TY - JOUR TI - A polyketide synthase gene cluster required for pathogenicity of Pseudocercospora fijiensis on banana AU - Thomas, Elizabeth AU - Noar, Roslyn D. AU - Daub, Margaret E. T2 - PLOS ONE AB - Pseudocercospora fijiensis is the causal agent of the highly destructive black Sigatoka disease of banana. Previous research has focused on polyketide synthase gene clusters in the fungus, given the importance of polyketide pathways in related plant pathogenic fungi. A time course study of expression of the previously identified PKS7-1, PKS8-2, and PKS10-2 gene clusters showed high expression of all three PKS genes and the associated clustered genes in infected banana plants from 2 weeks post-inoculation through 9 weeks. Engineered transformants silenced for PKS8-2 and PKS10-2 were developed and tested for pathogenicity. Inoculation of banana plants with silencing transformants for PKS10-2 showed significant reduction in disease symptoms and severity that correlated with the degree of silencing in the conidia used for inoculation, supporting a critical role for PKS10-2 in disease development. Unlike PKS10-2, a clear role for PKS8-2 could not be determined. Two of four PKS8-2 silencing transformants showed reduced disease development, but disease did not correlate with the degree of PKS8-2 silencing in the transformants. Overall, the degree of silencing obtained for the PKS8-2 transformants was less than that obtained for the PKS10-2 transformants, which may have limited the utility of the silencing strategy to identify a role for PKS8-2 in disease. Orthologous PKS10-2 clusters had previously been identified in the related banana pathogens Pseudocercospora musae and Pseudocercospora eumusae. Genome analysis identified orthologous gene clusters to that of PKS10-2 in the newly sequenced genomes of Pseudocercospora fuligena and Pseudocercospora cruenta, pathogens of tomato and cowpea, respectively. Our results support an important role for the PKS10-2 polyketide pathway in pathogenicity of Pseudocercospora fijiensis, and suggest a possible role for this pathway in disease development by other Pseudocercospora species. DA - 2021/10/27/ PY - 2021/10/27/ DO - 10.1371/journal.pone.0258981 VL - 16 IS - 10 SP - SN - 1932-6203 ER - TY - JOUR TI - Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species AU - Tawa, Gregory J. AU - Braisted, John AU - Gerhold, David AU - Grewal, Gurmit AU - Mazcko, Christina AU - Breen, Matthew AU - Sittampalam, Gurusingham AU - LeBlanc, Amy K. T2 - PLOS COMPUTATIONAL BIOLOGY AB - Understanding relationships between spontaneous cancer in companion (pet) canines and humans can facilitate biomarker and drug development in both species. Towards this end we developed an experimental-bioinformatic protocol that analyzes canine transcriptomics data in the context of existing human data to evaluate comparative relevance of canine to human cancer. We used this protocol to characterize five canine cancers: melanoma, osteosarcoma, pulmonary carcinoma, B- and T-cell lymphoma, in 60 dogs. We applied an unsupervised, iterative clustering method that yielded five co-expression modules and found that each cancer exhibited a unique module expression profile. We constructed cancer models based on the co-expression modules and used the models to successfully classify the canine data. These canine-derived models also successfully classified human tumors representing the same cancers, indicating shared cancer biology between canines and humans. Annotation of the module genes identified cancer specific pathways relevant to cells-of-origin and tumor biology. For example, annotations associated with melanin production (PMEL, GPNMB, and BACE2), synthesis of bone material (COL5A2, COL6A3, and COL12A1), synthesis of pulmonary surfactant (CTSH, LPCAT1, and NAPSA), ribosomal proteins (RPL8, RPS7, and RPLP0), and epigenetic regulation (EDEM1, PTK2B, and JAK1) were unique to melanoma, osteosarcoma, pulmonary carcinoma, B- and T-cell lymphoma, respectively. In total, 152 biomarker candidates were selected from highly expressing modules for each cancer type. Many of these biomarker candidates are under-explored as drug discovery targets and warrant further study. The demonstrated transferability of classification models from canines to humans enforces the idea that tumor biology, biomarker targets, and associated therapeutics, discovered in canines, may translate to human medicine. DA - 2021/9// PY - 2021/9// DO - 10.1371/journal.pcbi.1009450 VL - 17 IS - 9 SP - SN - 1553-7358 ER - TY - JOUR TI - Research Design, Protocol, and Participant Characteristics of COLEAFS: A Cluster Randomized Controlled Trial of a Childcare Garden Intervention AU - Cosco, Nilda Graciela AU - Wells, Nancy M. AU - Monsur, Muntazar AU - Goodell, Lora Suzanne AU - Zhang, Daowen AU - Xu, Tong AU - Hales, Derek AU - Moore, Robin Clive T2 - INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH AB - Childcare garden interventions may be an effective strategy to increase fruit and vegetable (FV) consumption and physical activity among young children. The objective of this paper is to describe the research design, protocol, outcome measures, and baseline characteristics of participants in the Childcare Outdoor Learning Environments as Active Food Systems ("COLEAFS") study, a cluster randomized controlled trial (RCT) examining the effect of a garden intervention on outcomes related to diet and physical activity. Fifteen childcare centers in low-income areas were randomly assigned to intervention (to receive garden intervention in Year 1), waitlist control (to receive garden intervention in Year 2), and control group (no intervention). The garden intervention comprised six raised beds planted with warm-season vegetables and fruits, and a garden activity booklet presenting 12 gardening activities. FV knowledge and FV liking were measured using a tablet-enabled protocol. FV consumption was measured by weighing FV before and after a snack session. Physical activity was measured using Actigraph GT3x+ worn by children for three consecutive days while at the childcare center. Of the 543 eligible children from the 15 childcare centers, 250 children aged 3-5 years received parental consent, assented, and participated in baseline data collection. By employing an RCT to examine the effect of a garden intervention on diet and physical activity among young children attending childcare centers within low-income communities, this study offers compelling research design and methods, addresses a critical gap in the empirical literature, and is a step toward evidence-based regulations to promote early childhood healthy habits. DA - 2021/12// PY - 2021/12// DO - 10.3390/ijerph182413066 VL - 18 IS - 24 SP - SN - 1660-4601 KW - children KW - childcare KW - gardening KW - randomized controlled trial KW - healthy eating KW - physical activity ER - TY - JOUR TI - Comparative Assessment of Pesticide Exposures in Domestic Dogs and Their Owners Using Silicone Passive Samplers and Biomonitoring AU - Wise, Catherine F. AU - Hammel, Stephanie C. AU - Herkert, Nicholas J. AU - Ospina, Maria AU - Calafat, Antonia M. AU - Breen, Matthew AU - Stapleton, Heather M. T2 - ENVIRONMENTAL SCIENCE & TECHNOLOGY AB - Pesticides are used extensively in residential settings for lawn maintenance and in homes to control household pests including application directly on pets to deter fleas and ticks. Pesticides are commonly detected in the home environment where people and pets can be subject to chronic exposure. Due to increased interest in using companion animals as sentinels for human environmental health studies, we conducted a comparative pesticide exposure assessment in 30 people and their pet dogs to determine how well silicone wristbands and silicone dog tags can predict urinary pesticide biomarkers of exposure. Using targeted gas chromatography-mass spectrometry analyses, we quantified eight pesticides in silicone samplers and used a suspect screening approach for additional pesticides. Urine samples were analyzed for 15 pesticide metabolite biomarkers. Several pesticides were detected in >70% of silicone samplers including permethrin, N,N-diethyl-meta-toluamide (DEET), and chlorpyrifos. Significant and positive correlations were observed between silicone sampler levels of permethrin and DEET with their corresponding urinary metabolites (rs = 0.50-0.96, p < 0.05) in both species. Significantly higher levels of fipronil were observed in silicone samplers from participants who reported using flea and tick products containing fipronil on their dog. This study suggests that people and their dogs have similar pesticide exposures in a home environment. DA - 2021/12/29/ PY - 2021/12/29/ DO - 10.1021/acs.est.1c06819 SP - SN - 1520-5851 KW - exposure KW - wristband KW - silicone KW - biomonitoring KW - pesticide KW - dog ER - TY - JOUR TI - Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population AU - Pereira, Guilherme da Silva AU - Mollinari, Marcelo AU - Qu, Xinshun AU - Thill, Christian AU - Zeng, Zhao-Bang AU - Haynes, Kathleen AU - Yencho, G. Craig T2 - PLANT DISEASE AB - Despite the negative impact of common scab (Streptomyces spp.) on the potato industry, little is known about the genetic architecture of resistance to this bacterial disease in the crop. We evaluated a mapping population (∼150 full sibs) derived from a cross between two tetraploid potatoes ('Atlantic' × B1829-5) in three environments (MN11, PA11, ME12) under natural common scab pressure. Three measures to common scab reaction, namely percentage of scabby tubers and disease area and lesion indices, were found to be highly correlated (>0.76). Because of the large environmental effect, heritability values were zero for all three traits in MN11, but moderate to high in PA11 and ME12 (∼0.44 to 0.79). We identified a single quantitative trait locus (QTL) for lesion index in PA11, ME12, and joint analyses on linkage group 3, explaining ∼22 to 30% of the total variation. The identification of QTL haplotypes and candidate genes contributing to disease resistance can support genomics-assisted breeding approaches in the crop.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license. DA - 2021/10// PY - 2021/10// DO - 10.1094/PDIS-10-20-2270-RE VL - 105 IS - 10 SP - 3048-3054 SN - 1943-7692 KW - disease resistance KW - polyploid QTL model KW - single-nucleotide polymorphism KW - Solanum tuberosum KW - Streptomyces spp ER - TY - JOUR TI - TIN2 is an architectural protein that facilitates TRF2-mediated trans- and cis-interactions on telomeric DNA AU - Kaur, Parminder AU - Barnes, Ryan AU - Pan, Hai AU - Detwiler, Ariana C. AU - Liu, Ming AU - Mahn, Chelsea AU - Hall, Jonathan AU - Messenger, Zach AU - You, Changjiang AU - Piehler, Jacob AU - Smart, Robert C. AU - Riehn, Robert AU - Opresko, Patricia L. AU - Wang, Hong T2 - NUCLEIC ACIDS RESEARCH AB - Abstract The telomere specific shelterin complex, which includes TRF1, TRF2, RAP1, TIN2, TPP1 and POT1, prevents spurious recognition of telomeres as double-strand DNA breaks and regulates telomerase and DNA repair activities at telomeres. TIN2 is a key component of the shelterin complex that directly interacts with TRF1, TRF2 and TPP1. In vivo, the large majority of TRF1 and TRF2 are in complex with TIN2 but without TPP1 and POT1. Since knockdown of TIN2 also removes TRF1 and TRF2 from telomeres, previous cell-based assays only provide information on downstream effects after the loss of TRF1/TRF2 and TIN2. Here, we investigated DNA structures promoted by TRF2–TIN2 using single-molecule imaging platforms, including tracking of compaction of long mouse telomeric DNA using fluorescence imaging, atomic force microscopy (AFM) imaging of protein–DNA structures, and monitoring of DNA–DNA and DNA–RNA bridging using the DNA tightrope assay. These techniques enabled us to uncover previously unknown unique activities of TIN2. TIN2S and TIN2L isoforms facilitate TRF2-mediated telomeric DNA compaction (cis-interactions), dsDNA–dsDNA, dsDNA–ssDNA and dsDNA–ssRNA bridging (trans-interactions). Furthermore, TIN2 facilitates TRF2-mediated T-loop formation. We propose a molecular model in which TIN2 functions as an architectural protein to promote TRF2-mediated trans and cis higher-order nucleic acid structures at telomeres. DA - 2021/12/16/ PY - 2021/12/16/ DO - 10.1093/nar/gkab1142 VL - 49 IS - 22 SP - 13000-13018 SN - 1362-4962 ER - TY - JOUR TI - Epistasis for head morphology in Drosophila melanogaster AU - Ozsoy, Ergi D. AU - Yilmaz, Murat AU - Patlar, Bahar AU - Emecen, Guzin AU - Durmaz, Esra AU - Magwire, Michael M. AU - Zhou, Shanshan AU - Huang, Wen AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - G3-GENES GENOMES GENETICS AB - Abstract Epistasis—gene–gene interaction—is common for mutations with large phenotypic effects in humans and model organisms. Epistasis impacts quantitative genetic models of speciation, response to natural and artificial selection, genetic mapping, and personalized medicine. However, the existence and magnitude of epistasis between alleles with small quantitative phenotypic effects are controversial and difficult to assess. Here, we use the Drosophila melanogaster Genetic Reference Panel of sequenced inbred lines to evaluate the magnitude of naturally occurring epistasis modifying the effects of mutations in jing and inv, two transcription factors that have subtle quantitative effects on head morphology as homozygotes. We find significant epistasis for both mutations and performed single marker genome-wide association analyses to map candidate modifier variants and loci affecting head morphology. A subset of these loci was significantly enriched for a known genetic interaction network, and mutations of the candidate epistatic modifier loci also affect head morphology. DA - 2021/10// PY - 2021/10// DO - 10.1093/g3journal/jkab285 VL - 11 IS - 10 SP - SN - 2160-1836 KW - Drosophila Genetic Reference Panel KW - genome-wide association analyses KW - modifier loci KW - genetic interaction network ER - TY - JOUR TI - Epigenetic modification associated with climate regulates betulin biosynthesis in birch AU - Wang, Jiang AU - Chen, Bowei AU - Ali, Shahid AU - Zhang, Tianxu AU - Wang, Yu AU - Zhang, He AU - Wang, Lishan AU - Zhang, Yonglan AU - Xie, Linan AU - Jiang, Tingbo AU - Yin, Jing AU - Sederoff, Heike W. AU - Zinta, Gaurav AU - Sederoff, Ronald R. AU - Li, Yuhua AU - Zhang, Qingzhu T2 - JOURNAL OF FORESTRY RESEARCH AB - Abstract The Betula genus contains pentacyclic triterpenoid betulin known for its environmental adaptation and medicinal properties. However, the mechanisms underlying betulin biosynthesis responding to climate change remain unclear. In this study, the role of epigenetic modification (DNA methylation) in betulin biosynthesis was examined and how climatic factors influence it. Whole-genome bisulfite sequencing was performed for greenhouse-grown Chinese white birch ( Betula platyphylla Sukaczev) treated with DNA methylation inhibitor zebularine (ZEB) and a natural birch population in Northeast China. ZEB treatment significantly affected the CHH methylation level of transposable elements and betulin content in a hormesis dose-dependent manner. The methylation and expression of bHLH9, a key transcriptional factor controlling betulin biosynthesis, were also consistently affected by ZEB treatment as a hormetic dose–response. In the natural population, there was a positive correlation between promoter methylation of bHLH9 and summer precipitation, while winter temperature was negatively correlated. Thus climate-dependent methylation of bHLH9 regulates the expression of downstream genes involved in betulin biosynthesis. This study highlights the role of environmental signals to induce epigenetic changes that result in betulin production, possibly helping to develop resilient plants to combat ongoing climate change and enhance secondary metabolite production. DA - 2021/12/4/ PY - 2021/12/4/ DO - 10.1007/s11676-021-01424-7 SP - SN - 1993-0607 KW - Epigenetics KW - DNA methylation KW - Betulin KW - bHLH9 transcription factor KW - Hormesis KW - Climate change KW - Secondary metabolite ER - TY - JOUR TI - Toward Sustainable Crop Protection: Aqueous Dispersions of Biodegradable Particles with Tunable Release and Rainfastness AU - Pirzada, Tahira AU - Sohail, Mariam AU - Tripathi, Anurodh AU - Farias, Barbara V AU - Mathew, Reny AU - Li, Chunying AU - Opperman, Charles H. AU - Khan, Saad A. T2 - ADVANCED FUNCTIONAL MATERIALS AB - Abstract Fabrication of aqueous particulate dispersions of biodegradable cellulose esters (CEs) as efficient carriers of agrochemical active‐ingredients (AIs) for foliar applications, is reported. The use of different ester substituent groups on CE permits modulation of particle morphology and size, from irregular shapes (<350 nm) to spheres (≈1.1 µm diameter), while maintaining stability as supported by minimal change in zeta potential and particle size over one year. Rainfastness is tested by simulating >50 mm h −1 rainfall on coated banana and tomato leaves and silicon. Surface coverage loss as low as 9%, based on the nature of leaf and formulation, confirms the rainfastness of the formulations. Variation in the release kinetics of a model AI fluopyram from different CEs can be attributed to the particle morphology and the nature of binding between fluopyram and various CEs. Thermodynamic analysis demonstrates spontaneous binding between fluopyram and multiple sites of CEs, justifying its two‐step release from CE particles. System functionalities are corroborated via in‐vitro fungal inhibition assays demonstrating a 100% inhibition of the fungal growth. This “lab‐to‐leaf” approach of materials development involving fundamental insights and functional performance reveals CE dispersions are promising green agricultural formulations with the potential to impact a myriad of crops around the globe. DA - 2021/11/27/ PY - 2021/11/27/ DO - 10.1002/adfm.202108046 SP - SN - 1616-3028 KW - cellulose ester dispersions KW - controlled release formulations KW - crop protection KW - fluopyram KW - rainfastness KW - solvent displacement KW - sustainable agriculture ER - TY - JOUR TI - BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021) AU - Wang, Qiao AU - Dai, Xinren AU - Pang, Hongying AU - Cheng, Yanxia AU - Huang, Xiong AU - Li, Hui AU - Yan, Xiaojing AU - Lu, Fachuang AU - Wei, Hairong AU - Sederoff, Ronald R. AU - Li, Quanzi T2 - FRONTIERS IN PLANT SCIENCE AB - CORRECTION article Front. Plant Sci., 09 September 2021 | https://doi.org/10.3389/fpls.2021.761291 DA - 2021/9/9/ PY - 2021/9/9/ DO - 10.3389/fpls.2021.761291 VL - 12 SP - SN - 1664-462X KW - lignin KW - BEL1-like homeodomain protein KW - transcription factor KW - yeast one hybrid ER - TY - JOUR TI - Bartonella spp. seroepidemiology and associations with clinicopathologic findings in dogs in the United States AU - Lashnits, Erin AU - Thatcher, Brendon AU - Carruth, Ariel AU - Mestek, Anton AU - Buch, Jesse AU - Beall, Melissa AU - Neupane, Pradeep AU - Chandrashekar, Ramaswamy AU - Breitschwerdt, Edward B. T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Improved understanding of Bartonella spp. serology in dogs may aid clinical decision making.Describe demographic and geographic patterns of Bartonella spp. seroreactivity in dogs, and describe hematologic and serum biochemical abnormalities in Bartonella spp. seroreactive and nonseroreactive dogs.Serum samples from 5957 dogs in the United States, previously submitted to IDEXX Reference Laboratories.Serum was tested using 3 indirect ELISAs for B. henselae, B. vinsonii subsp. berkhoffii, and B. koehlerae. Complete blood count and serum biochemistry panel results were reviewed retrospectively.Overall, 6.1% of dogs were Bartonella spp. seroreactive. Toy breeds were less likely to be seroreactive (3.9%) than mixed breeds (7.5%; adjusted odds ratio [aOR], 0.48; 95% confidence interval [CI], 0.32-0.72), and dogs <1 year old were less likely to be seroreactive (3.4%) than dogs 1 to 5.5 years of age (7.3%; aOR, 0.42; 95% CI, 0.23-0.72). Dogs in the West South Central (9.8%) and South Atlantic (8.8%) regions were more likely than dogs elsewhere in the United States to be seroreactive (aOR, 2.22; 95% CI, 1.31-3.87; aOR, 2.44; 95% CI, 1.38-4.36).Demographic and geographic findings for Bartonella spp. exposure were broadly comparable to previously reported patterns. DA - 2021/11/17/ PY - 2021/11/17/ DO - 10.1111/jvim.16311 VL - 11 SP - SN - 1939-1676 KW - bartonellosis KW - canine KW - seroreactivity KW - vector-borne KW - zoonoses ER - TY - JOUR TI - Phase I/II Trial of Vemurafenib in Dogs with Naturally Occurring, BRAF-mutated Urothelial Carcinoma AU - Rossman, Paul AU - Zabka, Tanja S. AU - Ruple, Audrey AU - Tuerck, Dietrich AU - Ramos-Vara, Jose A. AU - Liu, Liling AU - Mohallem, Rodrigo AU - Merchant, Mark AU - Franco, Jackeline AU - Fulkerson, Christopher M. AU - Bhide, Ketaki P. AU - Breen, Matthew AU - Aryal, Uma K. AU - Murray, Elaine AU - Dybdal, Noel AU - Utturkar, Sagar M. AU - Fourez, Lindsey M. AU - Enstrom, Alexander W. AU - Dhawan, Deepika AU - Knapp, Deborah W. T2 - MOLECULAR CANCER THERAPEUTICS AB - BRAF-targeted therapies including vemurafenib (Zelboraf) induce dramatic cancer remission; however, drug resistance commonly emerges. The purpose was to characterize a naturally occurring canine cancer model harboring complex features of human cancer, to complement experimental models to improve BRAF-targeted therapy. A phase I/II clinical trial of vemurafenib was performed in pet dogs with naturally occurring invasive urothelial carcinoma (InvUC) harboring the canine homologue of human BRAFV600E The safety, MTD, pharmacokinetics, and antitumor activity were determined. Changes in signaling and immune gene expression were assessed by RNA sequencing and phosphoproteomic analyses of cystoscopic biopsies obtained before and during treatment, and at progression. The vemurafenib MTD was 37.5 mg/kg twice daily. Anorexia was the most common adverse event. At the MTD, partial remission occurred in 9 of 24 dogs (38%), with a median progression-free interval of 181 days (range, 53-608 days). In 18% of the dogs, new cutaneous squamous cell carcinoma and papillomas occurred, a known pharmacodynamic effect of vemurafenib in humans. Upregulation of genes in the classical and alternative MAPK-related pathways occurred in subsets of dogs at cancer progression. The most consistent transcriptomic changes were the increase in patterns of T lymphocyte infiltration during the first month of vemurafenib, and of immune failure accompanying cancer progression. In conclusion, the safety, antitumor activity, and cutaneous pharmacodynamic effects of vemurafenib, and the development of drug resistance in dogs closely mimic those reported in humans. This suggests BRAF-mutated canine InvUC offers an important complementary animal model to improve BRAF-targeted therapies in humans. DA - 2021/11// PY - 2021/11// DO - 10.1158/1535-7163.MCT-20-0893 VL - 20 IS - 11 SP - 2177-2188 SN - 1538-8514 ER - TY - JOUR TI - Development of a Multiplex Droplet Digital PCR Assay for the Detection of Babesia, Bartonella, and Borrelia Species AU - Maggi, Ricardo AU - Breitschwerdt, Edward B. AU - Qurollo, Barbara AU - Miller, Jennifer C. T2 - PATHOGENS AB - We describe the development, optimization, and validation of a multiplex droplet digital PCR (ddPCR) assay for the simultaneous detection of Babesia, Bartonella, and Borrelia spp. DNA from several sample matrices, including clinical blood samples from animals and humans, vectors, in-vitro infected human and animal cell lines, and tissues obtained from animal models (infected with Bartonella and/or B. burgdorferi). The multiplex ddPCR assay was able to detect 31 Bartonella, 13 Borrelia, and 24 Babesia species, including Theileria equi, T. cervi, and Cytauxzoon felis. No amplification of Treponema or Leptospira spp. was observed. Sensitivity of 0.2-5 genome equivalent DNA copies per microliter was achieved for different members of the Bartonella and Borrelia genus, depending on the species or matrix type (water or spiked blood DNA) tested. The ddPCR assay facilitated the simultaneous detection of co-infections with two and three vector-borne pathogens comprising four different genera (Babesia, Bartonella, Borrelia, and Theileria) from clinical and other sample sources. DA - 2021/11// PY - 2021/11// DO - 10.3390/pathogens10111462 VL - 10 IS - 11 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10111462 KW - Babesia KW - Bartonella KW - Borrelia KW - Cytauxzoon KW - Piroplasma KW - Theileria KW - clinical diagnostics KW - molecular detection KW - digital droplet PCR KW - digital PCR ER - TY - JOUR TI - Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa AU - Lin, Chien-Yuan AU - Sun, Yi AU - Song, Jina AU - Chen, Hsi-Chuan AU - Shi, Rui AU - Yang, Chenmin AU - Liu, Jie AU - Tunlaya-Anukit, Sermsawat AU - Liu, Baoguang AU - Loziuk, Philip L. AU - Williams, Cranos M. AU - Muddiman, David C. AU - Lin, Ying-Chung Jimmy AU - Sederoff, Ronald R. AU - Wang, Jack P. AU - Chiang, Vincent L. T2 - FRONTIERS IN PLANT SCIENCE AB - Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa , two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa . The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa . DA - 2021/10/6/ PY - 2021/10/6/ DO - 10.3389/fpls.2021.727932 VL - 12 SP - SN - 1664-462X KW - protein interaction KW - monolignol biosynthesis KW - wood formation KW - Populus trichocarpa KW - BiFC KW - metabolic flux ER - TY - JOUR TI - A New Type of Satellite Associated with Cassava Mosaic Begomoviruses AU - Aimone, Catherine D. AU - De Leon, Leandro AU - Dallas, Mary M. AU - Ndunguru, Joseph AU - Ascencio-Ibanez, Jose T. AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGY AB - Cassava mosaic disease (CMD), which is caused by single-stranded DNA begomoviruses, severely limits cassava production across Africa. A previous study showed that CMD symptom severity and viral DNA accumulation increase in cassava in the presence of a DNA sequence designated SEGS-2 (sequence enhancing geminivirus symptoms). We report here that when SEGS-2 is coinoculated with African cassava mosaic virus (ACMV) onto Arabidopsis thaliana, viral symptoms increase. Transgenic Arabidopsis with an integrated copy of SEGS-2 inoculated with ACMV also display increased symptom severity and viral DNA levels. Moreover, SEGS-2 enables Cabbage leaf curl virus (CaLCuV) to infect a geminivirus-resistant Arabidopsis thaliana accession. Although SEGS-2 is related to cassava genomic sequences, an earlier study showed that it occurs as episomes and is packaged into virions in CMD-infected cassava and viruliferous whiteflies. We identified SEGS-2 episomes in SEGS-2 transgenic Arabidopsis. The episomes occur as both double-stranded and single-stranded DNA, with the single-stranded form packaged into virions. In addition, SEGS-2 episomes replicate in tobacco protoplasts in the presence, but not the absence, of ACMV DNA-A. SEGS-2 episomes contain a SEGS-2 derived promoter and an open reading frame with the potential to encode a 75-amino acid protein. An ATG mutation at the beginning of the SEGS-2 coding region does not enhance ACMV infection in A. thaliana. Together, the results established that SEGS-2 is a new type of begomovirus satellite that enhances viral disease through the action of an SEGS-2-encoded protein that may also be encoded by the cassava genome. IMPORTANCE Cassava is an important root crop in the developing world and a food and income crop for more than 300 million African farmers. Cassava is rising in global importance and trade as the demands for biofuels and commercial starch increase. More than half of the world's cassava is produced in Africa, where it is primarily grown by smallholder farmers, many of whom are from the poorest villages. Although cassava can grow under high temperature, drought, and poor soil conditions, its production is severely limited by viral diseases. Cassava mosaic disease (CMD) is one of the most important viral diseases of cassava and can cause up to 100% yield losses. We provide evidence that SEGS-2, which was originally isolated from cassava crops displaying severe and atypical CMD symptoms in Tanzanian fields, is a novel begomovirus satellite that can compromise the development of durable CMD resistance. DA - 2021/11// PY - 2021/11// DO - 10.1128/JVI.00432-21 VL - 95 IS - 21 SP - SN - 1098-5514 KW - Arabidopsis KW - begomovirus KW - cassava mosaic disease KW - SEGS ER - TY - JOUR TI - A calmodulin-binding transcription factor links calcium signaling to antiviral RNAi defense in plants AU - Wang, Yunjing AU - Gong, Qian AU - Wu, Yuyao AU - Huang, Fan AU - Ismayil, Asigul AU - Zhang, Danfeng AU - Li, Huangai AU - Gu, Hanqing AU - Ludman, Marta AU - Fatyol, Karoly AU - Qi, Yijun AU - Yoshioka, Keiko AU - Hanley-Bowdoin, Linda AU - Hong, Yiguo AU - Liu, Yule T2 - CELL HOST & MICROBE AB - RNA interference (RNAi) is an across-kingdom gene regulatory and defense mechanism. However, little is known about how organisms sense initial cues to mobilize RNAi. Here, we show that wounding to Nicotiana benthamiana cells during virus intrusion activates RNAi-related gene expression through calcium signaling. A rapid wound-induced elevation in calcium fluxes triggers calmodulin-dependent activation of calmodulin-binding transcription activator-3 (CAMTA3), which activates RNA-dependent RNA polymerase-6 and Bifunctional nuclease-2 (BN2) transcription. BN2 stabilizes mRNAs encoding key components of RNAi machinery, notably AGONAUTE1/2 and DICER-LIKE1, by degrading their cognate microRNAs. Consequently, multiple RNAi genes are primed for combating virus invasion. Calmodulin-, CAMTA3-, or BN2-knockdown/knockout plants show increased susceptibility to geminivirus, cucumovirus, and potyvirus. Notably, Geminivirus V2 protein can disrupt the calmodulin-CAMTA3 interaction to counteract RNAi defense. These findings link Ca2+ signaling to RNAi and reveal versatility of host antiviral defense and viral counter-defense. DA - 2021/9/8/ PY - 2021/9/8/ DO - 10.1016/j.chom.2021.07.003 VL - 29 IS - 9 SP - 1393-+ SN - 1934-6069 ER - TY - JOUR TI - Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Leaf Color Change in Chokecherry (Padus virginiana) AU - Li, Xiang AU - Li, Yan AU - Zhao, Minghui AU - Hu, Yanbo AU - Meng, Fanjuan AU - Song, Xingshun AU - Tigabu, Mulualem AU - Chiang, Vincent L. AU - Sederoff, Ronald AU - Ma, Wenjun AU - Zhao, Xiyang T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - Chokecherry (Padus virginiana L.) is an important landscaping tree with high ornamental value because of its colorful purplish-red leaves (PRL). The quantifications of anthocyanins and the mechanisms of leaf color change in this species remain unknown. The potential biosynthetic and regulatory mechanisms and the accumulation patterns of anthocyanins in P. virginiana that determine three leaf colors were investigated by combined analysis of the transcriptome and the metabolome. The difference of chlorophyll, carotenoid and anthocyanin content correlated with the formation of P. virginiana leaf color. Using enrichment and correlation network analysis, we found that anthocyanin accumulation differed in different colored leaves and that the accumulation of malvidin 3-O-glucoside (violet) and pelargonidin 3-O-glucoside (orange-red) significantly correlated with the leaf color change from green to purple-red. The flavonoid biosynthesis genes (PAL, CHS and CHI) and their transcriptional regulators (MYB, HD-Zip and bHLH) exhibited specific increased expression during the purple-red periods. Two genes encoding enzymes in the anthocyanin biosynthetic pathway, UDP glucose-flavonoid 3-O-glucosyl-transferase (UFGT) and anthocyanidin 3-O-glucosyltransferase (BZ1), seem to be critical for suppressing the formation of the aforesaid anthocyanins. In PRL, the expression of the genes encoding for UGFT and BZ1 enzymes was substantially higher than in leaves of other colors and may be related with the purple-red color change. These results may facilitate genetic modification or selection for further improvement in ornamental qualities of P. virginiana. DA - 2021/10// PY - 2021/10// DO - 10.3390/ijms221910697 VL - 22 IS - 19 SP - SN - 1422-0067 KW - Padus virginiana KW - leaf color KW - anthocyanin biosynthesis KW - transcriptomics KW - metabolomic ER - TY - JOUR TI - Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus AU - Li, Hui AU - Dai, Xinren AU - Huang, Xiong AU - Xu, Mengxuan AU - Wang, Qiao AU - Yan, Xiaojing AU - Sederoff, Ronald R. AU - Li, Quanzi T2 - JOURNAL OF INTEGRATIVE PLANT BIOLOGY AB - Abstract High‐throughput single‐cell RNA sequencing (scRNA‐seq) has advantages over traditional RNA‐seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop‐seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa . The scRNA‐seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high‐resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation. DA - 2021/10/4/ PY - 2021/10/4/ DO - 10.1111/jipb.13159 SP - SN - 1744-7909 KW - differentiating trajectory KW - differentiating xylem KW - marker genes KW - Populus alba x Populus glandulosa KW - single-cell RNA-seq KW - wood formation ER - TY - JOUR TI - Synthesis of AD-Dihydrodipyrrins Equipped with Latent Substituents of Native Chlorophylls and Bacteriochlorophylls AU - Wang, Pengzhi AU - Lindsey, Jonathan S. T2 - JOURNAL OF ORGANIC CHEMISTRY AB - Native chlorophylls and bacteriochlorophylls share a common trans-substituted pyrroline ring D (17-propionic acid, 18-methyl), whereas diversity occurs in ring A particularly at the 3-position. Two dihydrodipyrrins equipped with native-like D-ring substituents and tailorable A-ring substituents have been synthesized. The synthesis relies on a Schreiber-modified Nicholas reaction to construct the stereochemically defined precursor to ring D, a dialkyl-substituted pent-4-ynoic acid. The carboxylic acid group of the intact propionic acid proved unworkable, whereupon protected propionate (-CO2tBu) and several latent propyl ethers were examined. The tert-butyldiphenylsilyl-protected propanol substituent proved satisfactory for reaction of the chiral N-acylated oxazolidinone, affording (2S,3S)-2-(3-((tert-butyldiphenylsilyl)oxy)propyl)-3-methylpent-4-ynoic acid in ∼30% yield over 8 steps. Two variants for ring A, 2-tert-butoxycarbonyl-3-Br/H-5-iodo-4-methylpyrrole, were prepared via the Barton-Zard route. Dihydrodipyrrin formation from the pyrrole and pentynoic acid entailed Jacobi Pd-mediated lactone formation, Petasis methenylation, and Paal-Knorr-type pyrroline formation. The two AD-dihydrodipyrrins bear the D-ring methyl and protected propanol groups with a stereochemical configuration identical to that of native (bacterio)chlorophylls, and a bromine or no substitution in ring A corresponding to the 3-position of (bacterio)chlorophylls. The analogous β-position of a lactone-pyrrole intermediate on the path to the dihydrodipyrrin also was successfully brominated, opening opportunities for late-stage diversification in the synthesis of (bacterio)chlorophylls. DA - 2021/9/3/ PY - 2021/9/3/ DO - 10.1021/acs.joc.1c01239 VL - 86 IS - 17 SP - 11794-11811 SN - 1520-6904 UR - http://dx.doi.org/10.1021/acs.joc.1c01239 ER - TY - JOUR TI - Single-minded 2 is required for left-right asymmetric stomach morphogenesis AU - Wyatt, Brent H. AU - Amin, Nirav M. AU - Bagley, Kristen AU - Wcisel, Dustin AU - Dush, Michael K. AU - Yoder, Jeffrey A. AU - Nascone-Yoder, Nanette M. T2 - DEVELOPMENT AB - The morphogenesis of left-right (LR) asymmetry is a critical phase of organogenesis. In the digestive tract, the development of anatomical asymmetry is first evident in the leftward curvature of the stomach. To elucidate the molecular events that shape this archetypal laterality, we performed transcriptome analyses of the left versus right sides of the developing stomach in frog embryos. Besides the known LR gene pitx2, the only gene found to be expressed asymmetrically throughout all stages of curvature was single-minded2 (sim2), a Down Syndrome-related transcription factor and homolog of a Drosophila gene (sim) required for LR asymmetric looping of the fly gut. We demonstrate that sim2 functions downstream of LR patterning cues to regulate key cellular properties and behaviors in the left stomach epithelium that drive asymmetric curvature. Our results reveal unexpected convergent cooption of single-minded genes during the evolution of LR asymmetric morphogenesis, and have implications for dose-dependent roles of laterality factors in non-laterality-related birth defects. DA - 2021/9// PY - 2021/9// DO - 10.1242/dev.199265 VL - 148 IS - 17 SP - SN - 1477-9129 KW - right asymmetry KW - Stomach KW - Morphogenesis KW - Pitx2 KW - Sim2 KW - Down syndrome KW - Frog ER - TY - JOUR TI - Electronic Structure and Excited-State Dynamics of Rylene-Tetrapyrrole Panchromatic Absorbers AU - Rong, Jie AU - Magdaong, Nikki Cecil M. AU - Taniguchi, Masahiko AU - Diers, James R. AU - Niedzwiedzki, Dariusz M. AU - Kirmaier, Christine AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - JOURNAL OF PHYSICAL CHEMISTRY A AB - Panchromatic absorbers have potential applications in molecular-based energy-conversion schemes. A prior porphyrin–perylene dyad (P-PMI, where “MI” denotes monoimide) coupled via an ethyne linker exhibits panchromatic absorption (350–700 nm) and a tetrapyrrole-like lowest singlet excited state with a relatively long singlet excited-state lifetime (τS) and increased fluorescence quantum yield (Φf) versus the parent porphyrin. To explore the extension of panchromaticity to longer wavelengths, three arrays have been synthesized: a chlorin–terrylene dyad (C-TMI), a bacteriochlorin–terrylene dyad (B-TMI), and a perylene–porphyrin–terrylene triad (PMI-P-TMI), where the terrylene, a π-extended homologue of perylene, is attached via an ethyne linker. Characterization of the spectra (absorption and fluorescence), excited-state properties (lifetime, yields, and rate constants of decay pathways), and molecular-orbital characteristics reveals unexpected subtleties. The wavelength of the red-region absorption band increases in the order C-TMI (705 nm) < PMI-P-TMI (749 nm) < B-TMI (774 nm), yet each array exhibits diminished Φf and shortened τS values. The PMI-P-TMI triad in toluene exhibits Φf = 0.038 and τS = 139 ps versus the all-perylene triad (PMI-P-PMI) for which Φf = 0.26 and τS = 2000 ps. The results highlight design constraints for auxiliary pigments with tetrapyrroles to achieve panchromatic absorption with retention of viable excited-state properties. DA - 2021/9/16/ PY - 2021/9/16/ DO - 10.1021/acs.jpca.1c05771 VL - 125 IS - 36 SP - 7900-7919 SN - 1520-5215 ER - TY - JOUR TI - Prevalence of Vector-Borne Pathogens in Reproductive and Non-Reproductive Tissue Samples from Free-Roaming Domestic Cats in the South Atlantic USA AU - Manvell, Charlotte AU - Ferris, Kelli AU - Maggi, Ricardo AU - Breitschwerdt, Edward B. AU - Lashnits, Erin T2 - PATHOGENS AB - Reservoir to multiple species of zoonotic pathogens, free-roaming cats (FRCs) interact with domestic and wild animals, vectors, and humans. To assess the potential for feline vector-borne pathogens to be vertically transmitted, this study surveyed ear tip and reproductive tissues of FRCs from two locations in the South Atlantic United States for Anaplasma, Bartonella, Ehrlichia, hemotropic Mycoplasma, and Rickettsia species. We collected ovary (n = 72), uterus (n = 54), testicle (n = 74), and ear tip (n = 73) tissue from 73 cats, and fetal (n = 20) and placental (n = 19) tissue from 11 queens. Pathogen DNA was amplified utilizing qPCR, confirmed by sequencing. Cats were more frequently Bartonella henselae positive on reproductive tissues (19%, 14/73) than ear tip (5%, 4/73; p = 0.02). B. henselae was amplified from fetus (20%, 4/20) and placenta samples (11%, 2/19). Bartonella spp. infection was more common in cats from North Carolina (76%, 26/34) than Virginia (13%, 5/39; p < 0.0001). Fourteen percent (10/73) of both ear tip and reproductive tissues were positive for hemotropic Mycoplasma spp. Anaplasma, Ehrlichia, and Rickettsia spp. DNA was not amplified from any cat/tissue. These findings suggest that B. henselae preferentially infected cats’ reproductive tissue and reinforces the importance of investigating the potential for B. henselae vertical transmission or induction of reproductive failure. DA - 2021/9// PY - 2021/9// DO - 10.3390/pathogens10091221 VL - 10 IS - 9 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10091221 KW - Bartonella spp KW - hemotropic Mycoplasma spp KW - reproduction KW - cats KW - prevalence ER - TY - JOUR TI - Recent Progress in Lyme Disease and Remaining Challenges AU - Bobe, Jason R. AU - Jutras, Brandon L. AU - Horn, Elizabeth J. AU - Embers, Monica E. AU - Bailey, Allison AU - Moritz, Robert L. AU - Zhang, Ying AU - Soloski, Mark J. AU - Ostfeld, Richard S. AU - Marconi, Richard T. AU - Aucott, John AU - Ma'ayan, Avi AU - Keesing, Felicia AU - Lewis, Kim AU - Ben Mamoun, Choukri AU - Rebman, Alison W. AU - McClune, Mecaila E. AU - Breitschwerdt, Edward B. AU - Reddy, Panga Jaipal AU - Maggi, Ricardo AU - Yang, Frank AU - Nemser, Bennett AU - Ozcan, Aydogan AU - Garner, Omai AU - Di Carlo, Dino AU - Ballard, Zachary AU - Joung, Hyou-Arm AU - Garcia-Romeu, Albert AU - Griffiths, Roland R. AU - Baumgarth, Nicole AU - Fallon, Brian A. T2 - FRONTIERS IN MEDICINE AB - Lyme disease (also known as Lyme borreliosis) is the most common vector-borne disease in the United States with an estimated 476,000 cases per year. While historically, the long-term impact of Lyme disease on patients has been controversial, mounting evidence supports the idea that a substantial number of patients experience persistent symptoms following treatment. The research community has largely lacked the necessary funding to properly advance the scientific and clinical understanding of the disease, or to develop and evaluate innovative approaches for prevention, diagnosis, and treatment. Given the many outstanding questions raised into the diagnosis, clinical presentation and treatment of Lyme disease, and the underlying molecular mechanisms that trigger persistent disease, there is an urgent need for more support. This review article summarizes progress over the past 5 years in our understanding of Lyme and tick-borne diseases in the United States and highlights remaining challenges. DA - 2021/8/18/ PY - 2021/8/18/ DO - 10.3389/fmed.2021.666554 VL - 8 SP - SN - 2296-858X KW - Lyme disease KW - pathogenesis KW - diagnosis KW - treatment KW - prevention KW - field building KW - PTLD KW - vaccine ER - TY - JOUR TI - A perspective on the redox properties of tetrapyrrole macrocycles AU - Diers, James R. AU - Kirmaier, Christine AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - PHYSICAL CHEMISTRY CHEMICAL PHYSICS AB - Understanding the redox properties of tetrapyrroles requires deep insights into how structural/electronic alterations affect all four frontier molecular orbitals. DA - 2021/9/7/ PY - 2021/9/7/ DO - 10.1039/d1cp01943k VL - 9 SP - SN - 1463-9084 ER - TY - JOUR TI - A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa AU - Matthews, Megan L. AU - Wang, Jack P. AU - Sederoff, Ronald AU - Chiang, Vincent L. AU - Williams, Cranos M. T2 - COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL AB - Understanding the mechanisms behind lignin formation is an important research area with significant implications for the bioenergy and biomaterial industries. Computational models are indispensable tools for understanding this complex process. Models of the monolignol pathway in Populus trichocarpa and other plants have been developed to explore how transgenic modifications affect important bioenergy traits. Many of these models, however, only capture one level of biological organization and are unable to capture regulation across multiple biological scales. This limits their ability to predict how gene modification strategies will impact lignin and other wood properties. While the first multiscale model of lignin biosynthesis in P. trichocarpa spanned the transcript, protein, metabolic, and phenotypic layers, it did not account for cross-regulatory influences that could impact abundances of untargeted monolignol transcripts and proteins. Here, we present a multiscale model incorporating these cross-regulatory influences for predicting lignin and wood traits from transgenic knockdowns of the monolignol genes. The three main components of this multiscale model are (1) a transcript-protein model capturing cross-regulatory influences, (2) a kinetic-based metabolic model, and (3) random forest models relating the steady state metabolic fluxes to 25 physical traits. We demonstrate that including the cross-regulatory behavior results in smaller predictive error for 23 of the 25 traits. We use this multiscale model to explore the predicted impact of novel combinatorial knockdowns on key bioenergy traits, and identify the perturbation of PtrC3H3 and PtrCAld5H1&2 monolignol genes as a candidate strategy for increasing saccharification efficiencies while reducing negative impacts on wood density and height. DA - 2021/// PY - 2021/// DO - 10.1016/j.csbj.2020.11.046 VL - 19 SP - 168-182 SN - 2001-0370 KW - Lignin biosynthesis KW - Multiscale modeling KW - Cross-regulatory influences KW - Random forests ER - TY - JOUR TI - An Overview of the Practices and Management Methods for Enhancing Seed Production in Conifer Plantations for Commercial Use AU - Li, Yan AU - Li, Xiang AU - Zhao, Ming-Hui AU - Pang, Zhong-Yi AU - Wei, Jia-Tong AU - Tigabu, Mulualem AU - Chiang, Vincent L. AU - Sederoff, Heike AU - Sederoff, Ronald AU - Zhao, Xi-Yang T2 - HORTICULTURAE AB - Flowering, the beginning of the reproductive growth, is a significant stage in the growth and development of plants. Conifers are economically and ecologically important, characterized by straight trunks and a good wood quality and, thus, conifer plantations are widely distributed around the world. In addition, conifer species have a good tolerance to biotic and abiotic stress, and a stronger survival ability. Seeds of some conifer species, such as Pinus koraiensis, are rich in vitamins, amino acids, mineral elements and other nutrients, which are used for food and medicine. Although conifers are the largest (giant sequoia) and oldest living plants (bristlecone pine), their growth cycle is relatively long, and the seed yield is unstable. In the present work, we reviewed selected literature and provide a comprehensive overview on the most influential factors and on the methods and techniques that can be adopted in order to improve flowering and seed production in conifers species. The review revealed that flowering and seed yields in conifers are affected by a variety of factors, such as pollen, temperature, light, water availability, nutrients, etc., and a number of management techniques, including topping off, pruning, fertilization, hormone treatment, supplementary pollination, etc. has been developed for improving cone yields. Furthermore, several flowering-related genes (FT, Flowering locus T and MADS-box, MCMI, AGAMOUS, DEFICIENCES and SRF) that play a crucial role in flowering in coniferous trees were identified. The results of this study can be useful for forest managers and for enhancing seed yields in conifer plantations for commercial use. DA - 2021/8// PY - 2021/8// DO - 10.3390/horticulturae7080252 VL - 7 IS - 8 SP - SN - 2311-7524 KW - conifers KW - flowering KW - seed production KW - pollination KW - phytohormones KW - tree management KW - nutrient fertilization ER - TY - JOUR TI - Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria AU - Jin, Xiaohe AU - Zhang, Yunlong AU - Zhang, Ran AU - Nguyen, Kathy-Uyen AU - Lindsey, Jonathan S. AU - Miller, Eric S. T2 - LIFE-BASEL AB - Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles. DA - 2021/8// PY - 2021/8// DO - 10.3390/life11080758 VL - 11 IS - 8 SP - SN - 2075-1729 KW - tolyporphins KW - tetrapyrroles KW - cyanobacteria KW - biosynthetic gene cluster KW - Brasilonema KW - Nostoc KW - Oculatella ER - TY - JOUR TI - Population structure of Phytophthora infestans collected on potato and tomato in Italy AU - Saville, Amanda C. AU - La Spada, Federico AU - Faedda, Roberto AU - Migheli, Quirico AU - Scanu, Bruno AU - Ermacora, Paolo AU - Gilardi, Giovanna AU - Fedele, Giorgia AU - Rossi, Vitorrio AU - Lenzi, Nicolo AU - Testa, Antonino AU - Allagui, Mohamed Bechir AU - Moumni, Marwa AU - Dongiovanni, Enza AU - Rekad, Fatma Zohra AU - Cooke, David E. L. AU - Pane, Antonella AU - Cacciola, Santa O. AU - Ristaino, Jean B. T2 - PLANT PATHOLOGY AB - Abstract Late blight caused by the oomycete Phytophthora infestans is a disease of potato and tomato of worldwide relevance and is widespread throughout Europe and the Mediterranean region. While pathogen populations in northern Europe have been sampled and characterized for many years, the genetic structure of populations from southern Europe, including Italy, has been less studied. Between 2018 and 2019, we collected 91 samples of P . infestans from potato and tomato crops in Italy, Algeria, and Tunisia on FTA cards and genotyped them using 12‐plex microsatellites. These samples were compared to genotypes of P . infestans previously collected within the framework of the EuroBlight network and from published sources. Four clonal lineages were identified: 13_A2 (Blue 13), 2_A1, 23_A1, and 36_A2. Two other isolates collected could not be matched to any currently known clonal lineage. The 13_A2 and 36_A2 lineages were found exclusively in southern Italy and Algeria, while 2_A1 was only found in Algeria. This is the first report of the 36_A2 lineage in Italy. Two isolates from Solanum nigrum were 13_A2, suggesting this weed host could be a reservoir of inoculum. The 23_A1 lineage was found widely on infected tomato crops in Italy and is the same as the lineage US‐23 that is widespread in North America. Differences in genotypes across the country suggests that there may be different sources of introduction into Italy, possibly via infected seed tubers from other countries in Europe, tubers for consumption from North Africa, or tomatoes. DA - 2021/8/29/ PY - 2021/8/29/ DO - 10.1111/ppa.13444 VL - 8 SP - SN - 1365-3059 KW - Mediterranean KW - microsatellites KW - Phytophthora infestans KW - population biology ER - TY - JOUR TI - The bowfin genome illuminates the developmental evolution of ray-finned fishes AU - Thompson, Andrew W. AU - Hawkins, M. Brent AU - Parey, Elise AU - Wcisel, Dustin J. AU - Ota, Tatsuya AU - Kawasaki, Kazuhiko AU - Funk, Emily AU - Losilla, Mauricio AU - Fitch, Olivia E. AU - Pan, Qiaowei AU - Feron, Romain AU - Louis, Alexandra AU - Montfort, Jerome AU - Milhes, Marine AU - Racicot, Brett L. AU - Childs, Kevin L. AU - Fontenot, Quenton AU - Ferrara, Allyse AU - David, Solomon R. AU - McCune, Amy R. AU - Dornburg, Alex AU - Yoder, Jeffrey A. AU - Guiguen, Yann AU - Crollius, Hugues Roest AU - Berthelot, Camille AU - Harris, Matthew P. AU - Braasch, Ingo T2 - NATURE GENETICS AB - The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era. DA - 2021/8/30/ PY - 2021/8/30/ DO - 10.1038/s41588-021-00914-y SP - SN - 1546-1718 ER - TY - JOUR TI - Discovery of a naturally-occurring allele of eIF4E1.S in Nicotiana tabacum and development of a co-dominant marker AU - Lin, Shifeng AU - Dewey, Ralph E. AU - Wang, Rengang AU - Yu, Jing AU - Long, Mingjin AU - Zhang, Jie AU - Yu, Shizhou AU - Zhang, Jishun AU - Wang, Zili AU - Ren, Xueliang T2 - EUPHYTICA AB - Potato virus Y (PVY) is one of the most problematic pathogens affecting tobacco production. Genetic resistance to PVY in cultivated tobacco is mediated by recessive mutations, including the locus designated VAM, and its derived mutant va, both of which were previously shown to contain large chromosomal deletions. Among the genes deleted in lines containing VAM or va is eIF4E1.S, a gene whose protein product has been shown to facilitate infection by certain potyviruses, including PVY. Because the extent of the deletions and the exact nature of their specific breakpoints have not been precisely established for VAM or va, it has not been possible to develop co-dominant markers to facilitate their transfer to elite varieties using molecular breeding technologies. Here, we report the discovery of a novel naturally-occurring allele of eIF4E1.S from the Chinese tobacco landrace Fuquanliuye, designated eIF4E1.Fu, which lacks a genomic region of approximately 27 kb, including the 3'-end of eIF4E1.S. Characterization of the deletion junction enabled the development of a co-dominant PCR-based marker specific for eIF4E1.Fu, which can distinguish eIF4E1.S/eIF4E1.Fu heterozygotes from both homozygous classes. Using this co-dominant marker, we genotyped F2 plants segregating for the mutant eIF4E1.Fu allele and confirmed the correlation between genotype and phenotype. This study describes a novel source of resistance and an ideal co-dominant marker that can be applied in breeding for resistance to PVY and other potyviruses. DA - 2021/7// PY - 2021/7// DO - 10.1007/s10681-021-02876-y VL - 217 IS - 7 SP - SN - 1573-5060 KW - Nicotiana tabacum KW - Potato virus Y KW - Naturally-occurring allele KW - S KW - Co-dominant marker ER - TY - JOUR TI - Genetic Variation and the Effect of Herbicide and Fertilization Treatments on Wood Quality Traits in Loblolly Pine AU - Grans, Daniel AU - Isik, Fikret AU - Purnell, Robert C. AU - Peszlen, Ilona M. AU - McKeand, Steven E. T2 - FOREST SCIENCE AB - Abstract The effect of silvicultural treatments (herbicide, fertilization, herbicide + fertilization) and the interactions with genetic effects were investigated for wood quality traits in a 16-year-old loblolly pine (Pinus taeda L.) genetic test established in southwest Georgia, USA. Fertilizer and herbicide treatment combinations were applied multiple times to main plots containing 25 open-pollinated families as sub plots. Significant differences among treatments were found for all traits. Squared acoustic velocity, used as a surrogate for wood stiffness, was higher in herbicide-only plots compared with other treatments. Wood density was considerably lower in fertilization plots. A large proportion of variance observed for wood quality traits was explained by additive genetic effects, with individual-tree heritabilities ranging from 0.78 (ring 7–16 section wood density) to 0.28 (ring 2–6 section wood density). Corresponding family-mean heritability values were well over 0.86. Genotype-by-treatment interactions were nonsignificant for all traits, indicating no need to match families to silvicultural treatments. Wood quality traits had weak genetic correlations with growth and stem quality traits (stem slenderness, sweep, and branch angle) with a range of −0.33 to 0.43, suggesting that recurrent selection on growth or stem quality traits would not adversely affect wood quality in loblolly pine. DA - 2021/10// PY - 2021/10// DO - 10.1093/forsci/fxab026 VL - 67 IS - 5 SP - 564-573 SN - 1938-3738 UR - https://doi.org/10.1093/forsci/fxab026 KW - Silviculture KW - Pinus taeda KW - genotype by environment interaction KW - X-ray densitometry KW - acoustic velocity ER - TY - JOUR TI - The persistent threat of emerging plant disease pandemics to global food security AU - Ristaino, Jean B. AU - Anderson, Pamela K. AU - Bebber, Daniel P. AU - Brauman, Kate A. AU - Cunniffe, Nik J. AU - Fedoroff, Nina V AU - Finegold, Cambria AU - Garrett, Karen A. AU - Gilligan, Christopher A. AU - Jones, Christopher M. AU - Martin, Michael D. AU - MacDonald, Graham K. AU - Neenan, Patricia AU - Records, Angela AU - Schmale, David G. AU - Tateosian, Laura AU - Wei, Qingshan T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Plant disease outbreaks are increasing and threaten food security for the vulnerable in many areas of the world. Now a global human pandemic is threatening the health of millions on our planet. A stable, nutritious food supply will be needed to lift people out of poverty and improve health outcomes. Plant diseases, both endemic and recently emerging, are spreading and exacerbated by climate change, transmission with global food trade networks, pathogen spillover, and evolution of new pathogen lineages. In order to tackle these grand challenges, a new set of tools that include disease surveillance and improved detection technologies including pathogen sensors and predictive modeling and data analytics are needed to prevent future outbreaks. Herein, we describe an integrated research agenda that could help mitigate future plant disease pandemics. DA - 2021/6/8/ PY - 2021/6/8/ DO - 10.1073/pnas.2022239118 VL - 118 IS - 23 SP - SN - 0027-8424 KW - emerging plant disease KW - plant pathology KW - food security ER - TY - JOUR TI - Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster AU - Baker, Brandon M. AU - Carbone, Mary Anna AU - Huang, Wen AU - Anholt, Robert R. H. AU - Mackay, Trudy F. C. T2 - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA AB - Significance The use of cocaine and methamphetamine presents significant socioeconomic problems. However, identifying the genetic underpinnings that determine susceptibility to substance use is challenging in human populations. The fruit fly, Drosophila melanogaster , presents a powerful genetic model since we can control the genetic background and environment, 75% of disease-causing genes in humans have a fly counterpart, and flies—like humans—exhibit adverse effects upon cocaine and methamphetamine exposure. We showed that the genetic architecture underlying variation in voluntary cocaine and methamphetamine consumption differs between sexes and is dominated by variants in genes associated with connectivity and function of the nervous system. Results obtained from the Drosophila gene discovery model can guide studies on substance abuse susceptibility in human populations. DA - 2021/6/8/ PY - 2021/6/8/ DO - 10.1073/pnas.2104131118 VL - 118 IS - 23 SP - SN - 0027-8424 KW - extreme QTL genome-wide association mapping KW - Drosophila Genetic Reference Panel KW - RNA interference KW - advanced intercross population ER - TY - JOUR TI - Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation AU - Aimone, Catherine D. AU - Lavington, Erik AU - Hoyer, J. Steen AU - Deppong, David O. AU - Mickelson-Young, Leigh AU - Jacobson, Alana AU - Kennedy, George G. AU - Carbone, Ignazio AU - Hanley-Bowdoin, Linda AU - Duffy, Siobain T2 - JOURNAL OF GENERAL VIROLOGY AB - Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression. DA - 2021/// PY - 2021/// DO - 10.1099/jgv.0.001622 VL - 102 IS - 7 SP - SN - 1465-2099 KW - cassava mosaic begomoviruses KW - vegetative propagation KW - viral diversity ER - TY - JOUR TI - Immunohistochemical evaluation of immune cell infiltration in canine gliomas AU - Krane, Gregory A. AU - Carly A. O'Dea, AU - Malarkey, David E. AU - Miller, Andrew D. AU - Miller, C. Ryan AU - Tokarz, Debra A. AU - Jensen, Heather L. AU - Janardhan, Kyathanahalli S. AU - Shockley, Keith R. AU - Flagler, Norris AU - Rainess, Brittani A. AU - Mariani, Christopher L. T2 - VETERINARY PATHOLOGY AB - Evasion of the immune response is an integral part of the pathogenesis of glioma. In humans, important mechanisms of immune evasion include recruitment of regulatory T cells (Tregs) and polarization of macrophages toward an M2 phenotype. Canine glioma has a robust immune cell infiltrate that has not been extensively characterized. The purpose of this study was to determine the distribution of immune cells infiltrating spontaneous intracranial canine gliomas. Seventy-three formalin-fixed, paraffin-embedded tumor samples were evaluated using immunohistochemistry for CD3, forkhead box 3 (FOXP3), CD20, Iba1, calprotectin (Mac387), CD163, and indoleamine 2,3-dioxygenase (IDO). Immune cell infiltration was present in all tumors. Low-grade and high-grade gliomas significantly differed in the numbers of FoxP3+ cells, Mac387+ cells, and CD163+ cells (P = .006, .01, and .01, respectively). Considering all tumors, there was a significant increase in tumor area fraction of CD163 compared to Mac387 (P < .0001), and this ratio was greater in high-grade tumors than in low-grade tumors (P = .005). These data warrant further exploration into the roles of macrophage repolarization or Treg interference therapy in canine glioma. DA - 2021/7/1/ PY - 2021/7/1/ DO - 10.1177/03009858211023946 SP - SN - 1544-2217 KW - astrocytoma KW - brain KW - dogs KW - cancer KW - immunohistochemistry KW - immunology KW - lymphocytes KW - macrophages KW - oligodendroglioma ER - TY - JOUR TI - Real-time monitoring of plant stresses via chemiresistive profiling of leaf volatiles by a wearable sensor AU - Li, Zheng AU - Liu, Yuxuan AU - Hossain, Oindrila AU - Paul, Rajesh AU - Yao, Shanshan AU - Wu, Shuang AU - Ristaino, Jean B. AU - Zhu, Yong AU - Wei, Qingshan T2 - MATTER AB - Determination of plant stresses such as infections by plant pathogens is currently dependent on time-consuming and complicated analytical technologies. Here, we report a leaf-attachable chemiresistive sensor array for real-time fingerprinting of volatile organic compounds (VOCs) that permits noninvasive and early diagnosis of plant diseases, such as late blight caused by Phytophthora infestans. The imperceptible sensor patch integrates an array of graphene-based sensing materials and flexible silver nanowire electrodes on a kirigami-inspired stretchable substrate, which can minimize strain interference. The sensor patch has been mounted on live tomato plants to profile key plant volatiles at low-ppm concentrations with fast response (<20 s). The multiplexed sensor array allows for accurate detection and classification of 13 individual plant volatiles with >97% classification accuracy. The wearable sensor patch was used to diagnose tomato late blight as early as 4 days post inoculation and abiotic stresses such as mechanical damage within 1 h. DA - 2021/7/7/ PY - 2021/7/7/ DO - 10.1016/j.matt.2021.06.009 VL - 4 IS - 7 SP - 2553-2570 SN - 2590-2385 ER - TY - JOUR TI - Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts AU - Nguyen, Kathy-Uyen AU - Zhang, Ran AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial-microbial holobiont (termed HT-58-2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a, complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH2 Cl2 /2-propanol, 1:1) of HT-58-2 cultures with NaBH4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17-dioxobacteriochlorins) exhibit a bathochromic shift (λabs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 131 -oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λem 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non-axenic cultures at microscale quantities (2 mL, 2 μm), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT-58-2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously. DA - 2021/7/16/ PY - 2021/7/16/ DO - 10.1111/php.13474 VL - 7 SP - SN - 1751-1097 ER - TY - JOUR TI - Suspected Bartonella osteomyelitis in a dog AU - Easley, Frankie AU - Taylor, Lindsay AU - Breitschwerdt, Edward B. T2 - CLINICAL CASE REPORTS AB - Abstract Bartonella associated osteomyelitis, while described in humans and a cat, has to our knowledge not been described in dogs. Infection with Bartonella spp. should be considered as a potential bacterial cause of osteomyelitis in dogs. DA - 2021/7// PY - 2021/7// DO - 10.1002/ccr3.4512 VL - 9 IS - 7 SP - SN - 2050-0904 UR - https://doi.org/10.1002/ccr3.4512 KW - bone KW - infection KW - kidney KW - polydipsia and polyuria ER - TY - JOUR TI - In Situ, Protein-Mediated Generation of a Photochemically Active Chlorophyll Analogue in a Mutant Bacterial Photosynthetic Reaction Center AU - Magdaong, Nikki Cecil M. AU - Buhrmaster, James C. AU - Faries, Kaitlyn M. AU - Liu, Haijun AU - Tira, Gregory A. AU - Lindsey, Jonathan S. AU - Hanson, Deborah K. AU - Holten, Dewey AU - Laible, Philip D. AU - Kirmaier, Christine T2 - BIOCHEMISTRY AB - All possible natural amino acids have been substituted for the native LeuL185 positioned near the B-side bacteriopheophytin (HB) in the bacterial reaction center (RC) from Rhodobacter sphaeroides. Additional mutations that enhance electron transfer to the normally inactive B-side cofactors are present. Approximately half of the isolated RCs with Glu at L185 contain a magnesium chlorin (CB) in place of HB. The chlorin is not the common BChl a oxidation product 3-desvinyl-3-acetyl chlorophyll a with a C–C bond in ring D and a C═C bond in ring B but has properties consistent with reversal of these bond orders, giving 17,18-didehydro BChl a. In such RCs, charge-separated state P+CB– forms in ∼5% yield. The other half of the GluL185-containing RCs have a bacteriochlorophyll a (BChl a) denoted βB in place of HB. Residues His, Asp, Asn, and Gln at L185 yield RCs with ≥85% βB in the HB site, while most other amino acids result in RCs that retain HB (≥95%). To the best of our knowledge, neither bacterial RCs that harbor five BChl a molecules and one chlorophyll analogue nor those with six BChl a molecules have been reported previously. The finding that altering the local environment within a cofactor binding site of a transmembrane complex leads to in situ generation of a photoactive chlorin with an unusual ring oxidation pattern suggests new strategies for amino acid control over pigment type at specific sites in photosynthetic proteins. DA - 2021/4/27/ PY - 2021/4/27/ DO - 10.1021/acs.biochem.1c00137 VL - 60 IS - 16 SP - 1260-1275 SN - 0006-2960 ER - TY - JOUR TI - Synthesis of model bacteriochlorophylls containing substituents of native rings A, C and E AU - Chung, Duy T. M. AU - Tran, Phuong Vy AU - Chau Nguyen, Khiem AU - Wang, Pengzhi AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - An established route to the bacteriochlorophyll skeleton from two dihydrodipyrrin halves has been extended to accommodate several substituents characteristic of the native bacteriochlorophyll a. DA - 2021/7/8/ PY - 2021/7/8/ DO - 10.1039/d1nj02469h VL - 7 SP - SN - 1369-9261 UR - http://dx.doi.org/10.1039/d1nj02469h ER - TY - JOUR TI - BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAl5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar AU - Wang, Qiao AU - Dai, Xinren AU - Pang, Hongying AU - Cheng, Yanxia AU - Huang, Xiong AU - Li, Hui AU - Yan, Xiaojing AU - Lu, Fachuang AU - Wei, Hairong AU - Sederoff, Ronald R. AU - Li, Quanzi T2 - FRONTIERS IN PLANT SCIENCE AB - Lignin is one of the major components of xylem cell walls in tree stems. The lignin in the wood of most flowering plants (dicotyledonous angiosperms) is typically polymerized from three monolignol precursors, coniferyl alcohol, sinapyl alcohol, and p -coumaroyl alcohol, resulting in guaiacyl (G), syringyl (S), and hydroxyphenyl (H) subunits, respectively. In this study, we focus on the transcriptional regulation of a coniferaldehyde 5-hydroxylase ( CAld5H2 ) gene, which encodes a key enzyme for sinapyl alcohol biosynthesis. We carried out a yeast one-hybrid (Y1H) screen to identify candidate upstream transcription factors (TFs) regulating CAld5H2 . We obtained 12 upstream TFs as potential regulators of CAld5H2 . One of these TF genes, BLH6a, encodes a BEL1-like homeodomain (BLH) protein and negatively regulated the CAld5H2 promoter activity. The direct regulation of CAld5H2 promoter by BLH6a was supported by chromatin immunoprecipitation–quantitative polymerase chain reaction (ChIP–qPCR) and dominant repression of BLH6a in transgenic plants. Luciferase complementation imaging analyses showed extensive protein – protein interactions among these 12 TFs. We propose that BLH6a is a negative regulator of CAld5H2 , which acts through combinatorial regulation of multiple TFs for sinapyl alcohol (S monolignol) biosynthesis in poplar. DA - 2021/6/25/ PY - 2021/6/25/ DO - 10.3389/fpls.2021.695223 VL - 12 SP - SN - 1664-462X KW - lignin KW - BEL1-like homeodomain protein KW - transcription factor KW - yeast one hybrid ER - TY - JOUR TI - Discovery of a novel eIF4E1.S allele conferring PVY resistance in Chinese tobacco (Nicotiana tabacum) landraces AU - Lin, Shifeng AU - Dewey, Ralph E. AU - Wang, Rengang AU - Ren, Xueliang AU - Wang, Zili AU - Zhang, Jishun AU - Long, Mingjin T2 - PLANT BREEDING AB - Abstract The tobacco eIF4E1 . S gene is a well‐recognized susceptibility factor for potato virus Y (PVY) and a dominant target locus for current PVY resistance breeding in tobacco. In this study, over 900 tobacco landraces from China were screened for resistance to PVY and the DNA sequence of eIF4E1 . S was analysed for all resistant accessions. Eight PVY‐resistant lines were identified from this screen, and a naturally occurring mutant allele of eIF4E1 . S carrying a single nucleotide insertion was discovered in seven, including a landrace called Kaiyangxiaoheiyan (Kaixiao), and designated eIF4E1.Kai . Knowledge of the mutant gene sequence enabled the development of a codominant PCR‐based marker that can distinguish eIF4E1.S/eIF4E1.Kai heterozygotes from both homozygous classes. Using this marker, we genotyped F 2 plants segregating for the eIF4E1 . Kai mutant and confirmed the relationship between genotype and phenotype. The results described here provide valuable genetic insights into Chinese tobacco landraces as a source of naturally occurring PVY resistance, as well as a powerful tool for the molecular marker‐assisted breeding of tobacco varieties containing the resistance source eIF4E1.Kai . DA - 2021/6/22/ PY - 2021/6/22/ DO - 10.1111/pbr.12919 SP - SN - 1439-0523 KW - co-dominant marker KW - S KW - naturally-occurring allele KW - Nicotiana tabacum KW - potato virus Y KW - susceptibility gene ER - TY - JOUR TI - Considerations of the biosynthesis and molecular diversity of tolyporphins AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - Tolyporphins, relatively new members of the pigments of life family found in a cyanobacterium, differ in the chromophores, pyrroline substituents, and stereochemistry, yet likely all derive from uroporphyrinogen III. DA - 2021/6/22/ PY - 2021/6/22/ DO - 10.1039/d1nj01761f VL - 6 SP - SN - 1369-9261 ER - TY - JOUR TI - Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution AU - Peart, Claire R. AU - Williams, Christina AU - Pophaly, Saurabh D. AU - Neely, Benjamin A. AU - Gulland, Frances M. D. AU - Adams, David J. AU - Ng, Bee Ling AU - Cheng, William AU - Goebel, Michael E. AU - Fedrigo, Olivier AU - Haase, Bettina AU - Mountcastle, Jacquelyn AU - Fungtammasan, Arkarachai AU - Formenti, Giulio AU - Collins, Joanna AU - Wood, Jonathan AU - Sims, Ying AU - Torrance, James AU - Tracey, Alan AU - Howe, Kerstin AU - Rhie, Arang AU - Hoffman, Joseph I AU - Johnson, Jeremy AU - Jarvis, Erich D. AU - Breen, Matthew AU - Wolf, Jochen B. W. T2 - MOLECULAR ECOLOGY RESOURCES AB - Abstract With the advent of chromatin‐interaction maps, chromosome‐level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome‐scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion ( Zalophus californianus ). Short‐read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi‐C and Chicago), and long‐read assemblies with three data types (Hi‐C, optical maps and 10X linked reads) following the “Vertebrate Genomes Project (VGP)” pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2 n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2 n = 32–36), ferret (2 n = 34), red panda (2 n = 36) and domestic dog (2 n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome‐integrated single‐locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad‐scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near‐perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high‐quality genomes of an emerging cancer model and highlights that even highly fragmented short‐read assemblies scaffolded with Hi‐C can yield reliable chromosome‐level scaffolds suitable for comparative genomic analyses. DA - 2021/6/27/ PY - 2021/6/27/ DO - 10.1111/1755-0998.13443 SP - SN - 1755-0998 KW - California sea lion (Zalophus californianus) KW - cancer KW - Carnivora KW - chromatin interaction mapping KW - genome assembly KW - genome evolution KW - Hi-C ER - TY - JOUR TI - Global historic pandemics caused by the FAM-1 genotype of Phytophthora infestans on six continents AU - Saville, Amanda C. AU - Ristaino, Jean B. T2 - SCIENTIFIC REPORTS AB - The FAM-1 genotype of Phytophthora infestans caused late blight in the 1840s in the US and Europe and was responsible for the Irish famine. We sampled 140 herbarium specimens collected between 1845 and 1991 from six continents and used 12-plex microsatellite genotyping (SSR) to identify FAM-1 and the mtDNA lineage (Herb-1/Ia) present in historic samples. FAM-1 was detected in approximately 73% of the historic specimens and was found on six continents. The US-1 genotype was found later than FAM-1 on all continents except Australia/Oceania and in only 27% of the samples. FAM-1 was the first genotype detected in almost all the former British colonies from which samples were available. The data from historic outbreak samples suggest the FAM-1 genotype was widespread, diverse, and spread to Asia and Africa from European sources. The famine lineage spread to six continents over 144 years, remained widespread and likely spread during global colonization from Europe. In contrast, modern lineages of P. infestans are rapidly displaced and sexual recombination occurs in some regions. DA - 2021/6/11/ PY - 2021/6/11/ DO - 10.1038/s41598-021-90937-6 VL - 11 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Comparison of Serological and Molecular Assays for Bartonella Species in Dogs with Hemangiosarcoma AU - Lashnits, Erin AU - Neupane, Pradeep AU - Bradley, Julie M. AU - Richardson, Toni AU - Maggi, Ricardo G. AU - Breitschwerdt, Edward B. T2 - PATHOGENS AB - Currently, a gold standard diagnostic test for Bartonella infection in dogs is lacking. This represents a critical limitation for the development and evaluation of new diagnostic tests, as well as for the diagnosis of, and research on, bartonellosis in dogs. This retrospective observational study aims to compare the results of commonly performed and newly-reported Bartonella spp. diagnostic tests in banked clinical specimens from 90 dogs with hemangiosarcoma (HSA) using composite reference standard (CRS) and random effects latent class analysis (RE-LCA) techniques. Samples from each dog were tested using six serological or molecular diagnostic assays, including indirect fluorescent antibody (IFA) and Western blot (WB) for the detection of antibodies in serum, and qPCR and droplet digital PCR (ddPCR) in blood and fresh frozen tissue biopsy samples (mainly splenic HSA tumors and histopathologically normal spleen or skin/adipose tissue). Bartonella infection prevalence was estimated to be 78% based on the CRS (parallel testing with all six assays), and 64% based on the RE-LCA model. The assay with the highest diagnostic accuracy was qPCR performed on fresh frozen tissue biopsy samples (sensitivity: 94% by RE-LCA and 80% by CRS; specificity: 100%). When comparing newly-reported to traditional Bartonella diagnostic assays, ddPCR was more sensitive for the detection of Bartonella DNA than qPCR when testing blood samples (36% vs. 0%, p < 0.0001). Dogs that were positive on serological assays alone with negative molecular assays were highly unlikely (<3%) to be classified as infected by the RE-LCA model. These data indicate that Bartonella spp. DNA can be PCR amplified from fresh frozen tissues from a majority of dogs with HSA using both qPCR and ddPCR, supporting the use of these methods for future controlled studies comparing the prevalence of Bartonella spp. DNA in the tissue of dogs with HSA to that of unaffected controls. DA - 2021/7// PY - 2021/7// DO - 10.3390/pathogens10070794 VL - 10 IS - 7 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10070794 KW - diagnostic testing KW - ddPCR KW - PCR KW - serology KW - sensitivity KW - specificity KW - tissue biopsy KW - latent class analysis ER - TY - JOUR TI - Tolyporphins A-R, unusual tetrapyrrole macrocycles in a cyanobacterium from Micronesia, assessed quantitatively from the culture HT-58-2 AU - Timothy J. O'Donnell, AU - Gurr, Joshua R. AU - Dai, Jingqiu AU - Taniguchi, Masahiko AU - Williams, Philip G. AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - Tolyporphins A–R are the newest additions to the family of native tetrapyrroles. LC-MS-dMRM and absorption spectroscopy have been employed for analysis of mixtures containing the 18 distinctive natural products. DA - 2021/6/8/ PY - 2021/6/8/ DO - 10.1039/d1nj02108g VL - 6 SP - SN - 1369-9261 ER - TY - JOUR TI - Integrated microneedle-smartphone nucleic acid amplification platform for in-field diagnosis of plant diseases AU - Paul, Rajesh AU - Ostermann, Emily AU - Chen, Yuting AU - Saville, Amanda C. AU - Yang, Yuming AU - Gu, Zhen AU - Whitfield, Anna E. AU - Ristaino, Jean B. AU - Wei, Qingshan T2 - BIOSENSORS & BIOELECTRONICS AB - We demonstrate an integrated microneedle (MN)-smartphone nucleic acid amplification platform for “sample-to-answer” diagnosis of multiplexed plant pathogens within 30 min. This portable system consists of a polymeric MN patch for rapid nucleic acid extraction within a minute and a 3D-printed smartphone imaging device for loop-mediated isothermal amplification (LAMP) reaction and detection. We expanded the extraction of the MN technology for DNA targets as in the previous study (ACS Nano, 2019, 13, 6540–6549) to more fragile RNA biomarkers, evaluated the storability of the extracted nucleic acid samples on MN surfaces, and developed a smartphone-based LAMP amplification and fluorescent reader device that can quantify four LAMP reactions on the same chip. In addition, we have found that the MN patch containing as few as a single needle tip successfully extracted enough RNA for RT-PCR or RT-LAMP analysis. Moreover, MN-extracted RNA samples remained stable on MN surfaces for up to three days. The MN-smartphone platform has been used to detect both Phytophthora infestans DNA and tomato spotted wilt virus (TSWV) RNA down to 1 pg, comparable to the results from a benchtop thermal cycler. Finally, multiplexed detection of P. infestans and TSWV through a single extraction from infected tomato leaves and amplification on the smartphone without benchtop equipment was demonstrated. DA - 2021/9/1/ PY - 2021/9/1/ DO - 10.1016/j.bios.2021.113312 VL - 187 SP - SN - 1873-4235 KW - Plant disease diagnostics KW - Nucleic acid extraction KW - Microneedle KW - Isothermal amplification KW - Smartphone ER - TY - JOUR TI - Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles AU - Kranse, Olaf AU - Beasley, Helen AU - Adams, Sally AU - Pires-daSilva, Andre AU - Bell, Christopher AU - Lilley, Catherine J. AU - Urwin, Peter E. AU - Bird, David AU - Miska, Eric AU - Smant, Geert AU - Gheysen, Godelieve AU - Jones, John AU - Viney, Mark AU - Abad, Pierre AU - Maier, Thomas R. AU - Baum, Thomas J. AU - Siddique, Shahid AU - Williamson, Valerie AU - Akay, Alper AU - Akker, Sebastian T2 - G3-GENES GENOMES GENETICS AB - Plant-parasitic nematodes are a continuing threat to food security, causing an estimated 100 billion USD in crop losses each year. The most problematic are the obligate sedentary endoparasites (primarily root knot nematodes and cyst nematodes). Progress in understanding their biology is held back by a lack of tools for functional genetics: forward genetics is largely restricted to studies of natural variation in populations and reverse genetics is entirely reliant on RNA interference. There is an expectation that the development of functional genetic tools would accelerate the progress of research on plant-parasitic nematodes, and hence the development of novel control solutions. Here, we develop some of the foundational biology required to deliver a functional genetic tool kit in plant-parasitic nematodes. We characterize the gonads of male Heterodera schachtii and Meloidogyne hapla in the context of spermatogenesis. We test and optimize various methods for the delivery, expression, and/or detection of exogenous nucleic acids in plant-parasitic nematodes. We demonstrate that delivery of macromolecules to cyst and root knot nematode male germlines is difficult, but possible. Similarly, we demonstrate the delivery of oligonucleotides to root knot nematode gametes. Finally, we develop a transient expression system in plant-parasitic nematodes by demonstrating the delivery and expression of exogenous mRNA encoding various reporter genes throughout the body of H. schachtii juveniles using lipofectamine-based transfection. We anticipate these developments to be independently useful, will expedite the development of genetic modification tools for plant-parasitic nematodes, and ultimately catalyze research on a group of nematodes that threaten global food security. DA - 2021/2// PY - 2021/2// DO - 10.1093/g3journal/jkaa058 VL - 11 IS - 2 SP - SN - 2160-1836 KW - plant-parasitic nematodes KW - transient expression KW - genetic modification KW - lipofection KW - transformation KW - germline ER - TY - JOUR TI - Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions AU - Kim, Jong Hyuk AU - Megquier, Kate AU - Thomas, Rachael AU - Sarver, Aaron L. AU - Song, Jung Min AU - Kim, Yoon Tae AU - Cheng, Nuojin AU - Schulte, Ashley J. AU - Linden, Michael A. AU - Murugan, Paari AU - Oseth, LeAnn AU - Forster, Colleen L. AU - Elvers, Ingegerd AU - Swofford, Ross AU - Turner-Maier, Jason AU - Karlsson, Elinor K. AU - Breen, Matthew AU - Lindblad-Toh, Kerstin AU - Modiano, Jaime F. T2 - MOLECULAR CANCER RESEARCH AB - Sporadic angiosarcomas are aggressive vascular sarcomas whose rarity and genomic complexity present significant obstacles in deciphering the pathogenic significance of individual genetic alterations. Numerous fusion genes have been identified across multiple types of cancers, but their existence and significance remain unclear in sporadic angiosarcomas. In this study, we leveraged RNA-sequencing data from 13 human angiosarcomas and 76 spontaneous canine hemangiosarcomas to identify fusion genes associated with spontaneous vascular malignancies. Ten novel protein-coding fusion genes, including TEX2-PECAM1 and ATP8A2-FLT1, were identified in seven of the 13 human tumors, with two tumors showing mutations of TP53. HRAS and NRAS mutations were found in angiosarcomas without fusions or TP53 mutations. We found 15 novel protein-coding fusion genes including MYO16-PTK2, GABRA3-FLT1, and AKT3-XPNPEP1 in 11 of the 76 canine hemangiosarcomas; these fusion genes were seen exclusively in tumors of the angiogenic molecular subtype that contained recurrent mutations in TP53, PIK3CA, PIK3R1, and NRAS. In particular, fusion genes and mutations of TP53 cooccurred in tumors with higher frequency than expected by random chance, and they enriched gene signatures predicting activation of angiogenic pathways. Comparative transcriptomic analysis of human angiosarcomas and canine hemangiosarcomas identified shared molecular signatures associated with activation of PI3K/AKT/mTOR pathways. Our data suggest that genome instability induced by TP53 mutations might create a predisposition for fusion events that may contribute to tumor progression by promoting selection and/or enhancing fitness through activation of convergent angiogenic pathways in this vascular malignancy. IMPLICATIONS: This study shows that, while drive events of malignant vasoformative tumors of humans and dogs include diverse mutations and stochastic rearrangements that create novel fusion genes, convergent transcriptional programs govern the highly conserved morphologic organization and biological behavior of these tumors in both species. DA - 2021/5/1/ PY - 2021/5/1/ DO - 10.1158/1541-7786.MCR-20-0937 VL - 19 IS - 5 SP - 847-861 SN - 1557-3125 ER - TY - JOUR TI - Haematological and biochemical abnormalities in hunting dogs infected with Acanthocheilonema reconditum, associated risk factors, and a European overview AU - Pacifico, Laura AU - Ferrari, Nicola AU - Romeo, Claudia AU - Buono, Francesco AU - Varuzza, Paolo AU - Sgroi, Giovanni AU - Neola, Benedetto AU - Buch, Jesse AU - Beall, Melissa AU - Breitschwerdt, Edward B. AU - Chandrashekar, Ramaswamy AU - Veneziano, Vincenzo AU - Piantedosi, Diego T2 - PARASITOLOGY RESEARCH AB - Abstract Acanthocheilonema reconditum is a filarial parasite transmitted by arthropods (fleas, lice, and ticks) that infect dogs. There is minimal published data available to date on potential haematological and biochemical changes associated with this parasitic infection. Study aims were (i) provide an overview of A. reconditum in Europe, (ii) define A. reconditum prevalence and risk factors in a specific dog population (hunting) from southern Italy, and (iii) assess the frequency of haemato-biochemical abnormalities associated with infection. Blood samples collected from 3020 dogs were tested by a modified Knott’s technique to count and identify microfilariae. Eighty-four dogs were infected by A. reconditum (2.78%; 95% CI 2.19–3.37%). Microfilariae ranged from 1 to 212/ml. Based on clinical examination, all but six dogs with non-specific symptoms were healthy. Haematological abnormalities included leucocytosis ( n = 15), with eosinophilia ( n = 14) and monocytosis ( n = 13). Serum biochemical abnormalities included increased total serum proteins ( n = 19), albumins ( n = 7), total globulins ( n = 14), ALT ( n = 1), and ALP ( n = 1); one dog was hypoalbuminemic, and BUN was mildly increased in 2 dogs. Risk factors included the province origin (Napoli, OR=5.4, 95%CI: 2.1–14.0; Caserta, OR=5.1, 95%CI: 2.5–10.6), hunting wild mammals (OR=2.8, 95% 95%CI: 1.6–4.8), and ectoparasite infestation (OR=1.9, 95%CI: 1.1–3.1). There was a negative correlation between microfilaraemic load and decreased albumin level (−0.37; p =0.021). Our results showed that A. reconditum circulates within the hunting dog population of southern Italy, with seemingly low pathogenic potential. DA - 2021/5/8/ PY - 2021/5/8/ DO - 10.1007/s00436-021-07179-8 VL - 5 SP - SN - 1432-1955 KW - Filarial nematodes KW - Acanthocheilonema spp KW - CVBDs KW - Hunting dogs ER - TY - JOUR TI - Heat shock proteins and small nucleolar RNAs are dysregulated in a Drosophila model for feline hypertrophic cardiomyopathy AU - Tallo, Christian A. AU - Duncan, Laura H. AU - Yamamoto, Akihiko H. AU - Slaydon, Joshua D. AU - Arya, Gunjan H. AU - Turlapati, Lavanya AU - Mackay, Trudy F. C. AU - Carbone, Mary A. T2 - G3-GENES GENOMES GENETICS AB - In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans. DA - 2021/1// PY - 2021/1// DO - 10.1093/g3journal/jkaa014 VL - 11 IS - 1 SP - SN - 2160-1836 KW - MYBPC3 KW - cMyBP-C KW - Drosophila melanogaster KW - feline HCM KW - hypertrophic cardiomyopathy ER - TY - JOUR TI - Genetic Parameters and Genotype-by-Environment Interactions in Regional Progeny Tests of Pinus taeda L. in the Southern USA AU - Lauer, Edwin AU - Sims, Andrew AU - McKeand, Steven AU - Isik, Fikret T2 - FOREST SCIENCE AB - Abstract Genetic parameters were estimated using a five-series multienvironment trial of Pinus taeda L. in the southern USA. There were 324 half-sib families planted in five test series across 37 locations. A set of six variance/covariance matrices for the genotype-by-environment (G × E) effect for tree height and diameter were compared on the basis of model fit. In single-series analysis, extended factor analytical models provided generally superior model fit to simpler models for both traits; however, in the combined-series analysis, diameter was optimally modeled using simpler variance/covariance structures. A three-way compound term for modeling G × E interactions among and within series yielded substantial improvements in terms of model fit and standard errors of predictions. Heritability of family means ranged between 0.63 and 0.90 for both height and diameter. Average additive genetic correlations among sites were 0.70 and 0.61 for height and diameter, respectively, suggesting the presence of some G × E interaction. Pairs of sites with the lowest additive genetic correlations were located at opposite ends of the latitude range. Latent factor regression revealed a small number of parents with large factor scores that changed ranks significantly between southern and northern environments. DA - 2021/2// PY - 2021/2// DO - 10.1093/forsci/fxaa035 VL - 67 IS - 1 SP - 60-71 SN - 1938-3738 KW - factor analytical mixed models KW - tree breeding KW - heritability KW - genetic variance components ER - TY - JOUR TI - Single-Fluorophore Single-Chain Nanoparticle Undergoes Fluorophore-Driven Assembly with Fluorescence Features Retained in Physiological Milieu AU - Liu, Sijia AU - Rong, Jie AU - Liu, Rui AU - Lindsey, Jonathan S. T2 - ACS APPLIED POLYMER MATERIALS AB - To address the longstanding problem of solubilization of hydrophobic fluorophores in aqueous solution, a recent design employed a single fluorophore attached to the terminus of a heterotelechelic, amphiphilic polymer that contained poly(ethylene glycol) (PEG), dodecyl, and sulfonate pendant groups (1:1:5 ratio). The resulting single-polymer–single-fluorophore construct folded in aqueous solution containing 1 M NaCl but is shown here to comprise a mixture of folded (i.e., unimer) and unfolded species in low ionic strength media (e.g., phosphate-buffered saline, PBS) characteristic of physiological milieu. To identify molecular designs that engender unimer formation in PBS solution, heterotelechelic amphiphilic polymers containing cyclododecyl (rather than PEG and dodecyl) and sulfonate pendant groups were synthesized via reversible addition-fragmentation chain-transfer polymerization with variation in (1) degree of polymerization (weight average molecular weight 10–34 kDa) and (2) ratios of pendant groups. A perylene-monoimide or chlorin was used as the hydrophobic fluorophore and attached to the polymer via a maleimide group. Unimer formation occurred quantitatively in PBS solution with polymers of ≥28 kDa, a ratio of cyclododecyl/sulfonate groups of 1:4 to 1:6, and an attached hydrophobic fluorophore. The hydrophobic fluorophore promoted folding of the attached polymer, thereby driving its own encapsulation even in low ionic strength media. The resulting single-chain nanoparticles bearing a single fluorophore in PBS solution retain a fluorescence quantum yield that is at least 70% of that of the hydrophobic fluorophore benchmark alone in a nonpolar solvent. The molecular designs presented herein appear well suited for aqueous solubilization of hydrophobic fluorophores in life science applications. DA - 2021/4/9/ PY - 2021/4/9/ DO - 10.1021/acsapm.0c01313 VL - 3 IS - 4 SP - 1767-1776 SN - 2637-6105 KW - single-chain nanoparticle KW - amphiphilic KW - hydrophobic fluorophore KW - unimer KW - fluorescence KW - physiological milieu ER - TY - JOUR TI - Functional Diversification, Redundancy, and Epistasis among Paralogs of the Drosophila melanogaster Obp50a-d Gene Cluster AU - Johnstun, Joel A. AU - Shankar, Vijay AU - Mokashi, Sneha S. AU - Sunkara, Lakshmi T. AU - Ihearahu, Ugonna E. AU - Lyman, Roberta L. AU - Mackay, Trudy F. C. AU - Anholt, Robert R. H. T2 - MOLECULAR BIOLOGY AND EVOLUTION AB - Large multigene families, such as the insect odorant-binding proteins (OBPs), are thought to arise through functional diversification after repeated gene duplications. Whereas many OBPs function in chemoreception, members of this family are also expressed in tissues outside chemosensory organs. Paralogs of the Obp50 gene cluster are expressed in metabolic and male reproductive tissues, but their functions and interrelationships remain unknown. Here, we report the genetic dissection of four members of the Obp50 cluster, which are in close physical proximity without intervening genes. We used CRISPR technology to excise the entire cluster while introducing a PhiC31 reintegration site to reinsert constructs in which different combinations of the constituent Obp genes were either intact or rendered inactive. We performed whole transcriptome sequencing and assessed sexually dimorphic changes in transcript abundances (transcriptional niches) associated with each gene-edited genotype. Using this approach, we were able to estimate redundancy, additivity, diversification, and epistasis among Obp50 paralogs. We analyzed the effects of gene editing of this cluster on organismal phenotypes and found a significant skewing of sex ratios attributable to Obp50a, and sex-specific effects on starvation stress resistance attributable to Obp50d. Thus, there is functional diversification within the Obp50 cluster with Obp50a contributing to development and Obp50d to stress resistance. The deletion-reinsertion approach we applied to the Obp50 cluster provides a general paradigm for the genetic dissection of paralogs of multigene families. DA - 2021/5// PY - 2021/5// DO - 10.1093/molbev/msab004 VL - 38 IS - 5 SP - 2030-2044 SN - 1537-1719 KW - multigene families KW - functional diversification KW - transcriptional niche KW - RNAseq KW - odorant-binding proteins KW - evolutionary genetics ER - TY - JOUR TI - MYB-Mediated Regulation of Anthocyanin Biosynthesis AU - Yan, Huiling AU - Pei, Xiaona AU - Zhang, Heng AU - Li, Xiang AU - Zhang, Xinxin AU - Zhao, Minghui AU - Chiang, Vincent L. AU - Sederoff, Ronald Ross AU - Zhao, Xiyang T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - Anthocyanins are natural water-soluble pigments that are important in plants because they endow a variety of colors to vegetative tissues and reproductive plant organs, mainly ranging from red to purple and blue. The colors regulated by anthocyanins give plants different visual effects through different biosynthetic pathways that provide pigmentation for flowers, fruits and seeds to attract pollinators and seed dispersers. The biosynthesis of anthocyanins is genetically determined by structural and regulatory genes. MYB (v-myb avian myeloblastosis viral oncogene homolog) proteins are important transcriptional regulators that play important roles in the regulation of plant secondary metabolism. MYB transcription factors (TFs) occupy a dominant position in the regulatory network of anthocyanin biosynthesis. The TF conserved binding motifs can be combined with other TFs to regulate the enrichment and sedimentation of anthocyanins. In this study, the regulation of anthocyanin biosynthetic mechanisms of MYB-TFs are discussed. The role of the environment in the control of the anthocyanin biosynthesis network is summarized, the complex formation of anthocyanins and the mechanism of environment-induced anthocyanin synthesis are analyzed. Some prospects for MYB-TF to modulate the comprehensive regulation of anthocyanins are put forward, to provide a more relevant basis for further research in this field, and to guide the directed genetic modification of anthocyanins for the improvement of crops for food quality, nutrition and human health. DA - 2021/3// PY - 2021/3// DO - 10.3390/ijms22063103 VL - 22 IS - 6 SP - SN - 1422-0067 KW - MYB KW - transcription factor KW - anthocyanin KW - positive regulation KW - negative regulation KW - environment KW - MBW complexes ER - TY - JOUR TI - Comprehensive review of photophysical parameters (epsilon, Phi(f), tau(s)) of tetraphenylporphyrin (H2TPP) and zinc tetraphenylporphyrin (ZnTPP) - Critical benchmark molecules in photochemistry and photosynthesis AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. AU - Bocian, David F. AU - Holten, Dewey T2 - JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS AB - Tetraphenylporphyrin (H2TPP) and zinc tetraphenylporphyrin (ZnTPP) are widely used benchmark molecules in diverse photochemical studies given facile synthetic access, rich visible-region spectra, and broad structural analogy to chlorophylls. Yet the literature values for each key photophysical parameter – the molar absorption coefficient (ε), fluorescence quantum yield (Φf), and also singlet excited-state lifetime (τS) – vary over an astonishing range. Here, a comprehensive literature review (∼1940–September 2020) encompassing 871 publications is reported for these essential parameters. Each parameter is determined by measurement with distinct instrumentation and suffers idiosyncratic sources of error. The best values for H2TPP are ε = 460,000 cm−1·M−1, Φf = 0.090, and τS = 12.8 ns in Ar- purged toluene (Φf = 0.070, τS = 9.9 ns in toluene in air); the best values for ZnTPP are ε = 560,000 cm−1·M−1, Φf = 0.030, and τS = 2.1 ns in Ar-purged toluene (Φf = 0.029, τS = 2.0 ns in toluene in air). The choice of values for such parameters has far-reaching consequences in photochemistry ranging from fluorescence (or Förster) resonance energy transfer (FRET) processes to assessments of molecular brightness. DA - 2021/3// PY - 2021/3// DO - 10.1016/j.jphotochemrev.2020.100401 VL - 46 ER - TY - JOUR TI - SnRK1: a versatile plant protein kinase that limits geminivirus infection AU - Shen, Wei AU - Hanley-Bowdoin, Linda T2 - CURRENT OPINION IN VIROLOGY AB - Geminiviruses are a family of single-stranded DNA viruses that infect many plant species and cause serious diseases in important crops. The plant protein kinase, SnRK1, has been implicated in host defenses against geminiviruses. Overexpression of SnRK1 makes plants more resistant to geminivirus infection, and knock-down of SnRK1 increases susceptibility to geminivirus infection. GRIK, the SnRK1 activating kinase, is upregulated by geminivirus infection, while the viral C2 protein inhibits the SnRK1 activity. SnRK1 also directly phosphorylates geminivirus proteins to reduce infection. These data suggest that SnRK1 is involved in the co-evolution of plant hosts and geminiviruses. DA - 2021/4// PY - 2021/4// DO - 10.1016/j.coviro.2020.12.002 VL - 47 SP - 18-24 SN - 1879-6265 ER - TY - JOUR TI - Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2 AU - Jin, Xiaohe AU - Miller, Eric S. AU - Lindsey, Jonathan S. T2 - LIFE-BASEL AB - Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols. DA - 2021/4// PY - 2021/4// DO - 10.3390/life11040356 VL - 11 IS - 4 SP - SN - 2075-1729 KW - anatoxin-a KW - homoanatoxin-a KW - hapalosin KW - heterocyst glycolipids KW - natural products KW - secondary metabolites KW - shinorine KW - tolypodiols KW - tolyporphins ER - TY - JOUR TI - Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas) AU - Oloka, Bonny Michael AU - Pereira, Guilherme da Silva AU - Amankwaah, Victor A. AU - Mollinari, Marcelo AU - Pecota, Kenneth V AU - Yada, Benard AU - Olukolu, Bode A. AU - Zeng, Zhao-Bang AU - Yencho, G. Craig T2 - THEORETICAL AND APPLIED GENETICS AB - Utilizing a high-density integrated genetic linkage map of hexaploid sweetpotato, we discovered a major dominant QTL for root-knot nematode (RKN) resistance and modeled its effects. This discovery is useful for development of a modern sweetpotato breeding program that utilizes marker-assisted selection and genomic selection approaches for faster genetic gain of RKN resistance. The root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) causes significant storage root quality reduction and yields losses in cultivated sweetpotato [Ipomoea batatas (L.) Lam.]. In this study, resistance to RKN was examined in a mapping population consisting of 244 progenies derived from a cross (TB) between 'Tanzania,' a predominant African landrace cultivar with resistance to RKN, and 'Beauregard,' an RKN susceptible major cultivar in the USA. We performed quantitative trait loci (QTL) analysis using a random-effect QTL mapping model on the TB genetic map. An RKN bioassay incorporating potted cuttings of each genotype was conducted in the greenhouse and replicated five times over a period of 10 weeks. For each replication, each genotype was inoculated with ca. 20,000 RKN eggs, and root-knot galls were counted ~62 days after inoculation. Resistance to RKN in the progeny was highly skewed toward the resistant parent, exhibiting medium to high levels of resistance. We identified one major QTL on linkage group 7, dominant in nature, which explained 58.3% of the phenotypic variation in RKN counts. This work represents a significant step forward in our understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding in sweetpotato breeding programs. DA - 2021/7// PY - 2021/7// DO - 10.1007/s00122-021-03797-z VL - 134 IS - 7 SP - 1945-1955 SN - 1432-2242 ER - TY - JOUR TI - A deleterious mutation in the ALMS1 gene in a naturally occurring model of hypertrophic cardiomyopathy in the Sphynx cat AU - Meurs, Kathryn M. AU - Williams, Brian G. AU - DeProspero, Dylan AU - Friedenberg, Steven G. AU - Malarkey, David E. AU - Ezzell, J. Ashley AU - Keene, Bruce W. AU - Adin, Darcy B. AU - DeFrancesco, Teresa C. AU - Tou, Sandra T2 - ORPHANET JOURNAL OF RARE DISEASES AB - Familial hypertrophic cardiomyopathy is a common inherited cardiovascular disorder in people. Many causal mutations have been identified, but about 40% of cases do not have a known causative mutation. Mutations in the ALMS1 gene are associated with the development of Alstrom syndrome, a multisystem familial disease that can include cardiomyopathy (dilated, restrictive). Hypertrophic cardiomyopathy has not been described. The ALMS1 gene is a large gene that encodes for a ubiquitously expressed protein. The function of the protein is not well understood although it is believed to be associated with energy metabolism and homeostasis, cell differentiation and cell cycle control. The ALMS1 protein has also been shown to be involved in the regulation of cell cycle proliferation in perinatal cardiomyocytes. Although cardiomyocyte cell division and replication in mammals generally declines soon after birth, inhibition of ALMS1 expression in mice lead to increased cardiomyocyte proliferation, and deficiency of Alstrom protein has been suggested to impair post-natal cardiomyocyte cell cycle arrest. Here we describe the association of familial hypertrophic cardiomyopathy in Sphynx cats with a novel ALMS1 mutation.A G/C variant was identified in exon 12 (human exon 13) of the ALMS1 gene in affected cats and was positively associated with the presence of hypertrophic cardiomyopathy in the feline population (p < 0.0001). The variant was predicted to change a highly conserved nonpolar Glycine to a positively charged Arginine. This was predicted to be a deleterious change by three in silico programs. Protein prediction programs indicated that the variant changed the protein structure in this region from a coil to a helix. Light microscopy findings included myofiber disarray with interstitial fibrosis with significantly more nuclear proliferative activity in the affected cats than controls (p < 0.0001).This study demonstrates a novel form of cardiomyopathy associated with ALMS1 in the cat. Familial hypertrophic cardiomyopathy is a disease of genetic heterogeneity; many of the known causative genes encoding for sarcomeric proteins. Our findings suggest that variants in genes involved with cardiac development and cell regulation, like the ALMS1 gene, may deserve further consideration for association with familial hypertrophic cardiomyopathy. DA - 2021/2/27/ PY - 2021/2/27/ DO - 10.1186/s13023-021-01740-5 VL - 16 IS - 1 SP - SN - 1750-1172 KW - Hypertrophic cardiomyopathy KW - ALMS1 KW - Feline KW - Mitogenic KW - Sphynx ER - TY - JOUR TI - Autocrine and paracrine interferon signalling as 'ring vaccination' and 'contact tracing' strategies to suppress virus infection in a host AU - Lavigne, G. Michael AU - Russell, Hayley AU - Sherry, Barbara AU - Ke, Ruian T2 - PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES AB - The innate immune response, particularly the interferon response, represents a first line of defence against viral infections. The interferon molecules produced from infected cells act through autocrine and paracrine signalling to turn host cells into an antiviral state. Although the molecular mechanisms of IFN signalling have been well characterized, how the interferon response collectively contribute to the regulation of host cells to stop or suppress viral infection during early infection remain unclear. Here, we use mathematical models to delineate the roles of the autocrine and the paracrine signalling, and show that their impacts on viral spread are dependent on how infection proceeds. In particular, we found that when infection is well-mixed, the paracrine signalling is not as effective; by contrast, when infection spreads in a spatial manner, a likely scenario during initial infection in tissue, the paracrine signalling can impede the spread of infection by decreasing the number of susceptible cells close to the site of infection. Furthermore, we argue that the interferon response can be seen as a parallel to population-level epidemic prevention strategies such as ‘contact tracing’ or ‘ring vaccination’. Thus, our results here may have implications for the outbreak control at the population scale more broadly. DA - 2021/2/24/ PY - 2021/2/24/ DO - 10.1098/rspb.2020.3002 VL - 288 IS - 1945 SP - SN - 1471-2954 KW - interferon KW - innate immunity KW - ring vaccination KW - partial differential equations KW - cellular automata ER - TY - JOUR TI - Schizophrenia and Bartonella spp. Infection: A Pilot Case-Control Study AU - Lashnits, Erin AU - Maggi, Ricardo AU - Jarskog, Fredrik AU - Bradley, Julie AU - Breitschwerdt, Edward AU - Frohlich, Flavio T2 - VECTOR-BORNE AND ZOONOTIC DISEASES AB - Recently, infections with emerging zoonotic bacteria of the genus Bartonella have been reported in association with a range of central nervous system (CNS) symptoms. Currently, it remains unknown if Bartonella spp. infection is associated with symptoms of schizophrenia/schizoaffective disorder (SCZ/SAD). The objective of this study was to determine if there is an association between Bartonella species infection and SCZ/SAD. A secondary objective was to determine if SCZ/SAD symptoms were more severe among participants with documented Bartonella spp. infection. Using a case–control study design, 17 cases and 13 controls were evaluated with a series of clinical and cognitive assessments. Blood samples were collected and tested for Bartonella spp. infection using serological, microbiological, and molecular techniques. People with SCZ/SAD were more likely than healthy volunteers to have Bartonella spp. DNA in their bloodstream, with 11 of 17 cases (65%) positive by Bartonella spp. droplet digital PCR (ddPCR). In comparison, only one healthy volunteer was Bartonella spp. ddPCR positive (8%, p = 0.0024). Based on serology, Bartonella spp. exposure was common among people with SCZ/SAD (12 of 17) as well as among healthy volunteers (12 of 13), with no significant difference between the groups (p = 0.196). Within the case group of people with SCZ/SAD, there was no significant difference in SCZ/SAD severity scores between people with and without ddPCR evidence of Bartonella spp. infection. This pilot study provides preliminary evidence in support of future investigations that should examine a potential contribution of Bartonella spp. infection to SCZ/SAD. DA - 2021/6/1/ PY - 2021/6/1/ DO - 10.1089/vbz.2020.2729 VL - 21 IS - 6 SP - 413-421 SN - 1557-7759 KW - vector-borne disease KW - infectious disease KW - cat KW - epidemiology KW - ddPCR KW - cat scratch disease ER - TY - JOUR TI - The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F-1 population AU - Pereira, Guilherme da Silva AU - Mollinari, Marcelo AU - Schumann, Mitchell J. AU - Clough, Mark E. AU - Zeng, Zhao-Bang AU - Yencho, G. Craig T2 - HEREDITY AB - There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2n = 4x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population (n = 156) derived from a cross involving 'Atlantic', a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species. DA - 2021/5// PY - 2021/5// DO - 10.1038/s41437-021-00416-x VL - 126 IS - 5 SP - 817-830 SN - 1365-2540 ER - TY - JOUR TI - Provenance and Family Variation in Biomass Potential of Loblolly Pine in the Piedmont of North Carolina AU - Maynor, Jessica A. AU - Isik, Fikret AU - Walker, Trevor D. AU - Whetten, Ross W. AU - Heine, Austin J. AU - Payn, Kitt G. AU - McKeand, Steven E. T2 - FOREST SCIENCE AB - Abstract Considerable genetic differences in loblolly pine (Pinus taeda L.) exist for growth, stem form, and wood quality traits that influence biomass/biofuel production. By planting genetically superior trees with desirable biomass/biofuel traits, it is possible to substantially increase the amount of biomass and potential sawtimber trees produced from plantations. Ten of the fastest growing loblolly pine families from two provenances, Atlantic Coastal Plain and Piedmont, were tested for their biomass potential in North Carolina on a Piedmont site. At this northern Piedmont site at age six years, there were no provenance differences for biomass production or for trees with sawtimber potential. Variation in volume and sawtimber potential was significant at the family level. For biomass plantations, risks can be mitigated because of shorter rotation length, allowing for a higher-risk seed lot to capture greater gains in terms of volume. For a longer-rotation sawtimber stand, a more conservative family deployment strategy should be considered to maintain stem quality at the end of the rotation. Understanding the different seed source families and harvest regimes is essential to ensure profitable returns from pine plantations. DA - 2021/6// PY - 2021/6// DO - 10.1093/forsci/fxaa056 VL - 67 IS - 3 SP - 312-320 SN - 1938-3738 UR - https://doi.org/10.1093/forsci/fxaa056 KW - bioenergy KW - genetics KW - Pinus taeda KW - wood quality ER - TY - JOUR TI - Constitutive activation of nitrate reductase in tobacco alters flowering time and plant biomass AU - Lu, Jianli AU - Chandrakanth, Niharika N. AU - Lewis, Ramsey S. AU - Andres, Karen AU - Bovet, Lucien AU - Goepfert, Simon AU - Dewey, Ralph E. T2 - SCIENTIFIC REPORTS AB - Pyridine alkaloids produced in tobacco can react with nitrosating agents such as nitrite to form tobacco-specific nitrosamines (TSNA), which are among the most notable toxicants present in tobacco smoke. The market type known as burley tobacco is particularly susceptible to TSNA formation because its corresponding cultivars exhibit a nitrogen-use-deficiency phenotype which results in high accumulation of nitrate, which, in turn, is converted to nitrite by leaf surface microbes. We have previously shown that expression of a constitutively activated nitrate reductase (NR) enzyme dramatically decreases leaf nitrate levels in burley tobacco, resulting in substantial TSNA reductions without altering the alkaloid profile. Here, we show that plants expressing a constitutively active NR construct, designated 35S:S523D-NR, display an early-flowering phenotype that is also associated with a substantial reduction in plant biomass. We hypothesized that crossing 35S:S523D-NR tobaccos with burley cultivars that flower later than normal would help mitigate the undesirable early-flowering/reduced-biomass traits while maintaining the desirable low-nitrate/TSNA phenotype. To test this, 35S:S523D-NR plants were crossed with two late-flowering cultivars, NC 775 and NC 645WZ. In both cases, the plant biomass at harvest was restored to levels similar to those in the original cultivar used for transformation while the low-nitrate/TSNA trait was maintained. Interestingly, the mechanism by which yield was restored differed markedly between the two crosses. Biomass restoration in F1 hybrids using NC 645WZ as a parent was associated with delayed flowering, as originally hypothesized. Unexpectedly, however, crosses with NC 775 displayed enhanced biomass despite maintaining the early-flowering trait of the 35S:S523D-NR parent. DA - 2021/2/19/ PY - 2021/2/19/ DO - 10.1038/s41598-021-83797-7 VL - 11 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Exposure of Domestic Cats to Three Zoonotic Bartonella Species in the United States AU - Osikowicz, Lynn M. AU - Horiuchi, Kalanthe AU - Goodrich, Irina AU - Breitschwerdt, Edward B. AU - Chomel, Bruno AU - Biggerstaff, Brad J. AU - Kosoy, Michael T2 - PATHOGENS AB - Cat-associated Bartonella species, which include B. henselae, B. koehlerae, and B. clarridgeiae, can cause mild to severe illness in humans. In the present study, we evaluated 1362 serum samples obtained from domestic cats across the U.S. for seroreactivity against three species and two strain types of Bartonella associated with cats (B. henselae type 1, B. henselae type 2, B. koehlerae, and B. clarridgeiae) using an indirect immunofluorescent assay (IFA). Overall, the seroprevalence at the cutoff titer level of ≥1:64 was 23.1%. Seroreactivity was 11.1% and 3.7% at the titer level cutoff of ≥1:128 and at the cutoff of ≥1:256, respectively. The highest observation of seroreactivity occurred in the East South-Central, South Atlantic, West North-Central, and West South-Central regions. The lowest seroreactivity was detected in the East North-Central, Middle Atlantic, Mountain, New England, and Pacific regions. We observed reactivity against all four Bartonella spp. antigens in samples from eight out of the nine U.S. geographic regions. DA - 2021/3// PY - 2021/3// DO - 10.3390/pathogens10030354 VL - 10 IS - 3 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10030354 KW - domestic cats KW - cat scratch disease KW - Bartonella henselae KW - Bartonella clarridgeiae KW - Bartonella koehlerae KW - serosurvey KW - IFA KW - vector-borne pathogens ER - TY - JOUR TI - Bartonella henselae Antibodies in Serum and Oral Fluid Specimens from Cats AU - Alvarez-Fernandez, Alejandra AU - Baxarias, Marta AU - Prandi, David AU - Breitschwerdt, Edward B. AU - Solano-Gallego, Laia T2 - PATHOGENS AB - Cats are the primary reservoir host for Bartonella henselae(B. henselae), an etiological agent of human bartonellosis, including cat scratch disease. Although Bartonella DNA has been amplified from salivary swabs from cats, dogs and humans, we are not aware of studies investigating Bartonella antibodies in oral fluid (OF). Using inhouse and commercial immunofluorescence antibody assays (IFA), the objective of this study was to detect and compare antibodies against B. henselae in paired OF and serum specimens from cats. Specimens were collected from shelter and client-owned cats. For serum specimens, B. henselae seroreactivity was 78% for both the inhouse and commercial IFA assays and 56.8% for OF specimens. Comparing serum and OF specimens, there was moderate Kappa agreement (Cohen’s k = 0.434) for detection of B. henselae antibodies. Oral fluid antibodies were more likely measurable in cats with high B. henselae serum antibody titers when compared with low antibody titers. In conclusion, B. henselae OF IFA antibody measurements were less sensitive compared to serum IFA measurements of ≥1:64. Oral fluid antibodies were detected more often in cats with high B. henselae serum antibody titers. Therefore, OF antibodies, detectable by IFA, is of limited utility for epidemiological or diagnostic testing in cats. DA - 2021/3// PY - 2021/3// DO - 10.3390/pathogens10030329 VL - 10 IS - 3 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10030329 KW - bartonellosis KW - feline KW - serology KW - immunofluorescence antibody assay KW - oral fluid ER - TY - JOUR TI - Bartonella henselae Detected in Malignant Melanoma, a Preliminary Study AU - Ericson, Marna E. AU - Breitschwerdt, Edward B. AU - Reicherter, Paul AU - Maxwell, Cole AU - Maggi, Ricardo G. AU - Melvin, Richard G. AU - Maluki, Azar H. AU - Bradley, Julie M. AU - Miller, Jennifer C. AU - Simmons, Glenn E., Jr. AU - Dencklau, Jamie AU - Joppru, Keaton AU - Peterson, Jack AU - Bae, Will AU - Scanlon, Janet AU - Bemis, Lynne T. T2 - PATHOGENS AB - Bartonella bacilliformis (B. bacilliformis), Bartonella henselae (B. henselae), and Bartonella quintana (B. quintana) are bacteria known to cause verruga peruana or bacillary angiomatosis, vascular endothelial growth factor (VEGF)-dependent cutaneous lesions in humans. Given the bacteria’s association with the dermal niche and clinical suspicion of occult infection by a dermatologist, we determined if patients with melanoma had evidence of Bartonella spp. infection. Within a one-month period, eight patients previously diagnosed with melanoma volunteered to be tested for evidence of Bartonella spp. exposure/infection. Subsequently, confocal immunohistochemistry and PCR for Bartonella spp. were used to study melanoma tissues from two patients. Blood from seven of the eight patients was either seroreactive, PCR positive, or positive by both modalities for Bartonella spp. exposure. Subsequently, Bartonella organisms that co-localized with VEGFC immunoreactivity were visualized using multi-immunostaining confocal microscopy of thick skin sections from two patients. Using a co-culture model, B. henselae was observed to enter melanoma cell cytoplasm and resulted in increased vascular endothelial growth factor C (VEGFC) and interleukin 8 (IL-8) production. Findings from this small number of patients support the need for future investigations to determine the extent to which Bartonella spp. are a component of the melanoma pathobiome. DA - 2021/3// PY - 2021/3// DO - 10.3390/pathogens10030326 VL - 10 IS - 3 SP - SN - 2076-0817 UR - https://doi.org/10.3390/pathogens10030326 KW - melanoma KW - A375 cells KW - Bartonella spp KW - Bartonella henselae KW - vector-borne pathogens KW - multi-immunostaining methods KW - confocal microscopy of thick sections KW - cancer microbiome KW - melanoma pathobiome ER - TY - JOUR TI - Demographics and travel history of imported and autochthonous cases of leishmaniosis in dogs in the United States and Canada, 2006 to 2019 AU - Gin, Taylor Estes AU - Lashnits, Erin AU - Wilson, James M. AU - Breitschwerdt, Edward B. AU - Qurollo, Barbara T2 - JOURNAL OF VETERINARY INTERNAL MEDICINE AB - Abstract Background Leishmania infantum infections are reported in foxhounds throughout the United States (US) and Canada, but only rarely in other dog breeds. A seroprevalence report from 2006 documented leishmaniosis in foxhounds (8.9%) tested in the US between 2000 and 2003. All other breeds were seronegative. Objective To reexamine demographics and travel history of L. infantum ‐infected dogs in the US and Canada, we hypothesize detection of L. infantum in more foxhounds than nonfoxhounds and that infected nonfoxhounds will have traveled to endemic regions. Animals A total of 125 dogs positive for L. infantum by immunofluorescent antibody, PCR, or both. Methods Retrospective, descriptive study of L. infantum ‐infected dogs between 4 January 2006 and 22 May 2019. Travel history and known lineage to foxhounds was collected from questionnaires. Results Leishmania infantum was detected in 125 (6.4%) of 1961 dogs tested between 4 January 2006 and 22 May 2019, of which 10 (8%) were foxhounds and 115 (92%) were nonfoxhound breeds. Travel history available for 69 (55%) dogs showed 60 (86.9%) dogs had traveled outside of the US or Canada. Nine (13%) dogs had not traveled outside of the US or Canada, 5 of which were nonfoxhounds. Conclusions and Clinical Importance The majority of L. infantum cases were detected in nonfoxhounds, many of which had traveled to L. infantum ‐endemic countries, and several nonfoxhound breeds had no travel history. Leishmania surveillance should be considered for dogs that return from L. infantum ‐endemic regions to monitor emergence of this zoonotic disease in the US and Canada. DA - 2021/3// PY - 2021/3// DO - 10.1111/jvim.16071 VL - 35 IS - 2 SP - 954-964 SN - 1939-1676 UR - https://doi.org/10.1111/jvim.16071 KW - dog KW - leishmania KW - lutzomyia ER - TY - JOUR TI - Protective plant immune responses are elicited by bacterial outer membrane vesicles AU - McMillan, Hannah M. AU - Zebell, Sophia G. AU - Ristaino, Jean B. AU - Dong, Xinnian AU - Kuehn, Meta J. T2 - CELL REPORTS AB - Bacterial outer membrane vesicles (OMVs) perform a variety of functions in bacterial survival and virulence. In mammalian systems, OMVs activate immune responses and are exploited as vaccines. However, little work has focused on the interactions of OMVs with plant hosts. Here, we report that OMVs from Pseudomonas syringae and P. fluorescens activate plant immune responses that protect against bacterial and oomycete pathogens. OMV-mediated immunomodulatory activity from these species displayed different sensitivity to biochemical stressors, reflecting differences in OMV content. Importantly, OMV-mediated plant responses are distinct from those triggered by conserved bacterial epitopes or effector molecules alone. Our study shows that OMV-induced protective immune responses are independent of the T3SS and protein, but that OMV-mediated seedling growth inhibition largely depends on proteinaceous components. OMVs provide a unique opportunity to understand the interplay between virulence and host response strategies and add a new dimension to consider in host-microbe interactions. DA - 2021/1/19/ PY - 2021/1/19/ DO - 10.1016/j.celrep.2020.108645 VL - 34 IS - 3 SP - SN - 2211-1247 ER - TY - JOUR TI - Foreword AU - Kaltofen, Erich L. T2 - JOURNAL OF SYMBOLIC COMPUTATION AB - We consider the problem of computing the nearest matrix polynomial with a non-trivial Smith Normal Form. We show that computing the Smith form of a matrix polynomial is amenable to numeric computation as an optimization problem. Furthermore, we describe an effective optimization technique to find a nearby matrix polynomial with a non-trivial Smith form. The results are then generalized to include the computation of a matrix polynomial having a maximum specified number of ones in the Smith Form (i.e., with a maximum specified McCoy rank).We discuss the geometry and existence of solutions and how our results can be used for an error analysis. We develop an optimization-based approach and demonstrate an iterative numerical method for computing a nearby matrix polynomial with the desired spectral properties. We also describe an implementation of our algorithms and demonstrate the robustness with examples in Maple. DA - 2021/// PY - 2021/// DO - 10.1016/j.jsc.2020.04.006 VL - 105 SP - 1-3 SN - 1095-855X ER - TY - JOUR TI - Study of conditions for streamlined assembly of a model bacteriochlorophyll from two dihydrodipyrrin halves AU - Nguyen, Khiem Chau AU - Wang, Pengzhi AU - Lindsey, Jonathan S. T2 - NEW JOURNAL OF CHEMISTRY AB - Knoevenagel condensation followed by double-ring closure (Nazarov cyclization, electrophilic aromatic substitution, elimination of methanol) and optional zinc insertion smoothly afford models of the native bacteriochlorophylls. DA - 2021/1/14/ PY - 2021/1/14/ DO - 10.1039/d0nj04855k VL - 45 IS - 2 SP - 569-581 SN - 1369-9261 UR - http://dx.doi.org/10.1039/d0nj04855k ER - TY - JOUR TI - On computing the degree of a Chebyshev Polynomial from its value AU - Imamoglu, Erdal AU - Kaltofen, Erich L. T2 - JOURNAL OF SYMBOLIC COMPUTATION AB - Algorithms for interpolating a polynomial f from its evaluation points whose running time depends on the sparsity t of the polynomial when it is represented as a linear combination of t Chebyshev Polynomials of the First Kind with non-zero scalar coefficients are given by Lakshman and Saunders (1995), Kaltofen and Lee (2003) and Arnold and Kaltofen (2015). The term degrees are computed from values of Chebyshev Polynomials of those degrees. We give an algorithm that computes those degrees in the manner of the Pohlig and Hellman algorithm (1978) for computing discrete logarithms modulo a prime number p when the factorization of p−1 (or p+1) has small prime factors, that is, when p−1 (or p+1) is smooth. Our algorithm can determine the Chebyshev degrees modulo such primes in bit complexity log⁡(p)O(1) times the squareroot of the largest prime factor of p−1 (or p+1). DA - 2021/// PY - 2021/// DO - 10.1016/j.jsc.2020.04.011 VL - 104 SP - 159-167 SN - 1095-855X KW - Algorithms KW - Discrete logarithms KW - Chebyshev Polynomials KW - Interpolation in terms of the Chebyshev KW - Polynomials of the First Kind ER - TY - JOUR TI - Sparse Interpolation With Errors in Chebyshev Basis Beyond Redundant-Block Decoding AU - Kaltofen, Erich L. AU - Yang, Zhi-Hong T2 - IEEE TRANSACTIONS ON INFORMATION THEORY AB - We present sparse interpolation algorithms for recovering a polynomial with ≤ B terms from N evaluations at distinct values for the variable when ≤ E of the evaluations can be erroneous. Our algorithms perform exact arithmetic in the field of scalars K and the terms can be standard powers of the variable or Chebyshev polynomials, in which case the characteristic of K is ≠ 2. Our algorithms return a list of valid sparse interpolants for the N support points and run in polynomial-time. For standard power basis our algorithms sample at N = ⌊4/3 E + 2⌋B points, which are fewer points than N = 2(E + 1)B - 1 given by Kaltofen and Pernet in 2014. For Chebyshev basis our algorithms sample at N = ⌊3/2E + 2⌋B points, which are also fewer than the number of points required by the algorithm given by Arnold and Kaltofen in 2015, which has N = 74⌊E/13 +1⌋ for B = 3 and E ≥ 222. Our method shows how to correct 2 errors in a block of 4B points for standard basis and how to correct 1 error in a block of 3B points for Chebyshev Basis. DA - 2021/1// PY - 2021/1// DO - 10.1109/TIT.2020.3027036 VL - 67 IS - 1 SP - 232-243 SN - 1557-9654 KW - Sparse polynomial interpolation KW - error correction KW - black box polynomial KW - list-decoding ER - TY - JOUR TI - Qu-2, a robust poplar suspension cell line for molecular biology AU - Liu, Caixia AU - Li, Kailong AU - Wang, Meng AU - Fan, Erqin AU - Yang, Chuanping AU - Wang, Junhui AU - Fu, Pengyue AU - Ge, Xiaolan AU - Sederoff, Heike W. AU - Sederoff, Ronald R. AU - Chiang, Vincent L. AU - Wang, Sui AU - Qu, Guanzheng T2 - JOURNAL OF FORESTRY RESEARCH AB - Abstract Populus spp. have long been used as model woody plant species for molecular biology research. However, tissues of poplar are often recalcitrant to experimental procedures for molecular studies. We generated a hormone autotrophic poplar suspension cell line from a hybrid of Populus alba × P. berolinensis ‘Yinzhong’, named Qu-2. Qu-2 cells are suitable as a model biological system for studying woody plants. Qu-2 cells have many advantages over suspension cell lines derived so far from any other woody plants. Qu-2 cells are very easy to cultivate and can grow on several common plant culture media without the addition of any plant hormone. They show exceptionally high growth rates, reaching an approximately 150-fold increase in biomass after one week of culturing. Another important unique characteristic of Qu-2 cells is that they can be cryopreserved and readily reactivated. Qu-2 cells are suitable for molecular manipulations such as protoplast production, transient transformation, and RNA-seq analysis. Therefore, Qu-2 cells have the great potential to be an excellent model cell line in tree molecular biological research, ranging from physiology to gene function. The Qu-2 cells will be made available to the plant community for research. DA - 2021/4// PY - 2021/4// DO - 10.1007/s11676-020-01266-9 VL - 32 IS - 2 SP - 733-740 SN - 1993-0607 KW - Qu-2 cell line KW - Suspension cell KW - Poplar KW - Protoplast isolation KW - Transient transformation ER - TY - JOUR TI - A protocol for genome-wide analysis of DNA replication timing in intact root tips AU - Mickelson-Young, Leigh AU - Wear, Emily E. AU - Song, Jawon AU - Zynda, Gregory J. AU - Hanley-Bowdoin, Linda AU - Thompson, William F. T2 - Methods in Molecular Biology series DA - 2021/// PY - 2021/// ER - TY - JOUR TI - Economic Significance of Continued Improvement of Loblolly Pine Genetics and Its Efficient Deployment to Landowners in the Southern United States AU - McKeand, Steven E. AU - Payn, Kitt G. AU - Heine, Austin J. AU - Abt, Robert C. T2 - JOURNAL OF FORESTRY AB - Abstract The economic consequence of continuing or increasing the tree improvement efforts for loblolly pine (Pinus taeda L.) in the southern United States is immense. For the more than one million acres planted each year with germplasm from the North Carolina State University Cooperative Tree Improvement Program, the present value of continuing current tree breeding efforts and deploying the genetic gains to landowners is estimated to be more than $1.7 billion at current prices. The present value of increasing the rate of genetic gain from 1% per year to 1.1% per year is $211 million. These analyses can be used to justify maintaining and even increasing efforts in tree improvement. With the aggressive fourth-cycle breeding program underway and plans for fifth-cycle breeding and deployment strategies being developed, we have every reason to believe that this trend for at least 1% gain per year will continue for decades, provided the resources to continue tree improvement efforts remain available. Even a modest increase in genetic gain per year would be justification for stakeholders to invest more than $12 million per year to realize this gain. DA - 2021/1// PY - 2021/1// DO - 10.1093/jofore/fvaa044 VL - 119 IS - 1 SP - 62-72 SN - 1938-3746 UR - https://doi.org/10.1093/jofore/fvaa044 KW - genetic gain KW - Pinus taeda KW - plantations KW - tree breeding ER - TY - JOUR TI - Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation AU - Borges, Filipe AU - Donoghue, Mark T. A. AU - LeBlanc, Chantal AU - Wear, Emily E. AU - Tanurdzic, Milos AU - Berube, Benjamin AU - Brooks, Ashley AU - Thompson, William F. AU - Hanley-Bowdoin, Linda AU - Martienssen, Robert A. T2 - CURRENT BIOLOGY AB - 5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones. DA - 2021/// PY - 2021/// DO - 10.1016/j.cub.2020.10.098 VL - 31 IS - 3 SP - 591-+ UR - https://doi.org/10.1016/j.cub.2020.10.098 ER - TY - JOUR TI - Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues AU - Taniguchi, Masahiko AU - Lindsey, Jonathan S. T2 - PHOTOCHEMISTRY AND PHOTOBIOLOGY AB - Abstract Absorption spectra and fluorescence spectra are essential for use across the photosciences, yet such spectra along with the all‐important values for molar absorption coefficient (ε) and fluorescence quantum yield (Φ f ) often are found with great difficulty. Here, a literature survey concerning the vital class of chlorophyll compounds has led to identification of spectra for 150 members. Spectra in print form have been digitized (with baseline corrections) and assembled into a database along with literature references, solvent identity and values for ε and Φ f (where available). The database encompasses photosynthetic tetrapyrroles wherein the chromophore is a porphyrin (e.g. chlorophyll c 1 , protochlorophyll a ), chlorin (e.g. chlorophyll a , bacteriochlorophyll c ) or bacteriochlorin (e.g. bacteriochlorophyll a ). Altogether, the database contains 305 absorption spectra (from 19 porphyrins, 109 chlorins and 22 bacteriochlorins) and 72 fluorescence spectra (from 10 porphyrins, 30 chlorins and 4 bacteriochlorins). The spectral database should facilitate comparisons and quantitative calculations. All spectra are available in print form in the Supporting Information. The entire database in digital form is available with the PhotochemCAD program for free downloading and further use at http://www.photochemcad.com . DA - 2021/1// PY - 2021/1// DO - 10.1111/php.13319 VL - 97 IS - 1 SP - 136-165 SN - 1751-1097 ER -