of many young colleagues in systematic and evolutionary botany. Professor Tang was a mentor of QY(J) Xiang, one of the editors of this special issue, from 1982 to 1989, and opened the door for her to enter the field of plant systematics. Prof. Tang is well remembered by his colleagues for his many contributions to plant systematic work in China, including contributing to the Flora of China project, promoting the development of cladistic approaches in China, and taxonomic revisions. His scholarly pursuit of systematic theories and methodology and his persistent curiosity on the frontiers of systematics and biogeography inspired discussions on concepts and controversies with many young colleagues and facilitated active, dynamic and interdisciplinary collaboration among his many friends and colleagues. In 1980, Professor Tang was the leading participant in the first collaborative project between Chinese and American botanists after diplomatic relations were reestablished between the two countries. That project, a field expedition to western Hubei, paved the way for the vast number of collaborative research projects between Chinese botanist and botanists from around the world. Professor Tang would have been immensely pleased that the 19th International Botanical Congress was held in China, in part due to the quiet but competent way he handled that first international collaboration. Wenheng Zhang Department of Biology, Virginia Commonwealth University, 1000 West Cary Street,Richmond, Virginia 23284, USA Qiu-Yun (Jenny) Xiang Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA Jun Wen Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC 20013, USA DA - 2017/11// PY - 2017/11// DO - 10.1111/jse.12274 VL - 55 IS - 6 SP - 485-486 SN - 1759-6831 ER - TY - JOUR TI - Evolution and developmental genetics of floral display-A review of progress: A review of progress in evo-devo of floral display AU - Ma, Qing AU - Zhang, Wenheng AU - Jenny Xiang, Qiu-Yun T2 - Journal of Systematics and Evolution AB - Abstract Angiosperms evolved a great diversity of ways to display their flowers for reproductive success by variation in floral color, size, shape, scent, arrangements, and flowering time. The various innovations in floral forms and the aggregation of flowers into different kinds of inflorescences can drive new ecological adaptations, speciation, and angiosperm diversification. Evolutionary developmental biology (evo‐devo) seeks to uncover the developmental and genetic basis underlying morphological diversification. Advances in the developmental genetics of floral display have provided a foundation for insights into the genetic basis of floral and inflorescence evolution. A number of regulatory genes controlling floral and inflorescence development have been identified in model plants (e.g., Arabidopsis thaliana , Antirrhinum majus ) using forward genetics and conserved functions of many of these genes across diverse non‐model species have been revealed by reverse genetics. Gene‐regulatory networks that mediated the developmental progresses of floral and inflorescence development have also been established in some plant species. Meanwhile, phylogeny‐based comparative analysis of morphological and genetic character has enabled the identification of key evolutionary events that lead to morphological complexity and diversification. Here we review the recent progress on evo‐devo studies of floral display including floral symmetry, petal fusion, floral color, floral scent, and inflorescences. We also review the molecular genetic approaches applied to plant evo‐devo studies and highlight the future directions of evo‐devo. DA - 2017/11// PY - 2017/11// DO - 10.1111/jse.12259 VL - 55 IS - 6 SP - 487-515 LA - en SN - 16744918 ST - Evolution and developmental genetics of floral display-A review of progress UR - http://doi.wiley.com/10.1111/jse.12259 DB - Crossref Y2 - 2019/1/29/ KW - evo-devo KW - floral display KW - genetic basis KW - morphological variation ER - TY - JOUR TI - Down regulation of APETALA 3 homolog resulted in defect of floral structure critical to explosive pollen release in Cornus canadensis: The role of APETALA3 homolog in Cornus AU - Liu, Xiang AU - Li, Lu AU - Jenny Xiang, Qiu-Yun T2 - Journal of Systematics and Evolution AB - Abstract In mature buds of the dwarf dogwood lineage (DW) of Cornus , petals and filaments form an “x”‐like box containing mechanical energy from the filaments to allow explosive pollen dispersal. As a start to understand the molecular mechanisms responsible for the origin of this unique structure in Cornus , we cloned and characterized the sequences of APETALA3 ( AP3 ) homologs from Cornus canadensis of the DW lineage and five other Cornus species, given the function of AP3 on petal and stamen development in Arabidopsis , and tested the function of CorcanAP3 using a stable Agrobacterium ‐mediated transformation system. The cloned CorAP3s ( AP3 ‐like genes in Cornus ) were confirmed to belong to the euAP3 lineage. qRT‐PCR analysis indicated strong increase of CorcanAP3 expression in floral buds of wildtype C. canadensis . A hairpin construct of CorcanAP3 was successfully introduced into wild type plants of C. canadensis , resulting in significant reduction of CorcanAP3 expression and abnormal floral development. The abnormal floral buds lost the “x” form and opened immaturely due to delay or retard of petal and stamen elongation and the push of style elongation. The results suggested CorcanAP3 may function to regulate the coordinated rate of development of petals and stamens in C. canadensis , necessary for the x‐structure formation, although the exact molecular mechanism remains unclear. Comparison among six Cornus species indicated a greater ratio of stamen to petal and style growth in C. canadensis , suggesting an evolutionary change of CorAP3 expression pattern in the DW lineage, leading to the greater growth of filaments to form the “x”‐box. DA - 2017/11// PY - 2017/11// DO - 10.1111/jse.12272 VL - 55 IS - 6 SP - 566-580 LA - en SN - 16744918 ST - Down regulation of APETALA UR - http://doi.wiley.com/10.1111/jse.12272 DB - Crossref Y2 - 2019/1/29/ KW - abnormality in floral development KW - Cornus canadensis KW - explosive pollen release KW - functional validation of APETALA3 homolog KW - gene expression KW - genetic transformation ER - TY - JOUR TI - Near infrared spectroscopic data handling and chemometric analysis with the R statistical programming language: A practical tutorial AU - Whitfield, Matthew B. AU - Chinn, Mari S. T2 - JOURNAL OF NEAR INFRARED SPECTROSCOPY AB - Near infrared spectroscopy is widely used for compositional analysis of bulk materials because it is inexpensive, fast, and non-destructive. However, the chemometric techniques required to produce near infrared calibrations are varied and complex. While there are a number of commercial applications capable of implementing these techniques, there has also been a recent proliferation of R packages for chemometrics. The R programming language has greater capabilities for data processing, automation of multiple analyses, and user development of new techniques than many of the closed-source, graphical user interface-based commercial chemometrics applications do. The R project is thus a powerful, open-source option for generating and testing near infrared calibrations, albeit with a longer learning curve than many of the commercial chemometric applications. The calibration techniques available in R have been widely demonstrated in both the primary literature and introductory texts, but less so the steps between the acquisition of the data and the calibration. This tutorial seeks to bridge that gap by demonstrating a practical approach to data transfer and handling, using R and several packages available on the Comprehensive R Archive Network ( https://cran.r-project.org/ ), and then illustrates the use of the resulting data framework in the generation of near infrared calibrations. DA - 2017/12// PY - 2017/12// DO - 10.1177/0967033517740768 VL - 25 IS - 6 SP - 363-380 SN - 1751-6552 KW - Near infrared spectroscopy KW - chemometrics KW - Rstudio KW - Comprehensive R Archive Network KW - R language KW - open source statistical programming language KW - Foss Vision KW - solid material composition KW - PLS KW - data pretreatment ER - TY - JOUR TI - Trait shifts associated with the subshrub life-history strategy in a tropical savanna AU - Giroldo, A. B. AU - Scariot, A. AU - Hoffmann, W. A. T2 - OECOLOGIA AB - Over the past 10 million years, tropical savanna environments have selected for small growth forms within woody plant lineages. The result has been the evolution of subshrubs (geoxyles), presumably as an adaptation to frequent fire. To evaluate the traits associated with the shift from tree to subshrub growth forms, we compared seed biomass, germination, survival, resprouting, biomass allocation, and photosynthesis between congeneric trees and subshrubs, and quantified phylogenetic conservatism. Despite large differences in adult morphology between trees and subshrub species, the differences are modest in seedlings, and most of the variation in traits was explained by genus, indicating considerable phylogenic conservatism. Regardless, tree seedlings invested more heavily in aboveground growth, compared to subshrubs, which is consistent with the adult strategy of savanna trees, which depend on a large resistant-fire stem. Subshrub seedlings also invest in greater non-structural carbohydrate reserves, likely as an adaptation to the high fire frequencies typical of tropical savannas. The modest differences as seedlings suggest that selective pressures during early development may not have contributed substantially to the evolution of the subshrub growth form and that the distinct allocation and life history must arise later in life. This is consistent with the interpretation that the subshrub growth form arose as a life-history strategy in which maturity is reached at a small stem size, allowing them to reproduce despite repeated fire-induced topkill. The convergent evolution of subshrubs within multiple tree lineages reaffirms the importance of fire in the origin and diversification of the flora of mesic savannas. DA - 2017/10// PY - 2017/10// DO - 10.1007/s00442-017-3930-4 VL - 185 IS - 2 SP - 281-291 SN - 1432-1939 KW - Subshrub vs tree KW - Brazilian Savanna KW - Savanna evolution KW - Fire adaptations KW - Traits phylogenetically conserved ER - TY - JOUR TI - Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria AU - Zhang, Yunlong AU - Zhang, Ran AU - Nazari, Milad AU - Bagley, Michael C. AU - Miller, Eric S. AU - Williams, Philip G. AU - Muddiman, David C. AU - Lindsey, Jonathan S. T2 - JOURNAL OF PORPHYRINS AND PHTHALOCYANINES AB - Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by the molecular ion and four characteristic fragments. The molecular ion of chlorophyll [Formula: see text] also was observed. The sheared and vortexed sample contained substantial numbers of intact cells as demonstrated by regrowth of the filamentous cyanobacterium–microbial culture. The semi-quantitative and rapid qualitative methods developed herein should facilitate examination of other tolyporphin-producing organisms among the vast worldwide strains of cyanobacteria as well as investigation of the biosynthesis of tolyporphins. DA - 2017/11// PY - 2017/11// DO - 10.1142/s108842461750078x VL - 21 IS - 11 SP - 759-768 SN - 1099-1409 KW - IR-MALDESI-FTMS KW - MS/MS KW - MALDI-TOF-MS KW - chlorophyll KW - bacteriochlorin KW - high-throughput screening ER - TY - JOUR TI - Evidence of mixotrophic carbon-capture by n-butanol-producer Clostridium beijerinckii AU - Sandoval-Espinola, W. J. AU - Chinn, M. S. AU - Thon, M. R. AU - Bruno-Bárcena, J. M. T2 - Scientific Reports AB - Recent efforts to combat increasing greenhouse gas emissions include their capture into advanced biofuels, such as butanol. Traditionally, biobutanol research has been centered solely on its generation from sugars. Our results show partial re-assimilation of CO2 and H2 by n-butanol-producer C. beijerinckii. This was detected as synchronous CO2/H2 oscillations by direct (real-time) monitoring of their fermentation gasses. Additional functional analysis demonstrated increased total carbon recovery above heterotrophic values associated to mixotrophic assimilation of synthesis gas (H2, CO2 and CO). This was further confirmed using 13C-Tracer experiments feeding 13CO2 and measuring the resulting labeled products. Genome- and transcriptome-wide analysis revealed transcription of key C-1 capture and additional energy conservation genes, including partial Wood-Ljungdahl and complete reversed pyruvate ferredoxin oxidoreductase / pyruvate-formate-lyase-dependent (rPFOR/Pfl) pathways. Therefore, this report provides direct genetic and physiological evidences of mixotrophic inorganic carbon-capture by C. beijerinckii. DA - 2017/10/6/ PY - 2017/10/6/ DO - 10.1038/s41598-017-12962-8 VL - 7 IS - 1 SP - J2 - Sci Rep LA - en OP - SN - 2045-2322 UR - http://dx.doi.org/10.1038/s41598-017-12962-8 DB - Crossref ER - TY - JOUR TI - Canalization of Seasonal Phenology in the Presence of Developmental Variation: Seed Dormancy Cycling in an Annual Weed AU - Edwards, Brianne AU - Burghardt, Liana T. AU - Kovach, Katherine E. AU - Donohue, Kathleen T2 - INTEGRATIVE AND COMPARATIVE BIOLOGY AB - Variation in the developmental timing in one life stage may ramify within and across generations to disrupt optimal phenology of other life stages. By focusing on a common mechanism of developmental arrest in plants-seed dormancy-we investigated how variation in flowering time influenced seed germination behavior and identified potential processes that can lead to canalized germination behavior despite variation in reproductive timing. We quantified effects of reproductive timing on dormancy cycling by experimentally manipulating the temperature during seed maturation and the seasonal timing of seed dispersal/burial, and by assessing temperature-dependent germination of un-earthed seeds over a seasonal cycle. We found that reproductive timing, via both seed-maturation temperature and the timing of dispersal, strongly influenced germination behavior in the weeks immediately following seed burial. However, buried seeds subsequently canalized their germination behavior, after losing primary dormancy and experiencing natural temperature and moisture conditions in the field. After the complete loss of primary dormancy, germination behavior was similar across seed-maturation and dispersal treatments, even when secondary dormancy was induced. Maternal effects themselves may contribute to the canalization of germination: first, by inducing stronger dormancy in autumn-matured seeds, and second by modifying the responses of those seeds to their ambient environment. Genotypes differed in dormancy cycling, with functional alleles of known dormancy genes necessary for the suppression of germination at warm temperatures in autumn through spring across multiple years. Loss of function of dormancy genes abolished almost all dormancy cycling. In summary, effects of reproductive phenology on dormancy cycling of buried seeds were apparent only as long as seeds retained primary dormancy, and a combination of genetically imposed seed dormancy, maternally induced seed dormancy, and secondary dormancy can mitigate variation in germination behavior imposed by variation in reproductive phenology. DA - 2017/11// PY - 2017/11// DO - 10.1093/icb/icx065 VL - 57 IS - 5 SP - 1021-1039 SN - 1557-7023 ER - TY - JOUR TI - The triple response assay and its use to characterize ethylene mutants in Arabidopsis AU - Merchante, C. AU - Stepanova, A. N. T2 - Ethylene signaling: methods and protocols DA - 2017/// PY - 2017/// VL - 1573 SP - 163-209 ER - TY - JOUR TI - The biodiversity cost of carbon sequestration in tropical savanna AU - Abreu, Rodolfo C. R. AU - Hoffmann, William A. AU - Vasconcelos, Heraldo L. AU - Pilon, Natashi A. AU - Rossatto, Davi R. AU - Durigan, Giselda T2 - SCIENCE ADVANCES AB - Forest expansion into Brazilian savanna due to fire suppression causes precipitous species loss. DA - 2017/8// PY - 2017/8// DO - 10.1126/sciadv.1701284 VL - 3 IS - 8 SP - SN - 2375-2548 ER - TY - JOUR TI - Redundant CArG Box Cis-motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development AU - Sehra, Bhupinder AU - Franks, Robert G. T2 - FRONTIERS IN PLANT SCIENCE AB - In the Arabidopsis thaliana seed pod, pod shatter and seed dispersal properties are in part determined by the development of a longitudinally-orientated dehiscence zone that derives from cells of the gynoecial valve margin. Transcriptional regulation of the MADS protein encoding transcription factors genes SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2) are critical for proper valve margin (VM) identity specification and later on for dehiscence zone (DZ) development. Current models of SHP1 and SHP2 regulation indicate that the transcription factors FRUITFULL (FUL) and REPLUMLESS (RPL) repress these SHP genes in the developing valve and replum domains, respectively. Thus the expression of the SHP genes is restricted to the VM. FUL encodes a MADS-box containing transcription factor that is predicted to act through CArG-box containing cis-regulatory motifs. Here we delimit functional modules within the SHP2 cis-regulatory region and examine the functional importance of CArG box motifs within these regulatory regions. We have characterized a 2.2kb region upstream of the SHP2 translation start site that drives early and late medial domain expression in the gynoecium, as well as expression within the VM and DZ. We identified two separable, independent cis-regulatory modules, a 1kb promoter region and a 700bp enhancer region, that are capable of giving valve margin and dehiscence zone expression. Our results argue for multiple independent cis-regulatory modules that support SHP2 expression during VM development and may contribute to the robustness of SHP2 expression in this tissue. Additionally, three closely positioned CArG box motifs located in the SHP2 upstream regulatory region were mutated in the context of the 2.2kb reporter construct. Mutating simultaneously all three CArG boxes caused a moderate de-repression of the SHP2 reporter that was detected within the valve domain, suggesting that these CArG boxes are involved in SHP2 repression in the valve. DA - 2017/10/16/ PY - 2017/10/16/ DO - 10.3389/fpls.2017.01712 VL - 8 SP - SN - 1664-462X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85034058138&partnerID=MN8TOARS KW - SHATTERPROOF genes KW - FRUITFULL KW - seedpod dehiscence KW - valve margin KW - fruit patterning KW - transcriptional regulation ER - TY - JOUR TI - Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips AU - Wear, Emily E. AU - Song, Jawon AU - Zynda, Gregory J. AU - LeBlanc, Chantal AU - Lee, Tae-Jin AU - Mickelson-Young, Leigh AU - Concia, Lorenzo AU - Mulvaney, Patrick AU - Szymanski, Eric S. AU - Allen, George C. AU - Martienssen, Robert A. AU - Vaughn, Matthew W. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. T2 - PLANT CELL AB - All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the “Repli-seq” assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ∼32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase. DA - 2017/9// PY - 2017/9// DO - 10.1105/tpc.17.00037 VL - 29 IS - 9 SP - 2126-2149 SN - 1532-298X UR - http://europepmc.org/abstract/med/28842533 ER - TY - JOUR TI - Photophysical Characterization of the Naturally Occurring Dioxobacteriochlorin Tolyporphin A and Synthetic Oxobacteriochlorin Analogues AU - Hood, Don AU - Niedzwiedzki, Dariusz M. AU - Zhang, Ran AU - Zhang, Yunlong AU - Dai, Jingqiu AU - Miller, Eric S. AU - Bocian, David F. AU - Williams, Philip G. AU - Lindsey, Jonathan S. AU - Holten, Dewey T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Tolyporphins are tetrapyrrole macrocycles produced by a cyanobacterium‐containing culture known as HT ‐58‐2. Tolyporphins A–J are free base dioxobacteriochlorins, whereas tolyporphin K is an oxochlorin. Here, the photophysical characterization is reported of tolyporphin A and two synthetic analogues, an oxobacteriochlorin and a dioxobacteriochlorin. The characterization (in toluene, diethyl ether, ethyl acetate, dichloromethane, 1‐pentanol, 2‐butanone, ethanol, methanol, N,N ‐dimethylformamide and dimethylsulfoxide) includes static absorption and fluorescence spectra, fluorescence quantum yields and time‐resolved data. The data afford the lifetime of the lowest singlet excited state and the yields of the nonradiative decay pathways (intersystem crossing and internal conversion). The three macrocycles exhibit only modest variation in spectroscopic and excited‐state photophysical parameters across the solvents. The long‐wavelength (Q y ) absorption band of tolyporphin A appears at ~680 nm and is remarkably narrow (full‐width‐at‐half‐maximum ~7 nm). The position of the long‐wavelength (Q y ) absorption band of tolyporphin A (~680 nm) more closely resembles that of chlorophyll a (662 nm) than bacteriochlorophyll a (772 nm). The absorption spectra of tolyporphins B–I, K (which were available in minute quantities) are also reported in methanol; the spectra of B–I closely resemble that of tolyporphin A. Taken together, tolyporphin A generally exhibits spectral and photophysical features resembling those of chlorophyll a . DA - 2017/10// PY - 2017/10// DO - 10.1111/php.12781 VL - 93 IS - 5 SP - 1204-1215 SN - 1751-1097 ER - TY - JOUR TI - Metabolomics reveal physiological changes in mayfly larvae (Neocloeon triangulifer) at ecological upper thermal limits AU - Chou, Hsuan AU - Pathmasiri, Wimal AU - Deese-Spruill, Jocelin AU - Sumner, Susan AU - Buchwalter, David B. T2 - JOURNAL OF INSECT PHYSIOLOGY AB - Aquatic insects play critical roles in freshwater ecosystems and temperature is a fundamental driver of species performance and distributions. However, the physiological mechanisms that determine the thermal performance of species remain unclear. Here we used a metabolomics approach to gain insights into physiological changes associated with a short-term, sublethal thermal challenge in the mayfly Neocloeon triangulifer (Ephemeroptera: Baetidae). Larvae were subjected to a thermal ramp (from 22 to 30 °C at a rate of 1 °C/h) and metabolomics analysis (both Nuclear Magnetic Resonance (NMR) Spectroscopy and Gas Chromatography coupled Time-of-Flight Mass Spectrometry (GC-TOF-MS)) indicated that processes related to energetics (sugar metabolism) and membrane stabilization primarily differentiated heat treated larvae from controls. Limited evidence of anaerobic metabolism was observed in the heat treated larvae at 30 °C, a temperature that is chronically lethal to larvae. DA - 2017/// PY - 2017/// DO - 10.1016/j.jinsphys.2017.07.008 VL - 101 SP - 107-112 SN - 1879-1611 KW - Aquatic insects KW - Mayfly KW - Thermal limits KW - Metabolomics KW - Temperature ER - TY - JOUR TI - Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community AU - Hughes, Rebecca-Ayme AU - Zhang, Yunlong AU - Zhang, Ran AU - Williams, Philip G. AU - Lindsey, Jonathan S. AU - Miller, Eric S. T2 - APPLIED AND ENVIRONMENTAL MICROBIOLOGY AB - ABSTRACT The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae , 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a , and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis. IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway. DA - 2017/10// PY - 2017/10// DO - 10.1128/aem.01068-17 VL - 83 IS - 19 SP - SN - 1098-5336 KW - cyanobacteria KW - genome analysis KW - phylogenetic analysis KW - tetrapyrroles KW - tolyporphin ER - TY - JOUR TI - Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem AU - Wendrich, Jos R. AU - Moller, Barbara K. AU - Li, Song AU - Saiga, Shunsuke AU - Sozzani, Rosangela AU - Benfey, Philip N. AU - De Rybel, Bert AU - Weijers, Dolf T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem, a group of slowly dividing quiescent center cells is thought to limit stem cell activity to directly neighboring cells, thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction to the more gradual changes in cell division potential and differentiation that occur as cells move further away from the quiescent center. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation. DA - 2017/10/17/ PY - 2017/10/17/ DO - 10.1073/pnas.1707400114 VL - 114 IS - 42 SP - E8922-E8929 SN - 0027-8424 KW - plant development KW - root meristem KW - Arabidopsis KW - transcriptional regulation ER - TY - JOUR TI - Vacuolar trafficking and biogenesis: a maturation in the field AU - Brillada, Carla AU - Rojas-Pierce, Marcela T2 - CURRENT OPINION IN PLANT BIOLOGY AB - The vacuole is a prominent organelle that is essential for plant viability. The vacuole size, and its role in ion homeostasis, protein degradation and storage, place significant demands for trafficking of vacuolar cargo along the endomembrane system. Recent studies indicate that sorting of vacuolar cargo initiates at the ER and Golgi, but not the trans-Golgi network/early endosome, as previously thought. Furthermore, maturation of the trans-Golgi network into pre-vacuolar compartments seems to contribute to a major route for plant vacuolar traffic that works by bulk flow and ends with membrane fusion between the pre-vacuolar compartment and the tonoplast. Here we summarize recent evidence that indicates conserved and plant-specific mechanisms involved in sorting and trafficking of proteins to this major organelle. DA - 2017/12// PY - 2017/12// DO - 10.1016/j.pbi.2017.08.005 VL - 40 SP - 77-81 SN - 1879-0356 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85028575104&partnerID=MN8TOARS ER - TY - JOUR TI - Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development AU - Lin, Jer-Young AU - Le, Brandon H. AU - Chen, Min AU - Henry, Kelli F. AU - Hur, Jungim AU - Hsieh, Tzung-Fu AU - Chen, Pao-Yang AU - Pelletier, Julie M. AU - Pellegrini, Matteo AU - Fischer, Robert L. AU - Harada, John J. AU - Goldberg, Robert B. T2 - Proceedings of the National Academy of Sciences AB - We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis-regulatory elements and their cognate transcription factors are organized in genetic regulatory networks. DA - 2017/10/23/ PY - 2017/10/23/ DO - 10.1073/pnas.1716758114 VL - 114 IS - 45 SP - E9730-E9739 J2 - Proc Natl Acad Sci USA LA - en OP - SN - 0027-8424 1091-6490 UR - http://dx.doi.org/10.1073/pnas.1716758114 DB - Crossref KW - seed development KW - DNA methylation KW - soybean KW - Arabidopsis KW - transposon ER - TY - JOUR TI - Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa AU - Lin, Ying-Chung Jimmy AU - Chen, Hao AU - Li, Quanzi AU - Li, Wei AU - Wang, Jack P. AU - Shi, Rui AU - Tunlaya-Anukit, Sermsawat AU - Shuai, Peng AU - Wang, Zhifeng AU - Ma, Hongyan AU - Li, Huiyu AU - Sun, Ying-Hsuan AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Secondary cell wall (SCW) biosynthesis is the biological process that generates wood, an important renewable feedstock for materials and energy. NAC domain transcription factors, particularly Vascular-Related NAC-Domain (VND) and Secondary Wall-Associated NAC Domain (SND) proteins, are known to regulate SCW differentiation. The regulation of VND and SND is important to maintain homeostasis for plants to avoid abnormal growth and development. We previously identified a splice variant, PtrSND1-A2IR , derived from PtrSND1-A2 as a dominant-negative regulator, which suppresses the transactivation of all PtrSND1 family members. PtrSND1-A2IR also suppresses the self-activation of the PtrSND1 family members except for its cognate transcription factor, PtrSND1-A2, suggesting the existence of an unknown factor needed to regulate PtrSND1-A2 Here, a splice variant, PtrVND6-C1IR , derived from PtrVND6-C1 was discovered that suppresses the protein functions of all PtrVND6 family members. PtrVND6-C1IR also suppresses the expression of all PtrSND1 members, including PtrSND1-A2, demonstrating that PtrVND6-C1IR is the previously unidentified regulator of PtrSND1-A2 We also found that PtrVND6-C1IR cannot suppress the expression of its cognate transcription factor, PtrVND6-C1PtrVND6-C1 is suppressed by PtrSND1-A2IR Both PtrVND6-C1IR and PtrSND1-A2IR cannot suppress their cognate transcription factors but can suppress all members of the other family. The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation. This reciprocal cross-regulation between families suggests a general mechanism among NAC domain proteins and likely other transcription factors, where intron-retained splice variants provide an additional level of regulation. DA - 2017/11/7/ PY - 2017/11/7/ DO - 10.1073/pnas.1714422114 VL - 114 IS - 45 SP - E9722-E9729 SN - 0027-8424 KW - reciprocal cross-regulation KW - NAC transcription factors KW - alternative splicing KW - wood formation KW - Populus trichocarpa ER - TY - JOUR TI - Invasibility of a fire-maintained savanna-wetland gradient by non-native, woody plant species AU - Just, Michael G. AU - Hohmann, Matthew G. AU - Hoffmann, William A. T2 - FOREST ECOLOGY AND MANAGEMENT AB - Fire-promoting, open-canopy ecosystems are under threat of conversion to a fire-deterring, closed-canopy condition due to woody encroachment. This conversion of vegetation structure has been fostered by introduced woody plant species. We performed a field experiment to quantify growth, survival, and establishment success of six invasive, woody species along a managed longleaf pine savanna–wetland gradient in the Sandhills of North Carolina, USA. We investigated the effects of prescribed fire, fire history, dispersal, and abiotic conditions on the invasibility of sites along the gradient. Across 18 study sites, seeds of the six woody species were sown using three sowing methods that mimicked primary and secondary dispersal; each site contained paired plots located in savanna and savanna-wetland ecotone vegetation communities. We identified sowing treatment, abiotic conditions, seedling size, and prescribed fire as important factors for controlling woody invasion, as they prevented 5 of 6 study species from establishing in the landscape. However, the landscape was not immune to invasion. At the end of the 42-month study period, three species had established in unburned sites. In sites burned after seedling emergence, only one species, Pyrus calleryana, survived and established. We found P. calleryana survival and establishment to be a function of seedling size, soil humic matter content, and sowing treatment. Successful invasion and establishment of woody individuals in open-canopied systems increases the likelihood of fire-deterrence and further woody encroachment, threatening ecosystem integrity. DA - 2017/12/1/ PY - 2017/12/1/ DO - 10.1016/j.foreco.2017.09.052 VL - 405 SP - 229-237 SN - 1872-7042 KW - Establishment limitation KW - Fire ecology KW - Pins palustris KW - Pyrus calletyana KW - Seedling recruitment KW - Streamhead pocosin ER - TY - JOUR TI - Comment on "The extent of forest in dryland biomes" AU - Griffith, D. M. AU - Lehmann, C. E. R. AU - Stromberg, C. A. E. AU - Parr, C. L. AU - Pennington, R. T. AU - Sankaran, M. AU - Ratnam, J. AU - Still, C. J. AU - Powell, R. L. AU - Hanan, N. P. AU - Nippert, J. B. AU - Osborne, C. P. AU - Good, S. P. AU - Anderson, T. M. AU - Holdo, R. M. AU - Veldman, J. W. T2 - Science DA - 2017/// PY - 2017/// VL - 358 IS - 6365 ER - TY - JOUR TI - Assessing species biomass contributions in microbial communities via metaproteomics AU - Kleiner, Manuel AU - Thorson, Erin AU - Sharp, Christine E. AU - Dong, Xiaoli AU - Liu, Dan AU - Li, Carmen AU - Strous, Marc T2 - NATURE COMMUNICATIONS AB - Abstract Microbial community structure can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. Methods for quantifying cell numbers are already available (e.g., fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing), yet high-throughput methods for assessing community structure in terms of biomass are lacking. Here we present metaproteomics-based methods for assessing microbial community structure using protein abundance as a measure for biomass contributions of individual populations. We optimize the accuracy and sensitivity of the method using artificially assembled microbial communities and show that it is less prone to some of the biases found in sequencing-based methods. We apply the method to communities from two different environments, microbial mats from two alkaline soda lakes, and saliva from multiple individuals. We show that assessment of species biomass contributions adds an important dimension to the analysis of microbial community structure. DA - 2017/11/16/ PY - 2017/11/16/ DO - 10.1038/s41467-017-01544-x VL - 8 SP - SN - 2041-1723 UR - https://www.nature.com/articles/s41467-017-01544-x ER - TY - JOUR TI - Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms AU - Ma, Qing AU - Liu, Xiang AU - Franks, Robert G. AU - Xiang, Qiu-Yun T2 - NEW PHYTOLOGIST AB - TFL1-, AP1- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages. DA - 2017/10// PY - 2017/10// DO - 10.1111/nph.14197 VL - 216 IS - 2 SP - 519-535 SN - 1469-8137 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84988892931&partnerID=MN8TOARS KW - CorAP1 KW - Cornus KW - CorTFL1 KW - evolutionary development KW - gene expression KW - inflorescence KW - in situ hybridization KW - quantitative real-time polymerase chain reaction (qRT-PCR) ER - TY - JOUR TI - A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae AU - Reyes, Maria Ines AU - Flores-Vergara, Miguel A. AU - Guerra-Peraza, Orlene AU - Rajabu, Cyprian AU - Desai, Jigar AU - Hiromoto-Ruiz, Yokiko H. AU - Ndunguru, Joseph AU - Hanley-Bowdoin, Linda AU - Kjemtrup, Susanne AU - Ascencio-Ibanez, Jose T. AU - Robertson, Dominique T2 - PLANT JOURNAL AB - Summary Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus‐resistant genes that derive from alterations in essential host factors. We used a virus‐induced gene silencing ( VIGS ) vector derived from the geminivirus Cabbage leaf curl virus (Ca LC uV) to assess natural variation in virus–host interactions in 190 Arabidopsis accessions. Silencing of CH ‐42 , encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS , and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS . One accession, Pla‐1, lacked both symptoms and silencing, and was immune to wild‐type infectious clones corresponding to Ca LC uV or Beet curly top virus ( BCTV ), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus ( TYLCV ). Quantitative trait locus mapping of a Pla‐1 X Col‐0 F 2 population was used to detect a major peak on chromosome 1, which is designated gip‐1 ( geminivirus immunity Pla‐1‐1 ). The recessive nature of resistance to Ca LC uV and the lack of obvious candidate genes near the gip‐1 locus suggest that a novel resistance gene(s) confers immunity. DA - 2017/12// PY - 2017/12// DO - 10.1111/tpj.13716 VL - 92 IS - 5 SP - 796-807 SN - 1365-313X KW - Arabidopsis KW - BCTV KW - CaLCuV KW - geminivirus KW - gip-1 KW - immunity KW - Pla-1 KW - VIGS ER - TY - JOUR TI - Repliscan: a tool for classifying replication timing regions AU - Zynda, Gregory J. AU - Song, Jawon AU - Concia, Lorenzo AU - Wear, Emily E. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. AU - Vaughn, Matthew W. T2 - BMC BIOINFORMATICS AB - Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing.To accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds.Repliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage. DA - 2017/8/7/ PY - 2017/8/7/ DO - 10.1186/s12859-017-1774-x VL - 18 SP - 1-14 SN - 1471-2105 UR - http://europepmc.org/abstract/med/28784090 KW - DNA replication KW - Repli-seq KW - Classification ER - TY - JOUR TI - Escherichia coli O157:H7 Acid Sensitivity Correlates with Flocculation Phenotype during Nutrient Limitation AU - Kay, Kathryn L. AU - Breidt, Frederick AU - Fratamico, Pina M. AU - Baranzoni, Gian M. AU - Kim, Gwang-Hee AU - Grunden, Amy M. AU - Oh, Deog-Hwan T2 - FRONTIERS IN MICROBIOLOGY AB - Shiga toxin producing Escherichia coli (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3.3 targeting acidified foods. Strains exhibiting flocculation were more acid sensitive and were designated FAS, for flocculation acid sensitive, while the acid resistant strain designated PAR for planktonic acid resistant. Flocculation was not observed for any strains during growth in complex medium (Luria Bertani broth). STEC strains B201 and B241 were chosen as representative FAS (2.4 log reduction) and PAR (0.15 log reduction) strains, respectively, due to differences in acid resistance and flocculation phenotype. Results from electron microscopy showed evidence of fimbriae production in B201, whereas fimbriae were not observed in B241.Curli fimbriae production was identified through plating on Congo red differential medium, and all FAS strains showed curli fimbriae production. Surprisingly, 5 PAR strains also had evidence of curli production. Transcriptomic and targeted gene expression data for B201 and B241indicated that csg and hde (curli and acid induced chaperone genes, respectively) expression positively correlated with the phenotypic differences observed for these strains. These data suggest that FAS strains grown in minimal medium express curli, resulting in a flocculation phenotype. This may be regulated by GcvB, which positively regulates curli fimbriae production and represses acid chaperone proteins. RpoS and other regulatory mechanisms may impact curli fimbriae production, as well. These findings may help elucidate mechanisms underlying differences among STEC strains in relating acid resistance and biofilm formation. DA - 2017/7/26/ PY - 2017/7/26/ DO - 10.3389/fmicb.2017.01404 VL - 8 SP - SN - 1664-302X KW - STEC KW - acid resistance KW - nutrient limitation KW - curli KW - GcvB ER - TY - JOUR TI - Transcriptomic Analysis in Strawberry Fruits Reveals Active Auxin Biosynthesis and Signaling in the Ripe Receptacle (vol 8, pg 889, 2017) AU - Estrada-Johnson, Elizabeth AU - Csukasi, Fabiana AU - Pizarro, Carmen M. AU - Vallarino, Jose G. AU - Kiryakova, Yulia AU - Vioque, Amalia AU - Merchante, Catharina AU - Brumos, Javier AU - Medina-Escobar, Nieves AU - Botella, Miguel A. AU - Alonso, Jose M. AU - Fernie, Alisdair R. AU - Sanchez-Sevilla, Jose F. AU - Osorio, Sonia AU - Valpuesta, Victoriano T2 - FRONTIERS IN PLANT SCIENCE AB - [This corrects the article on p. 889 in vol. 8, PMID: 28611805.]. DA - 2017/7/24/ PY - 2017/7/24/ DO - 10.3389/fpls.2017.01305 VL - 8 SP - SN - 1664-462X KW - auxin KW - fruit KW - strawberry KW - transcriptome regulation KW - ripening ER - TY - JOUR TI - Physiological responses to short-term thermal stress in mayfly (Neocloeon triangulifer) larvae in relation to upper thermal limits AU - Kim, Kyoung Sun AU - Chou, Hsuan AU - Funk, David H. AU - Jackson, John K. AU - Sweeney, Bernard W. AU - Buchwalter, David B. T2 - JOURNAL OF EXPERIMENTAL BIOLOGY AB - Understanding species' thermal limits and their physiological determinants is critical in light of climate change and other human activities that warm freshwater ecosystems. Here, we ask whether oxygen limitation determines the chronic upper thermal limits in larvae of the mayfly Neocloeon triangulifer, an emerging model for ecological and physiological studies. Our experiments are based on a robust understanding of the upper acute (∼40°C) and chronic thermal limits of this species (>28°C, ≤30°C) derived from full life cycle rearing experiments across temperatures. We tested two related predictions derived from the hypothesis that oxygen limitation sets the chronic upper thermal limits: (1) aerobic scope declines in mayfly larvae as they approach and exceed temperatures that are chronically lethal to larvae; and (2) genes indicative of hypoxia challenge are also responsive in larvae exposed to ecologically relevant thermal limits. Neither prediction held true. We estimated aerobic scope by subtracting measurements of standard oxygen consumption rates from measurements of maximum oxygen consumption rates, the latter of which was obtained by treating with the metabolic uncoupling agent carbonyl cyanide-4-(trifluoromethoxy) pheylhydrazone (FCCP). Aerobic scope was similar in larvae held below and above chronic thermal limits. Genes indicative of oxygen limitation (LDH, EGL-9) were only upregulated under hypoxia or during exposure to temperatures beyond the chronic (and more ecologically relevant) thermal limits of this species (LDH). Our results suggest that the chronic thermal limits of this species are likely not driven by oxygen limitation, but rather are determined by other factors, e.g. bioenergetics costs. We caution against the use of short-term thermal ramping approaches to estimate critical thermal limits (CTmax) in aquatic insects because those temperatures are typically higher than those that occur in nature. DA - 2017/7/15/ PY - 2017/7/15/ DO - 10.1242/jeb.156919 VL - 220 IS - 14 SP - 2598-2605 SN - 1477-9145 KW - Temperature KW - Aerobic scope KW - Hypoxia KW - Aquatic insect KW - Gene expression ER - TY - JOUR TI - Overexpression of a type-I isopentenyl pyrophosphate isomerase of Artemisia annua in the cytosol leads to high arteannuinB production and artemisinin increase AU - Ma, D. M. AU - Li, G. AU - Alejos-Gonzalez, F. AU - Zhu, Y. AU - Xue, Z. AU - Wang, A. M. AU - Zhang, H. AU - Li, X. AU - Ye, H. C. AU - Wang, H. AU - Liu, B. Y. AU - DE-YU, XIE T2 - Plant Journal AB - Summary We recently characterized a gene–terpene network that is associated with artemisinin biosynthesis in self‐pollinated ( SP ) Artemisia annua , an effective antimalarial plant. We hypothesize that an alteration of gene expression in the network may improve the production of artemisinin and its precursors. In this study, we cloned an isopentenyl pyrophosphate isomerase ( IPPI ) cDNA , Aa IPPI 1 , from Artemisia annua (Aa). The full‐length cDNA encodes a type‐I IPPI containing a plastid transit peptide ( PTP ) at its amino terminus. After the removal of the PTP , the recombinant truncated Aa IPPI 1 isomerized isopentenyl pyrophosphate ( IPP ) to dimethyl allyl pyrophosphate ( DMAPP ) and vice versa . The steady‐state equilibrium ratio of IPP / DMAPP in the enzymatic reactions was approximately 1:7. The truncated Aa IPPI 1 was overexpressed in the cytosol of the SP A. annua variety. The leaves of transgenic plants produced approximately 4% arteannuin B (g g −1 , dry weight, dw) and 0.17–0.25% artemisinin (g g −1 , dw), the levels of which were significantly higher than those in the leaves of wild‐type plants. In addition, transgenic plants showed an increase in artemisinic acid production of more than 1% (g g −1 , dw). In contrast, isoprene formation was significantly reduced in transgenic plants. These results provide evidence that overexpression of AaIPPI1 in the cytosol can lead to metabolic alterations of terpenoid biosynthesis, and show that these transgenic plants have the potential to yield high production levels of arteannuin B as a new precursor source for artemisinin. DA - 2017/// PY - 2017/// DO - 10.1111/tpj.13583 VL - 91 IS - 3 SP - 466–479 ER - TY - JOUR TI - Construction and setup of a bench-scale algal photosynthetic bioreactor with temperature, light, and pH monitoring for kinetic growth tests AU - Karam, A.L. AU - McMillan, C.C. AU - Lai, Y.-C. AU - De Los Reyes, F.L. AU - Sederoff, H.W. AU - Grunden, A.M. AU - Ranjithan, R.S. AU - Levis, J.W. AU - Ducoste, J.J. T2 - Journal of Visualized Experiments AB - The optimal design and operation of photosynthetic bioreactors (PBRs) for microalgal cultivation is essential for improving the environmental and economic performance of microalgae-based biofuel production. Models that estimate microalgal growth under different conditions can help to optimize PBR design and operation. To be effective, the growth parameters used in these models must be accurately determined. Algal growth experiments are often constrained by the dynamic nature of the culture environment, and control systems are needed to accurately determine the kinetic parameters. The first step in setting up a controlled batch experiment is live data acquisition and monitoring. This protocol outlines a process for the assembly and operation of a bench-scale photosynthetic bioreactor that can be used to conduct microalgal growth experiments. This protocol describes how to size and assemble a flat-plate, bench-scale PBR from acrylic. It also details how to configure a PBR with continuous pH, light, and temperature monitoring using a data acquisition and control unit, analog sensors, and open-source data acquisition software. DA - 2017/// PY - 2017/// DO - 10.3791/55545 VL - 2017 IS - 124 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85021241433&partnerID=MN8TOARS KW - Bioengineering KW - Issue 124 KW - Photosynthetic bioreactors KW - microalgae KW - growth kinetics KW - biofuel KW - temperature KW - light KW - pH KW - automated monitoring ER - TY - JOUR TI - Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells AU - Balaguer, M. A. D. AU - Fisher, A. P. AU - Clark, N. M. AU - Fernandez-Espinosa, M. G. AU - Moller, B. K. AU - Weijers, D. AU - Lohmann, J. U. AU - Williams, C. AU - Lorenzo, O. AU - Sozzani, Rosangela AU - al. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells. DA - 2017/9/5/ PY - 2017/9/5/ DO - 10.1073/pnas.1707566114 VL - 114 IS - 36 SP - E7632-E7640 SN - 0027-8424 KW - root stem cell KW - root development KW - cell-type expression profile KW - gene regulatory network KW - modeling ER - TY - JOUR TI - Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii AU - Coneva, Viktoriya AU - Frank, Margaret H. AU - Balaguer, Maria A. de Luis AU - Li, Mao AU - Sozzani, Rosangela AU - Chitwood, Daniel H. T2 - PLANT PHYSIOLOGY AB - Thicker leaves allow plants to grow in water-limited conditions. However, our understanding of the genetic underpinnings of this highly functional leaf shape trait is poor. We used a custom-built confocal profilometer to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato Solanum pennellii and identified quantitative trait loci. We report evidence of a complex genetic architecture of this trait and roles for both genetic and environmental factors. Several ILs with thick leaves have dramatically elongated palisade mesophyll cells and, in some cases, increased leaf ploidy. We characterized the thick IL2-5 and IL4-3 in detail and found increased mesophyll cell size and leaf ploidy levels, suggesting that endoreduplication underpins leaf thickness in tomato. Next, we queried the transcriptomes and inferred dynamic Bayesian networks of gene expression across early leaf ontogeny in these lines to compare the molecular networks that pattern leaf thickness. We show that thick ILs share S. pennellii-like expression profiles for putative regulators of cell shape and meristem determinacy as well as a general signature of cell cycle-related gene expression. However, our network data suggest that leaf thickness in these two lines is patterned at least partially by distinct mechanisms. Consistent with this hypothesis, double homozygote lines combining introgression segments from these two ILs show additive phenotypes, including thick leaves, higher ploidy levels, and larger palisade mesophyll cells. Collectively, these data establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thickness in desert-adapted tomato. DA - 2017/9// PY - 2017/9// DO - 10.1104/pp.17.00790 VL - 175 IS - 1 SP - 376-391 SN - 1532-2548 ER - TY - JOUR TI - Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root AU - Di Mambro, Riccardo AU - De Ruvo, Micol AU - Pacifici, Elena AU - Salvi, Elena AU - Sozzani, Rosangela AU - Benfey, Philip N. AU - Busch, Wolfgang AU - Novak, Ondrej AU - Ljung, Karin AU - Di Paola, Luisa AU - Maree, Athanasius F. M. AU - Costantino, Paolo AU - Grieneisen, Veronica A. AU - Sabatini, Sabrina T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin's control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size. DA - 2017/9/5/ PY - 2017/9/5/ DO - 10.1073/pnas.1705833114 VL - 114 IS - 36 SP - E7641-E7649 SN - 0027-8424 KW - plant hormones KW - cell differentiation KW - root meristem KW - computational modeling ER - TY - JOUR TI - A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens AU - Yang, Qin AU - He, Yijian AU - Kabahuma, Mercy AU - Chaya, Timothy AU - Kelly, Amy AU - Borrego, Eli AU - Bian, Yang AU - El Kasmi, Farid AU - Yang, Li AU - Teixeira, Paulo AU - Kolkman, Judith AU - Nelson, Rebecca AU - Kolomiets, Michael AU - Dangl, Jeffery L. AU - Wisser, Randall AU - Caplan, Jeffrey AU - Li, Xu AU - Lauter, Nick AU - Balint-Kurti, Peter T2 - NATURE GENETICS AB - Alleles that confer multiple disease resistance (MDR) are valuable in crop improvement, although the molecular mechanisms underlying their functions remain largely unknown. A quantitative trait locus, qMdr9.02, associated with resistance to three important foliar maize diseases-southern leaf blight, gray leaf spot and northern leaf blight-has been identified on maize chromosome 9. Through fine-mapping, association analysis, expression analysis, insertional mutagenesis and transgenic validation, we demonstrate that ZmCCoAOMT2, which encodes a caffeoyl-CoA O-methyltransferase associated with the phenylpropanoid pathway and lignin production, is the gene within qMdr9.02 conferring quantitative resistance to both southern leaf blight and gray leaf spot. We suggest that resistance might be caused by allelic variation at the level of both gene expression and amino acid sequence, thus resulting in differences in levels of lignin and other metabolites of the phenylpropanoid pathway and regulation of programmed cell death. DA - 2017/9// PY - 2017/9// DO - 10.1038/ng.3919 VL - 49 IS - 9 SP - 1364-+ SN - 1546-1718 ER - TY - JOUR TI - Effects of highway pollution on forest lichen community structure in western Wake County, North Carolina, USA AU - Perlmutter, G. B. AU - Blank, G. B. AU - Wentworth, T. R. AU - Lowman, M. D. AU - Neufeld, H. S. AU - Plata, E. R. T2 - Bryologist AB - We studied lichen communities along forest edge-to-interior gradients on opposite sides of a major highway and along a remote lakeshore in central North Carolina, U.S.A., to investigate highway pollution effects on this sensitive ecosystem component. At each site we sampled lichens on trees at 10 m intervals along each of five parallel transects established at the forest edge and at 25, 60, 100, and 150 m into the forest in the highway sites, with a similar layout along a nonlinear lakeshore in a similar forest type, from which transect distances from the forest edge were estimated using average tree distances from the nearest shoreline. Lichen communities were inventoried on tree trunks from the base up to 1.5 m height, then compared both among and within sites. Species richness was highest in the control site, and did not differ between the two highway sites. The highway sites were more similar to one another than either was to the control site, based on Bray-Curtis similarity indices. No associations were detected among sites and sampled lichen biotic components in terms of growth form, photobiont type or reproductive mode. In the highway sites, total transect species richness increased from the forest edge to 150 m distant. In the control site, species richness decreased from the forest edge to the most distant transect. Findings suggest a negative effect of highway pollution on species richness of lichen communities, but not on species composition by habit, photobiont type or reproductive mode. Despite the elevated NOx concentrations recorded along the highway, known nitrophilous species were largely absent, suggesting that other factors, including other pollutants, were affecting community structure near the highway. DA - 2017/// PY - 2017/// DO - 10.1639/0007-2745-120.1.001 VL - 120 IS - 1 SP - 1-10 ER - TY - JOUR TI - Thiazolopyridines Improve Adipocyte Function by Inhibiting 11 Beta-HSD1 Oxoreductase Activity AU - Rathinasabapathy, Thirumurugan AU - Palatini Jackson, Kimberly Marie AU - Thor, Yiwen AU - Buru, Ayuba Sunday AU - Esposito, Debora AU - Li, Xu AU - Pichika, Mallikarjuna Rao AU - Hamzah, Ahmad Sazali AU - Komarnytsky, Slavko T2 - Journal of Chemistry AB - Background . Glucocorticoid excess has been linked to clinical observations associated with the pathophysiology of metabolic syndrome. The intracellular glucocorticoid levels are primarily modulated by 11 β -hydroxysteroid dehydrogenase type 1 (11 β -HSD1) enzyme that is highly expressed in key metabolic tissues including fat, liver, and the central nervous system. Methods . In this study we synthesized a set of novel tetrahydrothiazolopyridine derivatives, TR-01–4, that specifically target 11 β -HSD1 and studied their ability to interfere with the glucocorticoid and lipid metabolism in the 3T3-L1 adipocytes. Results . Based on the docking model and structure-activity relationships, tetrahydrothiazolopyridine derivatives TR-02 and TR-04 showed the highest potency against 11 β -HSD1 by dose-dependently inhibiting conversion of cortisone to cortisol (IC 50 values of 1.8 μ M and 0.095 μ M, resp.). Incubation of fat cells with 0.1–10 μ M TR-01–4 significantly decreased cortisone-induced lipid accumulation in adipocytes and suppressed 11 β -HSD1 mRNA expression. Observed reduction in adipocyte fat stores could be partially explained by decreased expression levels of adipogenic markers (PPAR- γ , aP2) and key enzymes of lipid metabolism, including fatty acid synthase (FAS), hormone sensitive lipase (HSL), and lipoprotein lipase (LPL). Conclusions . The tetrahydrothiazolopyridine moiety served as an active pharmacophore for inhibiting 11 β -HSD1 and offered a novel therapeutic strategy to ameliorate metabolic alterations found in obesity and diabetes. DA - 2017/// PY - 2017/// DO - 10.1155/2017/3182129 VL - 2017 SP - 1-10 J2 - Journal of Chemistry LA - en OP - SN - 2090-9063 2090-9071 UR - http://dx.doi.org/10.1155/2017/3182129 DB - Crossref ER - TY - JOUR TI - Antibacterial activity of medicinal plants from The Physicians of Myddvai, a 14th century Welsh medical manuscript AU - Wagner, Charles Stephen AU - De Gezelle, Jillian AU - Robertson, Maureen AU - Robertson, Keith AU - Wilson, Mickey AU - Komarnytsky, Slavko T2 - JOURNAL OF ETHNOPHARMACOLOGY AB - Antimicrobial drug resistance is a growing threat to global public health. Historical records and herbal texts relating to traditional Celtic medicine indicate an extensive pharmacopeia of plants for treating infections likely caused by microbes. However, a major barrier for successful integration of these remedies into mainstream practice is the current lack of accurate interpretation and scientific validation. We investigated the flora of the Isle of Arran, Scotland, via in situ targeted screening of 83 out of 138 plants identified in Meddygion Myddvai (a 14th century Welsh manuscript) to treat conditions related to microbial infections, and an additional 18 plants from modern ethnobotanical knowledge on the island (Scottish School of Herbal Medicine). In a follow-up proof-of-concept study, bioassay-guided fractionation was performed to identify bioactive constituents from two high scoring hits that inhibited Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative) bacterial growth. 67 historical plants (80.7%) and 14 modern plants (77.8%) were found to have detectable levels of antimicrobial activity when tested using Mobile Discovery kits, with human saliva as a source of bacteria for screening. Sabinene, a natural bicyclic monoterpene from juniper “berries” (Juniperus communis L.) and alliin, a natural sulfoxide from garlic cloves (Allium sativum L.), were isolated and confirmed as primary antibacterial leads. Using historical medical sources such as those associated with traditional Celtic medicine to guide rigorous, evidence-based scientific investigation, provides additional leads for new and alternative bioactive molecules for combating bacterial diseases. DA - 2017/5/5/ PY - 2017/5/5/ DO - 10.1016/j.jep.2017.03.039 VL - 203 SP - 171-181 SN - 1872-7573 KW - Traditional use KW - ethnobotany KW - medicinal plants KW - microbial infections KW - antibiotics ER - TY - JOUR TI - Functional Characterization of Tea (Camellia sinensis) MYB4a Transcription Factor Using an Integrative Approach AU - Li, Mingzhuo AU - Li, Yanzhi AU - Guo, Lili AU - Gong, Niandi AU - Pang, Yongzheng AU - Jiang, Wenbo AU - Liu, Yajun AU - Jiang, Xiaolan AU - Zhao, Lei AU - Wang, Yunsheng AU - Xie, De-Yu AU - Gao, Liping AU - Xia, Tao T2 - FRONTIERS IN PLANT SCIENCE AB - Green tea (Camellia sinensis, Cs) abundantly produces a diverse array of phenylpropanoid compounds benefiting human health. To date, the regulation of the phenylpropanoid biosynthesis in tea remains to be investigated. Here, we report a cDNA isolated from leaf tissues, which encodes a R2R3-MYB transcription factor. Amino acid sequence alignment and phylogenetic analysis indicate that it is a member of the MYB4-subgroup and named as CsMYB4a. Transcriptional and metabolic analyses show that the expression profile of CsMYB4a is negatively correlated to the accumulation of six flavan-3-ols and other phenolic acids. GFP fusion analysis shows CsMYB4a’s localization in the nucleus. Promoters of five tea phenylpropanoid pathway genes are isolated and characterized to contain four types of AC-elements, which are targets of MYB4 members. Interaction of CsMYB4a and five promoters shows that CsMYB4a decreases all five promoters’ activity. To further characterize its function, CsMYB4a is overexpressed in tobacco plants. The resulting transgenic plants show dwarf, shrinking and yellowish leaf, and early senescence phenotypes. A further genome-wide transcriptomic analysis reveals that the expression levels of 20 tobacco genes involved in the shikimate and the phenylpropanoid pathways are significantly downregulated in transgenic tobacco plants. UPLC-MS and HPLC based metabolic profiling reveals significant reduction of total lignin content, rutin, chlorogenic acid, and phenylalanine in CsMYB4a transgenic tobacco plants. Promoter sequence analysis of the 20 tobacco genes characterizes four types of AC-elements. Further CsMYB4a-AC element and CsMYB4a-promoter interaction analyses indicate that the negative regulation of CsMYB4a on the shikimate and phenylpropanoid pathways in tobacco is via reducing promoter activity. Taken together, all data indicate that CsMYB4a negatively regulates the phenylpropanoid and shikimate pathways. DA - 2017/6/12/ PY - 2017/6/12/ DO - 10.3389/fpls.2017.00943 VL - 8 SP - SN - 1664-462X KW - tea KW - Camellia sinensis KW - R2R3-MYB KW - transcription factor KW - phenylpropanoids KW - shikimate pathway ER - TY - JOUR TI - Amino Acids Are an Ineffective Fertilizer for Dunaliella spp. Growth AU - Murphree, C. A. AU - Dums, J. T. AU - Jain, S. K. AU - Zhao, C. S. AU - Young, D. Y. AU - Khoshnoodi, N. AU - Tikunov, A. AU - Macdonald, J. AU - Pilot, G. AU - Sederoff, Heike AU - al. T2 - FRONTIERS IN PLANT SCIENCE AB - Autotrophic microalgae are a promising bioproducts platform. However, the fundamental requirements these organisms have for nitrogen fertilizer severely limit the impact and scale of their cultivation. As an alternative to inorganic fertilizers, we investigated the possibility of using amino acids from deconstructed biomass as a nitrogen source in the genus Dunaliella. We found that only four amino acids (glutamine, histidine, cysteine, and tryptophan) rescue Dunaliella spp. growth in nitrogen depleted media, and that supplementation of these amino acids altered the metabolic profile of Dunaliella cells. Our investigations revealed that histidine is transported across the cell membrane, and that glutamine and cysteine are not transported. Rather, glutamine, cysteine, and tryptophan are degraded in solution by a set of oxidative chemical reactions, releasing ammonium that in turn supports growth. Utilization of biomass-derived amino acids is therefore not a suitable option unless additional amino acid nitrogen uptake is enabled through genetic modifications of these algae. DA - 2017/5/26/ PY - 2017/5/26/ DO - 10.3389/fpls.2017.00847 VL - 8 SP - SN - 1664-462X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85021390666&partnerID=MN8TOARS KW - Dunaliella KW - nitrogen recycling KW - lipids KW - biofuel KW - amino acids KW - sustainability ER - TY - JOUR TI - A naturally occurring conditional albino mutant in rice caused by defects in the plastid-localized OsABCI8 transporter AU - Zeng, X. Y. AU - Tang, R. AU - Guo, H. R. AU - Ke, S. W. AU - Teng, B. AU - Hung, Y. H. AU - Xu, Z. J. AU - Xie, X. M. AU - Hsieh, Tzung-Fu AU - Zhang, X. Q. AU - al. T2 - Plant Molecular Biology DA - 2017/3/11/ PY - 2017/3/11/ DO - 10.1007/s11103-017-0598-4 VL - 94 IS - 1-2 SP - 137-148 J2 - Plant Mol Biol LA - en OP - SN - 0167-4412 1573-5028 UR - http://dx.doi.org/10.1007/s11103-017-0598-4 DB - Crossref KW - Rice KW - ABC transporter KW - Iron transport KW - Chloroplast development ER - TY - JOUR TI - Vibrio Phage KVP40 Encodes a Functional NAD(+) Salvage Pathway AU - Lee, Jae Yun AU - Li, Zhiqun AU - Miller, Eric S. T2 - JOURNAL OF BACTERIOLOGY AB - ABSTRACT The genome of T4-type Vibrio bacteriophage KVP40 has five genes predicted to encode proteins of pyridine nucleotide metabolism, of which two, nadV and natV , would suffice for an NAD + salvage pathway. NadV is an apparent nicotinamide phosphoribosyltransferase (NAmPRTase), and NatV is an apparent bifunctional nicotinamide mononucleotide adenylyltransferase (NMNATase) and nicotinamide-adenine dinucleotide pyrophosphatase (Nudix hydrolase). Genes encoding the predicted salvage pathway were cloned and expressed in Escherichia coli , the proteins were purified, and their enzymatic properties were examined. KVP40 NadV NAmPRTase is active in vitro , and a clone complements a Salmonella mutant defective in both the bacterial de novo and salvage pathways. Similar to other NAmPRTases, the KVP40 enzyme displayed ATPase activity indicative of energy coupling in the reaction mechanism. The NatV NMNATase activity was measured in a coupled reaction system demonstrating NAD + biosynthesis from nicotinamide, phosphoribosyl pyrophosphate, and ATP. The NatV Nudix hydrolase domain was also shown to be active, with preferred substrates of ADP-ribose, NAD + , and NADH. Expression analysis using reverse transcription-quantitative PCR (qRT-PCR) and enzyme assays of infected Vibrio parahaemolyticus cells demonstrated nadV and natV transcription during the early and delayed-early periods of infection when other KVP40 genes of nucleotide precursor metabolism are expressed. The distribution and phylogeny of NadV and NatV proteins among several large double-stranded DNA (dsDNA) myophages, and also those from some very large siphophages, suggest broad relevance of pyridine nucleotide scavenging in virus-infected cells. NAD + biosynthesis presents another important metabolic resource control point by large, rapidly replicating dsDNA bacteriophages. IMPORTANCE T4-type bacteriophages enhance DNA precursor synthesis through reductive reactions that use NADH/NADPH as the electron donor and NAD + for ADP-ribosylation of proteins involved in transcribing and translating the phage genome. We show here that phage KVP40 encodes a functional pyridine nucleotide scavenging pathway that is expressed during the metabolic period of the infection cycle. The pathway is conserved in other large, dsDNA phages in which the two genes, nadV and natV , share an evolutionary history in their respective phage-host group. DA - 2017/5// PY - 2017/5// DO - 10.1128/jb.00855-16 VL - 199 IS - 9 SP - SN - 1098-5530 KW - NAD KW - bacteriophages KW - genomics KW - metabolism ER - TY - JOUR TI - Translation regulation in plants: an interesting past, an exciting present and a promising future AU - Merchante, Catharina AU - Stepanova, Anna N. AU - Alonso, Jose M. T2 - PLANT JOURNAL AB - Summary Changes in gene expression are at the core of most biological processes, from cell differentiation to organ development, including the adaptation of the whole organism to the ever‐changing environment. Although the central role of transcriptional regulation is solidly established and the general mechanisms involved in this type of regulation are relatively well understood, it is clear that regulation at a translational level also plays an essential role in modulating gene expression. Despite the large number of examples illustrating the critical role played by translational regulation in determining the expression levels of a gene, our understanding of the molecular mechanisms behind such types of regulation has been slow to emerge. With the recent development of high‐throughput approaches to map and quantify different critical parameters affecting translation, such as RNA structure, protein–RNA interactions and ribosome occupancy at the genome level, a renewed enthusiasm toward studying translation regulation is warranted. The use of these new powerful technologies in well‐established and uncharacterized translation‐dependent processes holds the promise to decipher the likely complex and diverse, but also fascinating, mechanisms behind the regulation of translation. DA - 2017/5// PY - 2017/5// DO - 10.1111/tpj.13520 VL - 90 IS - 4 SP - 628-653 SN - 1365-313X UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85017002891&partnerID=MN8TOARS KW - translation KW - upstream open reading frames KW - internal ribosomal entry sites KW - gene-specific translation KW - global regulation of translation KW - RNA-binding protein ER - TY - JOUR TI - Transcriptomic analysis in strawberry fruits reveals active auxin biosynthesis and signaling in the ripe receptacle AU - Estrada-Johnson, E. AU - Csukasi, F. AU - Pizarro, C. M. AU - Vallarino, J. G. AU - Kiryakova, Y. AU - Vioque, A. AU - Brumos, J. AU - Medina-Escobar, N. AU - Botella, M. A. AU - Alonso, J. M. AU - Fernie, A. R. AU - Sanchez-Sevilla, J. F. AU - Osorio, S. AU - Valpuesta, V. T2 - Frontiers in Plant Science DA - 2017/// PY - 2017/// VL - 8 ER - TY - JOUR TI - Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa AU - Shi, Rui AU - Wang, Jack P. AU - Lin, Ying-Chung AU - Li, Quanzi AU - Sun, Ying-Hsuan AU - Chen, Hao AU - Sederoff, Ronald R. AU - Chiang, Vincent L. T2 - PLANTA DA - 2017/5// PY - 2017/5// DO - 10.1007/s00425-016-2640-1 VL - 245 IS - 5 SP - 927-938 SN - 1432-2048 KW - Wood formation KW - Transcriptome KW - Fiber cells KW - Vessel elements KW - Cell wall biosynthesis KW - Co-expression network ER - TY - JOUR TI - Linking physiological mechanisms to thermally driven life history outcomes in the Mayfly Neocloeon triangulifer AU - Chou, H. AU - Pathmasiri, W. AU - Sumner, S. AU - Buchwalter, D. T2 - Integrative and Comparative Biology DA - 2017/// PY - 2017/// VL - 57 SP - E225-225 ER - TY - JOUR TI - Keep breathing: Linking respiration to thermally regulated life history outcomes in the Mayfly Neocloeon triangulifer AU - Chou, H. AU - Funk, D. AU - Buchwalter, D. T2 - Integrative and Comparative Biology DA - 2017/// PY - 2017/// VL - 57 SP - E225-225 ER - TY - JOUR TI - Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain AU - Whitham, Jason M. AU - Schulte, Mark J. AU - Bobay, Benjamin G. AU - Bruno-Barcena, Jose M. AU - Chinn, Mari S. AU - Flickinger, Michael C. AU - Pawlak, Joel J. AU - Grunden, Amy M. T2 - APPLIED MICROBIOLOGY AND BIOTECHNOLOGY DA - 2017/2// PY - 2017/2// DO - 10.1007/s00253-016-7978-6 VL - 101 IS - 4 SP - 1615-1630 SN - 1432-0614 UR - https://doi.org/10.1007/s00253-016-7978-6 KW - Acetyl-coA KW - Carbon monoxide dehydrogenase KW - Clostridium ljungdahlii KW - Ethanol KW - Wood-Ljungdahl pathway ER - TY - JOUR TI - Overexpression and Suppression of Artemisia annua 4-Hydroxy-3-Methylbut-2-enyl Diphosphate Reductase 1 Gene (AaHDR1) Differentially Regulate Artemisinin and Terpenoid Biosynthesis AU - Ma, Dongming AU - Li, Gui AU - Zhu, Yue AU - Xie, De-Yu T2 - FRONTIERS IN PLANT SCIENCE AB - 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR) catalyzes the last step of the 2-C-methyl-D-erythritol 4- phosphate (MEP) pathway to synthesize isopentenyl pyrophosphate (IPP) and dimethylallyl diphosphate (DMAPP). To date, little is known regarding effects of an increase or a decrease of a HDR expression on terpenoid and other metabolite profiles in plants. In our study, an Artemisia annua HDR cDNA (namely AaHDR1) was cloned from leaves. Expression profiling showed it was highly expressed in leaves, roots, stems, and flowers with different levels. Green florescence protein fusion and confocal microscope analyses showed that AaHDR1 was localized in chloroplasts. The overexpression of AaHDR1 increased contents of artemisinin, arteannuin B and other sesquiterpenes, and multiple monoterpenes. By contrast, the suppression of AaHDR1 by anti-sense of led to opposite results. In addition, an untargeted metabolic profiling showed that the overexpression and suppression altered non-polar metabolite profiles. In conclusion, the overexpression and suppression of AaHDR1 protein level in plastids differentially affect artemisinin and other terpenoid biosynthesis, and alter non-polar metabolite profiles of A. annua. Particularly, its overexpression leading to the increase of artemisinin production is informative to future metabolic engineering of this antimalarial medicine. DA - 2017/1/31/ PY - 2017/1/31/ DO - 10.3389/fpls.2017.00077 VL - 8 SP - SN - 1664-462X KW - Artemisia annua KW - artemisinin KW - arteannuin B KW - 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase KW - methylerythritol phosphate pathway KW - terpene ER - TY - JOUR TI - Identification of a residue responsible for UDP-sugar donor selectivity of a dihydroxybenzoic acid glycosyltransferase from Arabidopsis natural accessions AU - Chen, Han-Yi AU - Li, Xu T2 - PLANT JOURNAL AB - Summary UDP ‐glycosyltransferase ( UGT ) plays a major role in the diversity and reactivity of plant specialized metabolites by catalyzing the transfer of the sugar moiety from activated UDP ‐sugars to various acceptors. Arabidopsis UGT 89A2 was previously identified from a genome‐wide association study as a key factor that affects the differential accumulation of dihydroxybenzoic acid ( DHBA ) glycosides in distinct Arabidopsis natural accessions, including Col‐0 and C24. The in vitro enzyme assays indicate that these distinct metabolic phenotypes reflect the divergence of UGT 89A2 enzyme properties in the Col‐0 and C24 accessions. UGT 89A2 from Col‐0 is highly selective toward UDP ‐xylose as the sugar donor, and the isoform from C24 can utilize both UDP ‐glucose and UDP ‐xylose but with a higher affinity to the glucose donor. The sequences of the two isozymes only differ at six amino acid residues. Examination of these amino acid residues in more natural accessions revealed a strong correlation between the amino acid polymorphism at position 153 and the DHBA glycoside accumulation pattern. Site‐directed mutagenesis that swapped residue 153 between UGT 89A2 from Col‐0 and C24 reversed the UDP ‐sugar preferences, indicating that residue 153 plays an important role in determining sugar donor specificity of UGT 89A2. This study provides insight into the key amino acid changes that confer sugar donor selectivity on UGT s, and demonstrates the usefulness of natural variation in understanding the structure–function relationship of enzymes involved in specialized metabolism. DA - 2017/1// PY - 2017/1// DO - 10.1111/tpj.13271 VL - 89 IS - 2 SP - 195-203 SN - 1365-313X KW - plant secondary metabolism KW - UGT KW - substrate specificity KW - natural variation KW - Arabidopsis thaliana KW - dihydroxybenzoic acid ER - TY - JOUR TI - Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing AU - Pais, Andrew L. AU - Whetten, Ross W. AU - Xiang, Qiu-Yun T2 - ECOLOGY AND EVOLUTION AB - Abstract Discovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next‐generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees ( Cornus florida L .) using genotyping by sequencing ( GBS ). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases. We analyzed subpopulations in divergent ecological habitats within North Carolina to uncover loci under local selection and associated with environmental–functional traits or disease infection. At this scale, we tested the effect of incorporating additional sequencing before scaling for a broader examination of the entire range. To test for biases of GBS , we sequenced two similarly sampled libraries independently from six populations of three ecological habitats. We obtained environmental–functional traits for each subpopulation to identify associations with genotypes via latent factor mixed modeling ( LFMM ) and gradient forests analysis. To test whether heterogeneity of abiotic pressures resulted in genetic differentiation indicative of local adaptation, we evaluated F st per locus while accounting for genetic differentiation between coastal subpopulations and Piedmont‐Mountain subpopulations. Of the 54 candidate loci with sufficient evidence of being under selection among both libraries, 28–39 were Arlequin–BayeScan F st outliers. For LFMM , 45 candidates were associated with climate (of 54), 30 were associated with soil properties, and four were associated with plant health. Reanalysis of combined libraries showed that 42 candidate loci still showed evidence of being under selection. We conclude environment‐driven selection on specific loci has resulted in local adaptation in response to potassium deficiencies, temperature, precipitation, and (to a marginal extent) disease. High allele turnover along ecological gradients further supports the adaptive significance of loci speculated to be under selection. DA - 2017/1// PY - 2017/1// DO - 10.1002/ece3.2623 VL - 7 IS - 1 SP - 441-465 SN - 2045-7758 KW - Cornus florida KW - genotyping by sequencing KW - local adaptation KW - single nucleotide polymorphisms ER - TY - JOUR TI - More than meets the eye: Emergent properties of transcription factors networks in Arabidopsis AU - Muhammad, Durreshahwar AU - Schmittling, Selene AU - Williams, Cranos AU - Long, Terri A. T2 - BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS AB - Uncovering and mathematically modeling Transcription Factor Networks (TFNs) are the first steps in engineering plants with traits that are better equipped to respond to changing environments. Although several plant TFNs are well known, the framework for systematically modeling complex characteristics such as switch-like behavior, oscillations, and homeostasis that emerge from them remain elusive. This review highlights literature that provides, in part, experimental and computational techniques for characterizing TFNs. This review also outlines methodologies that have been used to mathematically model the dynamic characteristics of TFNs. We present several examples of TFNs in plants that are involved in developmental and stress response. In several cases, advanced algorithms capture or quantify emergent properties that serve as the basis for robustness and adaptability in plant responses. Increasing the use of mathematical approaches will shed new light on these regulatory properties that control plant growth and development, leading to mathematical models that predict plant behavior. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. DA - 2017/1// PY - 2017/1// DO - 10.1016/j.bbagrm.2016.07.017 VL - 1860 IS - 1 SP - 64-74 SN - 0006-3002 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-84995470767&partnerID=MN8TOARS KW - Transcription factor networks (TFNs) KW - Emergent properties KW - Mathematical modeling ER - TY - JOUR TI - Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.) AU - Andres, R. J. AU - Coneva, V. AU - Frank, M. H. AU - Tuttle, J. R. AU - Samayoa, L. F. AU - Han, S. W. AU - Kaur, B. AU - Zhu, L. L. AU - Fang, Hui AU - Bowman, D. T. AU - Rojas-Pierce, Marcela AU - Haigler, C. H. AU - Jones, D. C. AU - Holland, J. B. AU - Chitwood, D. H. AU - Kuraparthy, V. T2 - Proceedings of the National Academy of Sciences of the United States of America AB - Abstract Leaf shape is spectacularly diverse. As the primary source of photo-assimilate in major crops, understanding the evolutionary and environmentally induced changes in leaf morphology are critical to improving agricultural productivity. The role of leaf shape in cotton domestication is unique, as breeders have purposefully selected for entire and lobed leaf morphs resulting from a single locus, okra ( L-D 1 ). The okra locus is not only of agricultural importance in cotton ( Gossypium hirsutum L.), but through pioneering chimeric and morphometric studies it has contributed to fundamental knowledge about leaf development. Here we show that the major leaf shapes of cotton at the L-D 1 locus are controlled by a HD-Zip transcription factor most similar to Late Meristem Identity1 (LMI1) gene. The classical okra leaf shape gene has133-bp tandem duplication in the promoter, correlated with elevated expression, while an 8-bp deletion in the third exon of the presumed wild-type normal leaf causes a frame-shifted and truncated coding sequence. Virus-induced gene silencing (VIGS) of this LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. An intermediate leaf shape allele, sub-okra , lacks both the promoter duplication and the exonic deletion. Our results indicate that sub-okra is the ancestral leaf shape of tetraploid cotton and normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. DA - 2017/// PY - 2017/// DO - 10.1101/062612 VL - 114 IS - 1 SP - E57–66 ER - TY - JOUR TI - Metabolic engineering of anthocyanins in dark tobacco varieties AU - He, Xianzhi AU - Li, Yong AU - Lawson, Darlene AU - Xie, De-Yu T2 - PHYSIOLOGIA PLANTARUM AB - In this study, we investigate the metabolic engineering of anthocyanins in two dark tobacco crops (Narrow Leaf Madole and KY171) and evaluate the effects on physiological features of plant photosynthesis. Arabidopsis PAP1 (production of anthocyanin pigment 1) gene (AtPAP1) encodes a R2R3-type MYB transcript factor that is a master component of regulatory complexes controlling anthocyanin biosynthesis. AtPAP1 was introduced to Narrow Leaf Madole and KY171 plants. Multiple transgenic plants developed red/purple pigmentation in different tissues. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the expression levels of six pathway genes were increased two- to eight-fold in AtPAP1 transgenic plants compared with vector control plants. Dihydroflavonol reductase and anthocyanidin synthase genes that were not expressed in wild-type plants were activated. Spectrophotometric measurement showed that the amount of anthocyanins in AtPAP1 transgenic plants were 400-800 µg g-1 fresh weight (FW). High-performance liquid chromatography (HPLC) analysis showed that one main anthocyanin molecule accounted for approximately 98% of the total anthocyanins. Tandem MS/MS analysis using HPLC coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry identified the main anthocyanin as cyanidin 3-O-rutinoside, an important medicinal anthocyanin. Analysis of photosynthesis rate, chlorophylls and carotenoids contents showed no differences between red/purple transgenic and control plants, indicating that this metabolic engineering did not alter photosynthetic physiological traits. This study shows that AtPAP1 is of significance for metabolic engineering of anthocyanins in crop plants for value-added traits. DA - 2017/1// PY - 2017/1// DO - 10.1111/ppl.12475 VL - 159 IS - 1 SP - 2-12 SN - 1399-3054 ER - TY - JOUR TI - Wood decay and the persistence of resprouting species in pyrophilic ecosystems AU - Just, Michael G. AU - Schafer, Jennifer L. AU - Hohmann, Matthew G. AU - Hoffmann, William A. T2 - TREES-STRUCTURE AND FUNCTION DA - 2017/2// PY - 2017/2// DO - 10.1007/s00468-016-1477-3 VL - 31 IS - 1 SP - 237-245 SN - 1432-2285 KW - Longleaf pine savanna KW - Phenolics KW - Quercus laevis KW - Streamhead pocosin KW - Wood rot KW - Wood density ER - TY - JOUR TI - Whole genome duplication and acceleration of molecular evolution is associated with the early diversification of the genus Cornus L. (Cornaceae): Insights from De Novo Assembled Transcriptome Sequences AU - Yu, Yan AU - Xiang, Qiuyun AU - Manos, Paul S. AU - Soltis, Douglas E. AU - Soltis, Pamela S. AU - Song, Bao-Hua AU - Cheng, Shifeng AU - Liu, Xin AU - Wong, Gane T2 - PLOS ONE AB - The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants. DA - 2017/2/22/ PY - 2017/2/22/ DO - 10.1371/journal.pone.0171361 VL - 12 IS - 2 SP - e0171361 J2 - PLoS ONE LA - en OP - SN - 1932-6203 UR - http://dx.plos.org/10.1371/journal.pone.0171361 DB - Crossref Y2 - 2019/1/29/ ER - TY - JOUR TI - Convergence of bark investment according to fire and climate structures ecosystem vulnerability to future change AU - Pellegrini, Adam F. A. AU - Anderegg, William R. L. AU - Paine, C. E. Timothy AU - Hoffmann, William A. AU - Kartzinel, Tyler AU - Rabin, Sam S. AU - Sheil, Douglas AU - Franco, Augusto C. AU - Pacala, Stephen W. T2 - ECOLOGY LETTERS AB - Abstract Fire regimes in savannas and forests are changing over much of the world. Anticipating the impact of these changes requires understanding how plants are adapted to fire. In this study, we test whether fire imposes a broad selective force on a key fire‐tolerance trait, bark thickness, across 572 tree species distributed worldwide. We show that investment in thick bark is a pervasive adaptation in frequently burned areas across savannas and forests in both temperate and tropical regions where surface fires occur. Geographic variability in bark thickness is largely explained by annual burned area and precipitation seasonality. Combining environmental and species distribution data allowed us to assess vulnerability to future climate and fire conditions: tropical rainforests are especially vulnerable, whereas seasonal forests and savannas are more robust. The strong link between fire and bark thickness provides an avenue for assessing the vulnerability of tree communities to fire and demands inclusion in global models. DA - 2017/3// PY - 2017/3// DO - 10.1111/ele.12725 VL - 20 IS - 3 SP - 307-316 SN - 1461-0248 KW - Bark thickness KW - fire ecology KW - forest KW - functional traits KW - global change KW - savanna ER - TY - JOUR TI - Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa AU - Hu, Zhaohui AU - Wu, Qian AU - Dalal, Jyoti AU - Vasani, Naresh AU - Lopez, Harry O. AU - Sederoff, Heike W. AU - Qu, Rongda T2 - PLOS ONE AB - With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production. DA - 2017/2/17/ PY - 2017/2/17/ DO - 10.1371/journal.pone.0172296 VL - 12 IS - 2 SP - SN - 1932-6203 UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85013067776&partnerID=MN8TOARS ER -