TY - JOUR TI - Functional annotation of proteins for signaling network inference in non-model species AU - Broeck, Lisa Van AU - Bhosale, Dinesh AU - Song, Kuncheng AU - Lima, Cássio Fonseca AU - Ashley, Michael AU - Zhu, Tingting AU - Zhu, Shanshuo AU - Cotte, Brigitte Van De AU - Neyt, Pia AU - Ortiz, Anna AU - Sikes, Tiffany AU - Aper, Jonas AU - Lootens, Peter AU - Locke, Anna AU - Smet, Ive De AU - Sozzani, Rosangela AB - Abstract Molecular biology aims to understand the molecular basis of cellular responses, unravel dynamic regulatory networks, and model complex biological systems. However, these studies remain challenging in non-model species as a result of poor functional annotation of regulatory proteins, like kinases or phosphatases. To overcome this limitation, we developed a multi-layer neural network that annotates proteins by determining functionality directly from the protein sequence. We annotated the kinases and phosphatases in the non-model species, Glycine max (soybean), achieving a prediction sensitivity of up to 97%. To demonstrate the applicability, we used our functional annotations in combination with Bayesian network principles to predict signaling cascades using time series phosphoproteomics. We shed light on phosphorylation cascades in soybean seedlings upon cold treatment and identified Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as predicted key temperature response regulators in soybean. Importantly, the network inference does not rely upon known upstream kinases, kinase motifs, or protein interaction data, enabling de novo identification of kinase-substrate interactions. In addition to high accuracy and strong generalization, we showed that our functional prediction neural network is scalable to other model and non-model species, including Oryza sativa (rice), Zea mays (maize), Sorghum bicolor (sorghum), and Triticum aestivum (wheat). Taking together, we demonstrated a data-driven systems biology approach for non-model species leveraging our predicted upstream kinases and phosphatases. DA - 2022/11/11/ PY - 2022/11/11/ DO - 10.21203/rs.3.rs-2201240/v1 UR - https://doi.org/10.21203/rs.3.rs-2201240/v1 ER - TY - JOUR TI - Polyethersulfone (PES) Membrane on Agar Plates as a Plant Growth Platform for Spaceflight AU - Meyers, Alexander AU - Land, Eric AU - Perera, Imara AU - Canaday, Emma AU - Wyatt, Sarah E. T2 - Gravitational and Space Research AB - Abstract Plant biology experiments in microgravity face many challenges, among which are the constraints of the growth platforms available on the International Space Station (ISS). Protocols for preservation and sample return to Earth often limit efficient dissection of seedlings for downstream tissue-specific analysis. The Advanced Plant Experiment (APEx)-07 spaceflight experiment required a large quantity of dissectible, well-preserved seedlings suitable for omics analysis. During preflight tests, protocols were developed for using an agar-polyethersulfone (PES) membrane platform for seedling growth that allowed for seedling germination and growth aboard the ISS and rapid freezing to provide intact seedlings for dissection and extraction of high-quality DNA, RNA, and protein. Each component of the growth setup was carefully examined: membrane color, hydration and growth substrate, capacity for delayed germination, growth duration, harvest approach, and preservation pipelines were all individually optimized. Sterilized Arabidopsis seeds were adhered to PES membrane with guar gum. Membranes were laid onto 0.8% agar containing 0.5x Murashige and Skoog (MS) in 10 cm square Petri dishes and held at 4 °C until the experiment was actuated by placing the Petri dishes at room temperature. Seedlings were grown vertically for 12 days. PES membranes were removed from the agar, placed in the Petri dish lid, wrapped in foil, and frozen at −80 °C. Seedlings were dissected into roots and shoots and provided high-quality DNA, RNA, and protein. The system is simple, potentially adaptable for seedlings of multiple species, scalable and cost effective, and offers added versatility to existing ISS plant growth capabilities. DA - 2022/1/1/ PY - 2022/1/1/ DO - 10.2478/gsr-2022-0004 UR - http://dx.doi.org/10.2478/gsr-2022-0004 ER - TY - JOUR TI - Editorial: The methane moment - Cross-boundary significance of methanogens: Preface AU - Lyu, Zhe AU - Rotaru, Amelia-Elena AU - Pimentel, Mark AU - Zhang, Cui-Jing AU - Rittmann, Simon K.-M. R. T2 - Frontiers in Microbiology AB - EDITORIAL article Front. Microbiol., 14 November 2022Sec. Biology of Archaea Volume 13 - 2022 | https://doi.org/10.3389/fmicb.2022.1055494 DA - 2022/11/14/ PY - 2022/11/14/ DO - 10.3389/fmicb.2022.1055494 VL - 13 UR - http://dx.doi.org/10.3389/fmicb.2022.1055494 ER - TY - JOUR TI - Rapid Multilocus Adaptation of Clonal Cabbage Leaf Curl Virus Populations to Arabidopsis thaliana AU - Hoyer, J. Steen AU - Wilkins, Olivia W. AU - Munshi, Aanandi AU - Wiese, Emma AU - Dubey, Divya AU - Renard, Savannah AU - Mortensen, Karoline Rosendal Harto AU - Dye, Anna E. AU - Carbone, Ignazio AU - Duffy, Siobain AU - Ascencio-Ibanez, Jose Trinidad T2 - PHYTOBIOMES JOURNAL AB - Cabbage leaf curl virus (CabLCV) has a bipartite single-stranded DNA genome and infects the model plant Arabidopsis thaliana. CabLCV serves as a model for the genus Begomovirus, members of which cause tremendous crop losses worldwide. We have used CabLCV as a model for within-plant virus evolution by inoculating individual plants with infectious clones of either a wild-type or mutagenized version of the CabLCV genome. Consistent with previous reports, detrimental substitutions in the replication-associated ( Rep) gene were readily compensated for by direct reversion or alternative mutations. A surprising number of common mutations were detected elsewhere in both viral segments (DNA-A and DNA-B), indicating convergent evolution and suggesting that CabLCV may not be as well adapted to A. thaliana as commonly presumed. Consistent with this idea, a spontaneous coat protein variant consistently rose to high allele frequency in susceptible accession Columbia-0, at a higher rate than in hypersusceptible accession Sei-0. Numerous high-frequency mutations were also detected in a candidate Rep binding site in DNA-B. Our results reinforce the fact that spontaneous mutation of this type of virus occurs rapidly and can change the majority consensus sequence of a within-plant virus population in weeks. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . DA - 2022/// PY - 2022/// DO - 10.1094/PBIOMES-12-21-0077-R VL - 6 IS - 3 SP - 227-235 SN - 2471-2906 KW - begomovirus mutation KW - genomics KW - molecular biology KW - plant pathology KW - rapid adaptation KW - virology KW - within-host population variability ER - TY - JOUR TI - Remnants of the "Grande Savane?" Insights from Soil Organic Matter at Two Sites in the Deep River Triassic Basin of North Carolina AU - Krings, Alexander AU - Szakacs, Alexandria D. AU - Hyland, Ethan G. T2 - CASTANEA AB - Narrative accounts and floristics suggest a broader historical distribution of Piedmont upland savannas and woodlands with a prairie-affinity flora than today, although dates of emergence, spatiotemporal extent, and historical dynamics remain unclear. To help address the question whether remnant prairie-affinity patches in the state represent at least historical, if not ancient, grasslands, we analyzed stable carbon isotopes from soil organic matter from two well-known localities hosting prairie-affinity heliophytes, both within the boundaries of historically mapped “Grande Savane”. Soil cores for δ13Corg analysis and radiocarbon dating were collected from five sites, hosting different present-day plant communities and spanning three soil orders. Recovered δ13Corg values suggest historical grasslands, likely savanna-type with some fluctuations in cover, were present at both localities essentially continuously over the past 2000 years until the more recent canopy closure over the past century. These findings are consistent with historical narrative accounts, although significant additional sampling is needed to determine its spatiotemporal extent. While the general trend at our localities transitions from open to closed systems, pronounced fluctuations are apparent in all profiles, particularly between 1254–1468 CE. Precipitation does not appear predominantly responsible, but available climatic reconstructions are from an adjacent basin. The timing of the pronounced vegetation class fluctuations is intriguingly coincidental to the timing of Siouan occupancy and intertribal movements, suggesting a need for more vigorous interdisciplinary investigations. DA - 2022/12// PY - 2022/12// DO - 10.2179/0008-7475.87.2.244 VL - 87 IS - 2 SP - 244-267 SN - 1938-4386 KW - C-3/C-4 KW - grasslands KW - heliophytes KW - "Piedmont prairie," soil organic matter (SOM) ER - TY - JOUR TI - Distinguishing Saplings of Pines of Piedmont Upland Grassland Systems AU - Krings, Alexander AU - Cabell, Hannah T2 - CASTANEA AB - The development and assessment of Piedmont upland grassland restoration efforts is hampered in part by continued challenges in identifying immature individuals of three associated pines, Pinus echinata, P. taeda, and P. virginiana, the penultimate of which is thought alien to the system. To help fill this gap, we studied three quantitative and 25 qualitative characters in 174, 2- to 5-year-old saplings in managed stands in Durham County (North Carolina) and 169 herbarium specimens of mature individuals from 94 Piedmont counties from Georgia to Virginia. Although mean short-shoot needle and fascicle sheath lengths differed significantly between lifestage classes of the three species (F8,335=185, p<0.0001 and F8,335=173.5, p<0.0001, respectively), there was substantial range overlap, likely contributing to diagnostic confusion in the field when existing keys are applied. For example, needle length ranges of all lifestage classes of all species overlapped with those of mature P. echinata and 2-year-old P. virginiana. In addition, at the apex of the previous season's growth, 2-year-old saplings of P. echinata and P. virginiana exhibited needles either predominantly or in higher percentages of threes, than the contrasting described preponderance of pairs for mature individuals. Of the 25 qualitative characters evaluated, we found (1) absence of decurrency glaucescence distinguishes 2- to 5-year-old saplings of P. taeda from P. echinata and P. virginiana, and (2) absence of stomatal plugs distinguishes P. virginiana from the others. A diagnostic key to saplings is provided. DA - 2022/12// PY - 2022/12// DO - 10.2179/0008-7475.87.2.211 VL - 87 IS - 2 SP - 211-223 SN - 1938-4386 KW - Dwarf shoot KW - juvenile trees KW - Pinaceae KW - prairie KW - savanna ER - TY - JOUR TI - Asymmetrical lineage introgression and recombination in populations of Aspergillus flavus: Implications for biological control AU - Molo, Megan S. AU - White, James B. AU - Cornish, Vicki AU - Gell, Richard M. AU - Baars, Oliver AU - Singh, Rakhi AU - Carbone, Mary Anna AU - Isakeit, Thomas AU - Wise, Kiersten A. AU - Woloshuk, Charles P. AU - Bluhm, Burton H. AU - Horn, Bruce W. AU - Heiniger, Ron W. AU - Carbone, Ignazio T2 - PLOS ONE AB - Aspergillus flavus is an agriculturally important fungus that causes ear rot of maize and produces aflatoxins, of which B 1 is the most carcinogenic naturally-produced compound. In the US, the management of aflatoxins includes the deployment of biological control agents that comprise two nonaflatoxigenic A . flavus strains, either Afla-Guard (member of lineage IB) or AF36 (lineage IC). We used genotyping-by-sequencing to examine the influence of both biocontrol agents on native populations of A . flavus in cornfields in Texas, North Carolina, Arkansas, and Indiana. This study examined up to 27,529 single-nucleotide polymorphisms (SNPs) in a total of 815 A . flavus isolates, and 353 genome-wide haplotypes sampled before biocontrol application, three months after biocontrol application, and up to three years after initial application. Here, we report that the two distinct A . flavus evolutionary lineages IB and IC differ significantly in their frequency distributions across states. We provide evidence of increased unidirectional gene flow from lineage IB into IC, inferred to be due to the applied Afla-Guard biocontrol strain. Genetic exchange and recombination of biocontrol strains with native strains was detected in as little as three months after biocontrol application and up to one and three years later. There was limited inter-lineage migration in the untreated fields. These findings suggest that biocontrol products that include strains from lineage IB offer the greatest potential for sustained reductions in aflatoxin levels over several years. This knowledge has important implications for developing new biocontrol strategies. DA - 2022/10/27/ PY - 2022/10/27/ DO - 10.1371/journal.pone.0276556 VL - 17 IS - 10 SP - SN - 1932-6203 ER - TY - JOUR TI - The double flower variant of yellowhorn is due to a LINE1 transposon-mediated insertion AU - Wang, Hanhui AU - Lu, Yanan AU - Zhang, Tianxu AU - Liu, Zhi AU - Cao, Li AU - Chang, Qiaoying AU - Liu, Yueying AU - Lu, Xin AU - Yu, Song AU - Li, Huiyu AU - Jiang, Jing AU - Liu, Guifeng AU - Sederoff, Heike W. AU - Sederoff, Ronald R. AU - Zhang, Qingzhu AU - Zheng, Zhimin T2 - PLANT PHYSIOLOGY AB - As essential organs of reproduction in angiosperms, flowers, and the genetic mechanisms of their development have been well characterized in many plant species but not in the woody tree yellowhorn (Xanthoceras sorbifolium). Here, we focused on the double flower phenotype in yellowhorn, which has high ornamental value. We found a candidate C-class gene, AGAMOUS1 (XsAG1), through bovine serum albumin sequencing and genetics analysis with a Long Interpersed Nuclear Elements 1 (LINE1) transposable element fragment (Xsag1-LINE1-1) inserted into its second intron that caused a loss-of-C-function and therefore the double flower phenotype. In situ hybridization of XsAG1 and analysis of the expression levels of other ABC genes were used to identify differences between single- and double-flower development processes. These findings enrich our understanding of double flower formation in yellowhorn and provide evidence that transposon insertions into genes can reshape plant traits in forest trees. DA - 2022/12/10/ PY - 2022/12/10/ DO - 10.1093/plphys/kiac571 VL - 12 SP - SN - 1532-2548 ER - TY - JOUR TI - Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape AU - Han, Qiang AU - Hung, Yu-Hung AU - Zhang, Changqing AU - Bartels, Arthur AU - Rea, Matthew AU - Yang, Hanwen AU - Park, Christine AU - Zhang, Xiang-Qian AU - Fischer, Robert L. L. AU - Xiao, Wenyan AU - Hsieh, Tzung-Fu T2 - FRONTIERS IN PLANT SCIENCE AB - The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-bound heterochromatins are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation. DA - 2022/12/22/ PY - 2022/12/22/ DO - 10.3389/fpls.2022.1070397 VL - 13 SP - SN - 1664-462X KW - epigenetics KW - DNA demethylation KW - gene imprinting KW - DNA glycosylase KW - linker histone H1 ER - TY - JOUR TI - Hyperspectral imaging with chemometrics for non-destructive determination of cannabinoids in floral and leaf materials of industrial hemp (Cannabis sativa L.) AU - Lu, Yuzhen AU - Li, Xu AU - Young, Sierra AU - Li, Xin AU - Linder, Eric AU - Suchoff, David T2 - COMPUTERS AND ELECTRONICS IN AGRICULTURE AB - With the passage of the 2018 Farm Bill, industrial hemp (Cannabis sativa L.) has become a legal and economically promising crop commodity for U.S. farmers. There has been a surge of interest in growing industrial hemp for producing cannabinoids, such as cannabidiol (CBD), because of their medical potential. Quantitative determination of cannabinoids in harvested materials (primarily floral tissues) is critical for cannabinoid production and compliance testing. The concentrations of cannabinoids in hemp materials are conventionally determined using wet-chemistry chromatographic methods, which require destructive sampling, and are time-consuming, costly, and thus not suitable for on-site rapid testing. This study presents a novel effort to utilize hyperspectral imaging technology for non-destructive quantification of major cannabinoids, including CBD, THC (tetrahydrocannabinol), CBG (cannabigerol) and their acid forms in fresh floral and leaf materials of industrial hemp on a dry weight basis. Hyperspectral images in the wavelength range of 400–1000 nm were acquired from floral and leaf tissues immediately after harvest from a total of 100 industrial hemp plants of five cultivars at varied growth stages. Linear discriminant analysis showed hyperspectral imaging could identify CBD-rich/poor and THC-legal/illegal flower samples with accuracies of 99% and 97%, respectively. Quantitative models based on full-spectrum PLS (partial least squares) achieved prediction accuracies of RPD (ratio of prediction to deviation) = 2.5 (corresponding R2 = 0.84) for CBD and THC in floral tissues. Similar accuracies were obtained for their acid forms in flower samples. The predictions for CBG and its acid form in floral tissues and all six cannabinoids in leaf tissues were unsatisfactory with noticeably lower RPD values. Consistently improved accuracies were obtained by parsimonious PLS models based on a wavelength selection procedure for minimized variable collinearity. The best RPD values of approximately 2.6 (corresponding R2 = 0.85) were obtained for CBD and THC in floral materials. This study demonstrates the utility of hyperspectral imaging as a potential valuable tool for rapid quantification of cannabinoids in industrial hemp. DA - 2022/11// PY - 2022/11// DO - 10.1016/j.compag.2022.107387 VL - 202 SP - SN - 1872-7107 KW - Imaging spectroscopy KW - Cannabis KW - Cannabinoids KW - Quantification KW - Wavelength selection ER - TY - JOUR TI - The challenges of using treatment solution properties to determine concentrations for the inhibition of seedling processes by monoprotic phenolic acids AU - Blum, Udo T2 - PLANT AND SOIL DA - 2022/12/14/ PY - 2022/12/14/ DO - 10.1007/s11104-022-05837-z VL - 12 SP - SN - 1573-5036 KW - Allelopathic agents KW - Neutral molecules KW - Monoprotic phenolic acids KW - Solution properties KW - % inhibition of seedling processes ER - TY - JOUR TI - Vector acquisition and co-inoculation of two plant viruses influences transmission, infection, and replication in new hosts AU - McLaughlin, Autumn A. AU - Hanley-Bowdoin, Linda AU - Kennedy, George G. AU - Jacobson, Alana L. T2 - SCIENTIFIC REPORTS AB - Abstract This study investigated the role of vector acquisition and transmission on the propagation of single and co-infections of tomato yellow leaf curl virus (TYLCV,) and tomato mottle virus (ToMoV) (Family: Geminiviridae, Genus: Begomovirus ) by the whitefly vector Bemisia tabaci MEAM1 (Gennadius) in tomato. The aim of this research was to determine if the manner in which viruses are co-acquired and co-transmitted changes the probability of acquisition, transmission and new host infections. Whiteflies acquired virus by feeding on singly infected plants, co-infected plants, or by sequential feeding on singly infected plants. Viral titers were also quantified by qPCR in vector cohorts, in artificial diet, and plants after exposure to viruliferous vectors. Differences in transmission, infection status of plants, and titers of TYLCV and ToMoV were observed among treatments. All vector cohorts acquired both viruses, but co-acquisition/co-inoculation generally reduced transmission of both viruses as single and mixed infections. Co-inoculation of viruses by the vector also altered virus accumulation in plants regardless of whether one or both viruses were propagated in new hosts. These findings highlight the complex nature of vector-virus-plant interactions that influence the spread and replication of viruses as single and co-infections. DA - 2022/11/27/ PY - 2022/11/27/ DO - 10.1038/s41598-022-24880-5 VL - 12 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Randomized placebo-controlled trial of feline-origin Enterococcus hirae probiotic effects on preventative health and fecal microbiota composition of fostered shelter kittens AU - Gookin, Jody L. L. AU - Strong, Sandra J. J. AU - Bruno-Barcena, Jose M. AU - Stauffer, Stephen H. H. AU - Williams, Shelby AU - Wassack, Erica AU - Azcarate-Peril, M. Andrea AU - Estrada, Marko AU - Seguin, Alexis AU - Balzer, Joerg AU - Davidson, Gigi T2 - FRONTIERS IN VETERINARY SCIENCE AB - Diarrhea is the second most common cause of mortality in shelter kittens. Studies examining prevention strategies in this population are lacking. Probiotics are of particular interest but studies in cats are largely limited to healthy adults or those with induced disease. Only one study in domestic cats describes the use of host-derived bacteria as a probiotic. We previously identified Enterococcus hirae as a dominant species colonizing the small intestinal mucosa in healthy shelter kittens. Oral administration of a probiotic formulation of kitten-origin E. hirae (strain 1002-2) mitigated the increase in intestinal permeability and fecal water loss resulting from experimental enteropathogenic E. coli infection in purpose-bred kittens. Based on these findings, we hypothesized that administration of kitten-origin E. hirae to weaned fostered shelter kittens could provide a measurable preventative health benefit.We conducted a randomized, placebo-controlled, blinded clinical trial to determine the impact of a freeze-dried E. hirae probiotic on body weight gain, incidence of diarrhea, carriage of potential diarrheal pathogens, and composition of the intestinal microbiota in weaned fostered shelter kittens.One-hundred thirty kittens completed the study. Fifty-eight kittens received the probiotic and 72 received the placebo. There were no significant differences in age, weight upon initiation of the study, number of days in the study, average daily gain in body weight, or weight at completion of the study. Kittens treated with E. hirae were 3.4 times less likely to develop diarrhea compared to kittens treated with placebo (odds ratio = 0.294, 95% CI 0.109-0.792, p = 0.022). A significant impact of E. hirae was not observed on the presence or abundance of 30 different bacterial, viral, protozoal, fungal, algal, and parasitic agents in feces examined by qPCR. With exception to a decrease in Megamonas, administration of the E. hirae probiotic did not alter the predominant bacterial phyla present in feces based on 16S rRNA gene amplicon sequencing.Decreased incidence of diarrhea associated with preventative administration of E. hirae to foster kittens supports a rationale for use of E. hirae for disease prevention in this young population at high risk for intestinal disease though additional studies are warranted. DA - 2022/11/17/ PY - 2022/11/17/ DO - 10.3389/fvets.2022.923792 VL - 9 SP - SN - 2297-1769 UR - https://doi.org/10.3389/fvets.2022.923792 KW - 16S rRNA gene amplicon sequencing KW - diarrheal pathogens KW - growth and survival KW - infection KW - polymerase chain reaction KW - shelter medicine ER - TY - JOUR TI - Dietary protein and the intestinal microbiota: An understudied relationship AU - Bartlett, Alexandria AU - Kleiner, Manuel T2 - ISCIENCE AB - Diet has a profound impact on the microbial community in the gastrointestinal tract, the intestinal microbiota, to the benefit or detriment of human health. To understand the influence of diet on the intestinal microbiota, research has focused on individual macronutrients. Some macronutrients (e.g. fiber) have been studied in great detail and have been found to strongly influence the intestinal microbiota. The relationship between dietary protein, a vital macronutrient, and the intestinal microbiota has gone largely unexplored. Emerging evidence suggests that dietary protein strongly impacts intestinal microbiota composition and function and that protein-microbiota interactions can have critical impacts on host health. In this review, we focus on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences. We highlight major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota. DA - 2022/11/18/ PY - 2022/11/18/ DO - 10.1016/j.isci.2022.105313 VL - 25 IS - 11 SP - SN - 2589-0042 ER - TY - JOUR TI - Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities AU - Beck, Ashley E. AU - Kleiner, Manuel AU - Garrell, Anna-Katharina T2 - FRONTIERS IN PLANT SCIENCE AB - With a growing world population and increasing frequency of climate disturbance events, we are in dire need of methods to improve plant productivity, resilience, and resistance to both abiotic and biotic stressors, both for agriculture and conservation efforts. Microorganisms play an essential role in supporting plant growth, environmental response, and susceptibility to disease. However, understanding the specific mechanisms by which microbes interact with each other and with plants to influence plant phenotypes is a major challenge due to the complexity of natural communities, simultaneous competition and cooperation effects, signalling interactions, and environmental impacts. Synthetic communities are a major asset in reducing the complexity of these systems by simplifying to dominant components and isolating specific variables for controlled experiments, yet there still remains a large gap in our understanding of plant microbiome interactions. This perspectives article presents a brief review discussing ways in which metabolic modelling can be used in combination with synthetic communities to continue progress toward understanding the complexity of plant-microbe-environment interactions. We highlight the utility of metabolic models as applied to a community setting, identify different applications for both flux balance and elementary flux mode simulation approaches, emphasize the importance of ecological theory in guiding data interpretation, and provide ideas for how the integration of metabolic modelling techniques with big data may bridge the gap between simplified synthetic communities and the complexity of natural plant-microbe systems. DA - 2022/6/20/ PY - 2022/6/20/ DO - 10.3389/fpls.2022.910377 VL - 13 SP - SN - 1664-462X KW - synthetic communities KW - plant microbiome KW - plant microbial interactions KW - metabolic modelling KW - flux balance analysis KW - elementary flux mode analysis ER - TY - JOUR TI - Greater evolutionary divergence of thermal limits within marine than terrestrial species AU - Sasaki, Matthew AU - Barley, Jordanna M. AU - Gignoux-Wolfsohn, Sarah AU - Hays, Cynthia G. AU - Kelly, Morgan W. AU - Putnam, Alysha B. AU - Sheth, Seema N. AU - Villeneuve, Andrew R. AU - Cheng, Brian S. T2 - NATURE CLIMATE CHANGE AB - There is considerable uncertainty regarding which ecosystems are most vulnerable to warming. Current understanding of organismal sensitivity is largely centred on species-level assessments that do not consider variation across populations. Here we used meta-analysis to quantify upper thermal tolerance variation across 305 populations from 61 terrestrial, freshwater, marine and intertidal taxa. We found strong differentiation in heat tolerance across populations in marine and intertidal taxa but not terrestrial or freshwater taxa. This is counter to the expectation that increased connectivity in the ocean should reduce intraspecific variation. Such adaptive differentiation in the ocean suggests there may be standing genetic variation at the species level to buffer climate impacts. Assessments of vulnerability to warming should account for variation in thermal tolerance among populations (or the lack thereof) to improve predictions about climate vulnerability. The authors quantify the thermal tolerance of 305 populations from 61 taxa by meta-analysis. They reveal strong population-level differentiation in marine and intertidal taxa, but not terrestrial or freshwater taxa, and highlight the need to consider such variation in climate vulnerability predictions. DA - 2022/12// PY - 2022/12// DO - 10.1038/s41558-022-01534-y VL - 12 IS - 12 SP - 1175-+ SN - 1758-6798 UR - https://doi.org/10.1038/s41558-022-01534-y ER - TY - JOUR TI - Legacies of precipitation influence primary production in Panicum virgatum AU - Heckman, Robert W. AU - Rueda, Austin AU - Bonnette, Jason E. AU - Aspinwall, Michael J. AU - Khasanova, Albina AU - Hawkes, Christine V. AU - Juenger, Thomas E. AU - Fay, Philip A. T2 - OECOLOGIA DA - 2022/11/14/ PY - 2022/11/14/ DO - 10.1007/s00442-022-05281-x VL - 11 SP - SN - 1432-1939 KW - Bud banks KW - Precipitation variability KW - Rainfall manipulation KW - Switchgrass KW - Tiller dynamics ER - TY - JOUR TI - The Effect of Harvest Date on Temporal Cannabinoid and Biomass Production in the Floral Hemp (Cannabis sativa L.) Cultivars BaOx and Cherry Wine AU - Linder, Eric R. AU - Young, Sierra AU - Li, Xu AU - Inoa, Shannon Henriquez AU - Suchoff, David H. T2 - HORTICULTURAE AB - The objectives of this study were to model the temporal accumulation of cannabidiol (CBD) and tetrahydrocannabinol (THC) in field-grown floral hemp in North Carolina and establish harvest timing recommendations to minimize non-compliant crop production. Field trials were conducted in 2020 and 2021 with BaOx and Cherry Wine cultivars. Harvest events started two weeks after floral initiation and occurred every two weeks for 12 weeks. Per-plant threshed biomass accumulation exhibited a linear plateau trend. The best fit model for temporal accumulation of THC was a beta growth curve. As harvest date was delayed, total THC concentrations increased until concentrations reached their maximum, then decreased as plants approached senescence. Logistic regression was the best fit model for temporal accumulation of CBD. CBD concentrations increased with later harvest dates. Unlike THC concentrations, there was no decline in total CBD concentrations. To minimize risk, growers should test their crop as early as possible within the USDA’s 30-day compliance window. We observed ‘BaOx’ and ‘Cherry Wine’ exceeding the compliance threshold 50 and 41 days after flower initiation, respectively. DA - 2022/10// PY - 2022/10// DO - 10.3390/horticulturae8100959 VL - 8 IS - 10 SP - SN - 2311-7524 KW - CBD KW - THC KW - hemp KW - Cannabis sativa KW - biomass KW - cannabinoids ER - TY - JOUR TI - Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium AU - Sato, Yui AU - Wippler, Juliane AU - Wentrup, Cecilia AU - Ansorge, Rebecca AU - Sadowski, Miriam AU - Gruber-Vodicka, Harald AU - Dubilier, Nicole AU - Kleiner, Manuel T2 - MICROBIOME AB - Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract. DA - 2022/10/22/ PY - 2022/10/22/ DO - 10.1186/s40168-022-01372-2 VL - 10 IS - 1 SP - SN - 2049-2618 KW - Microbiome KW - Animal-bacterial symbiosis KW - Symbiont transmission KW - Phylosymbiosis KW - Intraspecific genetic variation ER - TY - JOUR TI - Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes AU - Salvato, Fernanda AU - Vintila, Simina AU - Finkel, Omri M. AU - Dangl, Jeffery L. AU - Kleiner, Manuel T2 - MOLECULAR PLANT-MICROBE INTERACTIONS AB - Metaproteomics is a powerful tool for the characterization of metabolism, physiology, and functional interactions in microbial communities, including plant-associated microbiota. However, the metaproteomic methods that have been used to study plant-associated microbiota are very laborious and require large amounts of plant tissue, hindering wider application of these methods. We optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species ( Arabidopsis and maize). Our main goal was to identify a method that would work with low amounts of input material (40 to 70 mg) and that would maximize the number of identified microbial proteins. We tested eight protocols, each comprising a different combination of physical lysis method, extraction buffer, and cell-enrichment method on roots from plants grown with synthetic microbial communities. We assessed the performance of the extraction protocols by liquid chromatography-tandem mass spectrometry–based metaproteomics and found that the optimal extraction method differed between the two species. For Arabidopsis roots, protein extraction by beating whole roots with small beads provided the greatest number of identified microbial proteins and improved the identification of proteins from gram-positive bacteria. For maize, vortexing root pieces in the presence of large glass beads yielded the greatest number of microbial proteins identified. Based on these data, we recommend the use of these two methods for metaproteomics with Arabidopsis and maize. Furthermore, detailed descriptions of the eight tested protocols will enable future optimization of protein extraction for metaproteomics in other dicot and monocot plants. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license . DA - 2022/11// PY - 2022/11// DO - 10.1094/MPMI-05-22-0116-TA VL - 35 IS - 11 SP - 977-988 SN - 1943-7706 UR - https://doi.org/10.1094/MPMI-05-22-0116-TA KW - endosphere KW - metaproteomics KW - microbiome KW - microbiota KW - phytobiome KW - plant-microbe interactions KW - rhizoplane ER - TY - JOUR TI - Local Adaptation: Causal Agents of Selection and Adaptive Trait Divergence AU - Wadgymar, Susana M. AU - DeMarche, Megan L. AU - Josephs, Emily B. AU - Sheth, Seema N. AU - Anderson, Jill T. T2 - ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS AB - Divergent selection across the landscape can favor the evolution of local adaptation in populations experiencing contrasting conditions. Local adaptation is widely observed in a diversity of taxa, yet we have a surprisingly limited understanding of the mechanisms that give rise to it. For instance, few have experimentally confirmed the biotic and abiotic variables that promote local adaptation, and fewer yet have identified the phenotypic targets of selection that mediate local adaptation. Here, we highlight critical gaps in our understanding of the process of local adaptation and discuss insights emerging from in-depth investigations of the agents of selection that drive local adaptation, the phenotypes they target, and the genetic basis of these phenotypes. We review historical and contemporary methods for assessing local adaptation, explore whether local adaptation manifests differently across life history, and evaluate constraints on local adaptation. DA - 2022/// PY - 2022/// DO - 10.1146/annurev-ecolsys-012722-035231 VL - 53 IS - 1 SP - 87-111 SN - 1545-2069 UR - http://dx.doi.org/10.1146/annurev-ecolsys-012722-035231 KW - genetic basis of local adaptation KW - manipulative experiment KW - provenance trial KW - reciprocal transplant experiment KW - target of selection KW - agent of selection ER - TY - JOUR TI - Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage AU - Ahmad, Jabeen AU - Zervas, Athanasios AU - Ellegaard-Jensen, Lea AU - Hennessy, Rosanna C. AU - Carbone, Ignazio AU - Cornish, Vicki AU - Muller-Stover, Dorette Sophie AU - Grunden, Amy AU - Jacobsen, Carsten S. AU - Nicolaisen, Mette Haubjerg T2 - MICROBIOLOGY RESOURCE ANNOUNCEMENTS AB - Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment. DA - 2022/10/6/ PY - 2022/10/6/ DO - 10.1128/mra.00663-22 VL - 10 SP - SN - 2576-098X ER - TY - JOUR TI - Populations of western North American monkeyflowers accrue niche breadth primarily via genotypic divergence in environmental optima AU - Coughlin, Aeran O. AU - Wooliver, Rachel AU - Sheth, Seema N. T2 - ECOLOGY AND EVOLUTION AB - Niche breadth, the range of environments that individuals, populations, and species can tolerate, is a fundamental ecological and evolutionary property, yet few studies have examined how niche breadth is partitioned across biological scales. We use a published dataset of thermal performance for a single population from each of 10 closely related species of western North American monkeyflowers (genus Mimulus) to investigate whether populations achieve broad thermal niches through general purpose genotypes, specialized genotypes with divergent environmental optima, and/or variation among genotypes in the degree of generalization. We found the strongest relative support for the hypothesis that populations with greater genetic variation for thermal optimum had broader thermal niches, and for every unit increase in among-family variance in thermal optimum, population-level thermal breadth increased by 0.508°C. While the niche breadth of a single genotype represented up to 86% of population-level niche breadth, genotype-level niche breadth had a weaker positive effect on population-level breadth, with every 1°C increase in genotypic thermal breadth resulting in a 0.062°C increase in population breadth. Genetic variation for thermal breadth was not predictive of population-level thermal breadth. These findings suggest that populations of Mimulus species have achieved broad thermal niches primarily through genotypes with divergent thermal optima and to a lesser extent via general-purpose genotypes. Future work examining additional biological hierarchies would provide a more comprehensive understanding of how niche breadth partitioning impacts the vulnerabilities of individuals, populations, and species to environmental change. DA - 2022/10// PY - 2022/10// DO - 10.1002/ece3.9434 VL - 12 IS - 10 SP - SN - 2045-7758 UR - https://doi.org/10.1002/ece3.9434 KW - environmental tolerance KW - genetic variation KW - Mimulus KW - niche optimum KW - specialization KW - thermal performance curve ER - TY - JOUR TI - Establishing a reproducible approach for the controllable deposition and maintenance of plants cells with 3D bioprinting AU - Broeck, Lisa Van AU - Schwartz, Michael F AU - Krishnamoorthy, Srikumar AU - Spurney, Ryan J AU - Tahir, Maimouna Abderamane AU - Melvin, Charles AU - Gobble, Mariah AU - Peters, Rachel AU - Muhammad, Atiyya AU - Li, Baochun AU - Stuiver, Maarten AU - Horn, Timothy AU - Sozzani, Rosangela AB - Abstract Capturing cell-to-cell and cell-to-environment signals in a defined 3 dimensional (3D) microenvironment is key to study cellular functions, including cellular reprogramming towards tissue regeneration. A major challenge in current culturing methods is that these methods cannot accurately capture this multicellular 3D microenvironment. In this study, we established the framework of 3D bioprinting with plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis root cells and soybean meristematic cells. To analyze the large image datasets generated during these long-term viability studies, we developed an open source high-throughput image analysis pipeline. Furthermore, we showed the cell cycle re-entry of the isolated Arabidopsis and soybean cells leading to the formation of microcalli. Finally, we showed that the identity of isolated cells of Arabidopsis roots expressing endodermal markers maintained longer periods of time. The framework established in this study paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle re-entry towards tissue regeneration. DA - 2022/3/27/ PY - 2022/3/27/ DO - 10.1101/2022.03.25.485804 VL - 3 UR - https://doi.org/10.1101/2022.03.25.485804 ER - TY - JOUR TI - Establishing a reproducible approach to study cellular functions of plant cells with 3D bioprinting AU - Broeck, Lisa Van AU - Schwartz, Michael F. AU - Krishnamoorthy, Srikumar AU - Tahir, Maimouna Abderamane AU - Spurney, Ryan J. AU - Madison, Imani AU - Melvin, Charles AU - Gobble, Mariah AU - Nguyen, Thomas AU - Peters, Rachel AU - Hunt, Aitch AU - Muhammad, Atiyya AU - Li, Baochun AU - Stuiver, Maarten AU - Horn, Timothy AU - Sozzani, Rosangela T2 - Science Advances AB - Capturing cell-to-cell signals in a three-dimensional (3D) environment is key to studying cellular functions. A major challenge in the current culturing methods is the lack of accurately capturing multicellular 3D environments. In this study, we established a framework for 3D bioprinting plant cells to study cell viability, cell division, and cell identity. We established long-term cell viability for bioprinted Arabidopsis and soybean cells. To analyze the generated large image datasets, we developed a high-throughput image analysis pipeline. Furthermore, we showed the cell cycle reentry of bioprinted cells for which the timing coincides with the induction of core cell cycle genes and regeneration-related genes, ultimately leading to microcallus formation. Last, the identity of bioprinted Arabidopsis root cells expressing endodermal markers was maintained for longer periods. The framework established here paves the way for a general use of 3D bioprinting for studying cellular reprogramming and cell cycle reentry toward tissue regeneration. DA - 2022/10/14/ PY - 2022/10/14/ DO - 10.1126/sciadv.abp9906 UR - https://doi.org/10.1126/sciadv.abp9906 ER - TY - JOUR TI - Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape AU - Hsieh, Tzung-Fu AU - Han, Qiang AU - Hung, Yu-Hung AU - Zhang, Changqing AU - Bartels, Arthur AU - Rea, Matthew AU - Yang, Hanwen AU - Park, Christine AU - Zhang, Xiang-Qian AU - Fsicher, Robert L. AU - Xiao, Wenyan AB - Abstract The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these target loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which how H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that unlike in the vegetative cell, both canonical histone H1 variants are present in the central cell. Our endosperm methylome analysis revealed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-containing nucleosomes are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation. DA - 2022/10/20/ PY - 2022/10/20/ DO - 10.1101/2022.10.17.512625 UR - https://doi.org/10.1101/2022.10.17.512625 ER - TY - JOUR TI - High-throughput detection of T-DNA insertion sites for multiple transgenes in complex genomes AU - Edwards, Brianne AU - Hornstein, Eli D. AU - Wilson, Nathan J. AU - Sederoff, Heike T2 - BMC GENOMICS AB - Genetic engineering of crop plants has been successful in transferring traits into elite lines beyond what can be achieved with breeding techniques. Introduction of transgenes originating from other species has conferred resistance to biotic and abiotic stresses, increased efficiency, and modified developmental programs. The next challenge is now to combine multiple transgenes into elite varieties via gene stacking to combine traits. Generating stable homozygous lines with multiple transgenes requires selection of segregating generations which is time consuming and labor intensive, especially if the crop is polyploid. Insertion site effects and transgene copy number are important metrics for commercialization and trait efficiency.We have developed a simple method to identify the sites of transgene insertions using T-DNA-specific primers and high-throughput sequencing that enables identification of multiple insertion sites in the T1 generation of any crop transformed via Agrobacterium. We present an example using the allohexaploid oil-seed plant Camelina sativa to determine insertion site location of two transgenes.This new methodology enables the early selection of desirable transgene location and copy number to generate homozygous lines within two generations. DA - 2022/10/5/ PY - 2022/10/5/ DO - 10.1186/s12864-022-08918-6 VL - 23 IS - 1 SP - SN - 1471-2164 KW - Transgene KW - Insertion site KW - Polyploid KW - T-DNA KW - Sequencing ER - TY - JOUR TI - Transcriptional and Metabolic Characterization of Feeding Ramie Growth Enhanced by a Combined Application of Gibberellin and Ethrel AU - Jie, Hongdong AU - Ma, Yushen AU - Xie, De-Yu AU - Jie, Yucheng T2 - INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES AB - Feeding ramie cultivars (Boehmaria nivea L.) are an important feedstock for livestock. Increasing their biomass and improving their nutritional values are essential for animal feeding. Gibberellin (GA3) and ethylene (ETH) are two plant hormones that regulate the growth, development, and metabolism of plants. Herein, we report effects of the GA3 and ETH application on the growth and plant metabolism of feeding ramie in the field. A combination of GA3 and ETH was designed to spray new plants. The two hormones enhanced the growth of plants to produce more biomass. Meanwhile, the two hormones reduced the contents of lignin in leaves and stems, while increased the content of flavonoids in leaves. To understand the potential mechanisms behind these results, we used RNA-seq-based transcriptomics and UPLC-MS/MS-based metabolomics to characterize gene expression and metabolite profiles associated with the treatment of GA3 and ETH. 1562 and 2364 differentially expressed genes (DEGs) were obtained from leaves and stems (treated versus control), respectively. Meanwhile, 99 and 88 differentially accumulated metabolites (DAMs) were annotated from treated versus control leaves and treated versus control stems, respectively. Data mining revealed that both DEGs and DAMs were associated with multiple plant metabolisms, especially plant secondary metabolism. A specific focus on the plant phenylpropanoid pathway identified candidates of DEGs and DEMs that were associated with lignin and flavonoid biosynthesis. Shikimate hydroxycinnamoyl transferase (HCT) is a key enzyme that is involved in the lignin biosynthesis. The gene encoding B. nivea HCT was downregulated in the treated leaves and stems. In addition, genes encoding 4-coumaryl CoA ligase (4CL) and trans-cinnamate 4-monooxygenase (CYP73A), two lignin pathway enzymes, were downregulated in the treated stems. Meanwhile, the reduction in lignin in the treated leaves led to an increase in cinnamic acid and p-coumaryl CoA, two shared substrates of flavonoids that are enhanced in contents. Taken together, these findings indicated that an appropriate combination of GA3 and ETH is an effective strategy to enhance plant growth via altering gene expression and plant secondary metabolism for biomass-enhanced and value-improved feeding ramie. DA - 2022/10// PY - 2022/10// DO - 10.3390/ijms231912025 VL - 23 IS - 19 SP - SN - 1422-0067 UR - https://doi.org/10.3390/ijms231912025 KW - GA(3) KW - ETH KW - transcriptomics KW - metabolomics KW - secondary metabolites ER - TY - JOUR TI - Effects and response of the Cerrado ground-layer to frost along the canopy cover gradient AU - Lima Pilon, Natashi A. AU - Cava, Mario G. B. AU - Hoffmann, William A. AU - Abreu, Rodolfo C. R. AU - Rossatto, Davi R. AU - Durigan, Giselda T2 - OECOLOGIA DA - 2022/9/21/ PY - 2022/9/21/ DO - 10.1007/s00442-022-05259-9 SP - SN - 1432-1939 KW - Frost KW - Litter accumulation KW - Neotropical savanna KW - Disturbance KW - Resilience ER - TY - JOUR TI - Reciprocal Inclusion of Microbiomes and Environmental Justice Contributes Solutions to Global Environmental Health Challenges AU - Choudoir, Mallory J. AU - Eggleston, Erin M. T2 - mSystems AB - Generations of colonialism, industrialization, intensive agriculture, and anthropogenic climate change have radically altered global ecosystems and by extension, their environmental microbiomes. The environmental consequences of global change disproportionately burden racialized communities, those with lower socioeconomic status, and other systematically underserved populations. Environmental justice seeks to balance the relationships between environmental burden, beneficial ecosystem functions, and local communities. Given their direct links to human and ecosystem health, microbes are embedded within social and environmental justice. Considering scientific and technological advances is becoming an important step in developing actionable solutions to global equity challenges. Here we identify areas where inclusion of microbial knowledge and research can support planetary health goals. We offer guidelines for strengthening a reciprocal integration of environmental justice into environmental microbiology research. Microbes form intimate relationships with the environment and society, thus microbiologists have numerous and unique opportunities to incorporate equity into their research, teaching, and community engagement. DA - 2022/6/28/ PY - 2022/6/28/ DO - 10.1128/msystems.01462-21 VL - 7 IS - 3 UR - http://dx.doi.org/10.1128/msystems.01462-21 KW - microbiome KW - environmental microbes KW - environmental justice KW - social equity KW - global change KW - stewardship KW - research ethics KW - microbiome stewardship ER - TY - JOUR TI - Streptomyces apricus sp. nov., isolated from soil AU - Hariharan, Janani AU - Choudoir, Mallory J. AU - Diebold, Peter AU - Panke-Buisse, Kevin AU - Buckley, Daniel H. T2 - International Journal of Systematic and Evolutionary Microbiology AB - A novel Streptomyces strain, SUN51T, was isolated from soils sampled in Wisconsin, USA, as part of a Streptomyces biogeography survey. Genome sequencing revealed that this strain had less than 90 % average nucleotide identity (ANI) to type species of Streptomyces: SUN51T was most closely related to Streptomyces dioscori A217T (99.5 % 16S rRNA gene identity, 89.4 % ANI). Genome size was estimated at 8.81 Mb, and the genome DNA G+C content was 72 mol%. The strain possessed the cellular fatty acids anteiso-C15 : 0, iso-C16 : 0, 16 : 1 ω7c, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0. The predominant menaquinones were MK-9 H4, MK-9 H6 and MK-9 H8. Strain SUN51T contained the polar lipids phosphatidic acid, phosphatidyl ethanolamine, phosphatidyl glycerol and diphosphatidyl glycerol. The cell wall contained ll-diaminopimelic acid. The strain could grow on a broad range of carbon sources and tolerate temperatures of up to 40 °C. The results of the polyphasic study confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces apricus sp. nov. is proposed. The type strain of this species is SUN51T (=NRRL B-65543T=JCM 33736T). DA - 2022/1/19/ PY - 2022/1/19/ DO - 10.1099/ijsem.0.005178 VL - 72 IS - 1 UR - https://doi.org/10.1099/ijsem.0.005178 KW - Streptomyces KW - soil KW - species description KW - apricus ER - TY - JOUR TI - Chitosan diet alters the microbiome of adult house flies AU - Schaal, Hila AU - Choudoir, Mallory J. AU - Diwanji, Vedang AU - Stoffolano, John, Jr. AU - DeAngelis, Kristen M. AB - Abstract House flies are disease vectors, carrying human pathogens which include Escherichia coli and Vibrio cholera . To explore the use of chitosan as a bioinsecticide, we evaluated the effects of a chitosan-amended diet on Musca domestica (house fly). We first conducted longevity experiments to understand the impact of chitosan on house fly longevity. We confirmed that chitosan diet amendment is associated with reduced longevity and that this is not due to starvation. We then extracted fly microbiome DNA and used 16S ribosomal RNA gene amplicon sequencing and quantitative PCR to assess the composition and load of the microbiome for flies fed chitosan-amended diets compared to controls. Diversity of the chitosan-fed fly microbiomes was lower than the control, with significant dissimilarities in community composition. Chitosan-fed flies showed lower Ralstonia relative abundance but increased relative abundance of Serratia . Both control and chitosan-fed flies had highly uneven communities, but the control flies were dominated by genera Ralstonia and Providencia , while the chitosan-fed flies were dominated by genera Serratia, Kosakonia , and Providencia . Contrary to our expected results, chitosan-fed flies also contained 56% more bacteria compared to controls. Gut microbiome changes appear to result from chitinolytic bacteria becoming more relatively abundant, and our results suggest that chitosan-amended diet alters the house fly microbiome resulting in higher fly mortality. DA - 2022/8/31/ PY - 2022/8/31/ DO - 10.1101/2022.08.31.502951 UR - https://doi.org/10.1101/2022.08.31.502951 ER - TY - JOUR TI - A framework for integrating microbial dispersal modes into soil ecosystem ecology AU - Choudoir, Mallory J. AU - DeAngelis, Kristen M. T2 - iScience AB - Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships. DA - 2022/3// PY - 2022/3// DO - 10.1016/j.isci.2022.103887 VL - 25 IS - 3 SP - 103887 UR - http://dx.doi.org/10.1016/j.isci.2022.103887 ER - TY - JOUR TI - Additive genetic variance for lifetime fitness and the capacity for adaptation in an annual plant (vol 73, pg 1746, 2019) AU - Geyer, Charles J. AU - Kulbaba, Mason W. AU - Sheth, Seema N. AU - Pain, Rachel E. AU - Eckhart, Vincent M. AU - Shaw, Ruth G. T2 - EVOLUTION DA - 2022/9/6/ PY - 2022/9/6/ DO - 10.1111/evo.14607 VL - 9 SP - SN - 1558-5646 UR - https://doi.org/10.1111/evo.14607 ER - TY - JOUR TI - Host induced gene silencing of Magnaporthe oryzae by targeting pathogenicity and development genes to control rice blast disease AU - Wang, Mengying AU - Dean, Ralph A. T2 - FRONTIERS IN PLANT SCIENCE AB - Rice blast disease caused by the hemi-biotrophic fungus Magnaporthe oryzae is the most destructive disease of rice world-wide. Traditional disease resistance strategies for the control of rice blast disease have not proved durable. HIGS (host induced gene silencing) is being developed as an alternative strategy. Six genes (CRZ1, PMC1, MAGB, LHS1, CYP51A, CYP51B) that play important roles in pathogenicity and development of M. oryzae were chosen for HIGS. HIGS vectors were transformed into rice calli through Agrobacterium-mediated transformation and T0, T1 and T2 generations of transgenic rice plants were generated. Except for PMC1 and LHS1, HIGS transgenic rice plants challenged with M. oryzae showed significantly reduced disease compared with non-silenced control plants. Following infection with M. oryzae of HIGS transgenic plants, expression levels of target genes were reduced as demonstrated by Quantitative RT-PCR. In addition, treating M. oryzae with small RNA derived from the target genes inhibited fungal growth. These findings suggest RNA silencing signals can be transferred from host to an invasive fungus and that HIGS has potential to generate resistant rice against M. oryzae. DA - 2022/8/11/ PY - 2022/8/11/ DO - 10.3389/fpls.2022.959641 VL - 13 SP - SN - 1664-462X KW - rice blast KW - host-induced gene silencing KW - transgenic plant KW - RNA silencing KW - cross-kingdom communication ER - TY - JOUR TI - Phylogenomics AND biogeography of Castanea (chestnut) and Hamamelis (witch-hazel) - Choosing between RAD-seq and Hyb-Seq approaches AU - Zhou, Wenbin AU - Xiang, Qiu-Yun T2 - MOLECULAR PHYLOGENETICS AND EVOLUTION AB - Hyb-Seq and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for plant phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed RAD-seq and Hyb-Seq of Angiosperms353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian (EA) -eastern North American (ENA) disjunct distribution, and compared them side by side. Our results showed congruences in phylogenetic inference and divergence time dating between the two data sets obtained through our customized procedures of library preparation and sequence trimming, although they differed in the number of loci and informative sites, the amount of missing data, and sampling within species. We provide recommendations regarding the selection of the two methods for phylogenomic study at generic level based on fund availability and sampling scale. If funds and time are not constrained, we recommend Hyb-Seq. If funds and time are somewhat limited and sampling is large, we recommend RAD-seq. However, we found greater conflict among gene trees from the RAD-seq data due to the short sequences per locus. Therefore, species tree building and network detecting with the RAD-seq data with short RAD-seq loci (e.g., <150 bp) should avoid using analytical methods relying on gene trees of individual locus, but using site-based methods such as SVDQuartets and D-statistic method. Our phylogenetic analyses of RAD-seq and Hyb-Seq data resulted in well-resolved species relationships. Analyses of the data using the D-statistic test and PhyloNet revealed ancient introgressions in both genera. Biogeographic analyses including fossil data using total evidence-based dated tree and DEC model applying specific inter-area dispersal probabilities revealed a complicated history for each genus, indicating multiple interareal dispersals and local extinctions within and outside areas of the taxa's modern ranges in both the Paleogene and Neogene. The study demonstrates the importance of including fossil taxa for a more accurate reconstruction of biogeographic histories of taxa to understand the EA and ENA floristic disjunction. Our results support a widespread ancestral range in EA-western North America (WNA) followed by early diversification in EA and expansion to North America (NA) and Europe for Castanea and a more widespread ancestral range in EA-ENA-WNA for Hamamelis. The origins of the modern EA-ENA disjunction in both genera were suggested to be the result of vicariance from widespread ancestors in Eurasia-ENA of the mid-Miocene and in EA-NA of the late Oligocene, respectively. DA - 2022/11// PY - 2022/11// DO - 10.1016/j.ympev.2022.107592 VL - 176 SP - SN - 1095-9513 KW - RAD-seq KW - Hyb-Seq KW - Angiosperms353 genes KW - Castanea KW - Hamamelis KW - America disjunction KW - Biogeography of eastern Asia-eastern North ER - TY - JOUR TI - The Effect of Transplant Date and Plant Spacing on Biomass Production for Floral Hemp (Cannabis sativa L.) AU - Linder, Eric R. AU - Young, Sierra AU - Li, Xu AU - Inoa, Shannon Henriquez AU - Suchoff, David H. T2 - AGRONOMY-BASEL AB - Floral hemp cultivated for the extraction of cannabinoids is a new crop in the United States, and agronomic recommendations are scarce. The objective of this study was to understand the effects of plant spacing and transplant date on floral hemp growth and biomass production. Field trials were conducted in North Carolina in 2020 and 2021 with the floral hemp cultivar BaOx. Transplant date treatments occurred every two weeks from 11 May to 7 July (±1 d). Plant spacing treatments were 0.91, 1.22, 1.52, and 1.83 m between plants. Weekly height and width data were collected throughout the vegetative period, and dry biomass was measured at harvest. Plant width was affected by transplant date and spacing. Plant height was affected by transplant date. Earlier transplant dates resulted in taller, wider plants, while larger plant spacing resulted in wider plants. Individual plant biomass increased with earlier transplant dates and larger plant spacing. On a per-hectare basis, biomass increased with earlier transplant dates and smaller transplant spacing. An economic analysis found that returns were highest with 1.22 m spacing and decreased linearly by a rate of −163.098 USD ha−1 d−1. These findings highlight the importance of earlier transplant timing to maximize harvestable biomass. DA - 2022/8// PY - 2022/8// DO - 10.3390/agronomy12081856 VL - 12 IS - 8 SP - SN - 2073-4395 KW - hemp KW - cannabis KW - biomass KW - cannabinoid KW - CBD KW - plant density ER - TY - JOUR TI - Microgravity enhances the phenotype of Arabidopsis zigzag-1 and reduces the Wortmannin-induced vacuole fusion in root cells AU - Wang, Mengying AU - Danz, Katherine AU - Ly, Vanessa AU - Rojas-Pierce, Marcela T2 - NPJ MICROGRAVITY AB - Abstract The spaceflight environment of the International Space Station poses a multitude of stresses on plant growth including reduced gravity. Plants exposed to microgravity and other conditions on the ISS display root skewing, changes in gene expression and protein abundance that may result in changes in cell wall composition, antioxidant accumulation and modification of growth anisotropy. Systematic studies that address the effects of microgravity on cellular organelles are lacking but altered numbers and sizes of vacuoles have been detected in previous flights. The prominent size of plant vacuoles makes them ideal models to study organelle dynamics in space. Here, we used Arabidopsis zigzag-1 ( zig-1 ) as a sensitized genotype to study the effect of microgravity on plant vacuole fusion. Wortmannin was used to induce vacuole fusion in seedlings and a formaldehyde-based fixation protocol was developed to visualize plant vacuole morphology after sample return, using confocal microscopy. Our results indicate that microgravity enhances the zig-1 phenotype by reducing hypocotyl growth and vacuole fusion in some cells. This study demonstrates the feasibility of chemical inhibitor treatments for plant cell biology experiments in space. DA - 2022/9/6/ PY - 2022/9/6/ DO - 10.1038/s41526-022-00226-3 VL - 8 IS - 1 SP - SN - 2373-8065 UR - https://doi.org/10.1038/s41526-022-00226-3 ER - TY - JOUR TI - Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice AU - Blakeley-Ruiz, J. Alfredo AU - McClintock, Carlee S. AU - Shrestha, Him K. AU - Poudel, Suresh AU - Yang, Zamin K. AU - Giannone, Richard J. AU - Choo, James J. AU - Podar, Mircea AU - Baghdoyan, Helen A. AU - Lydic, Ralph AU - Hettich, Robert L. T2 - ISME Communications AB - There are known associations between opioids, obesity, and the gut microbiome, but the molecular connection/mediation of these relationships is not understood. To better clarify the interplay of physiological, genetic, and microbial factors, this study investigated the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice. Samples of feces, urine, colon tissue, and plasma were analyzed using targeted LC-MS/MS quantification of metabolites, immunoassays of inflammatory cytokine levels, genome-resolved metagenomics, and metaproteomics. Genetic obesity, diet-induced obesity, and morphine treatment in lean mice each showed increases in distinct inflammatory cytokines. Metagenomic assembly and binning uncovered over 400 novel gut bacterial genomes and species. Morphine administration impacted the microbiome's composition and function, with the strongest effect observed in lean mice. This microbiome effect was less pronounced than either diet or genetically driven obesity. Based on inferred microbial physiology from the metaproteome datasets, a high-fat diet transitioned constituent microbes away from harvesting diet-derived nutrients and towards nutrients present in the host mucosal layer. Considered together, these results identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome. DA - 2022/8/5/ PY - 2022/8/5/ DO - 10.1038/s43705-022-00131-6 VL - 2 IS - 1 UR - http://dx.doi.org/10.1038/s43705-022-00131-6 ER - TY - JOUR TI - POPEYE intercellular localization mediates cell-specific iron deficiency responses AU - Muhammad, DurreShahwar AU - Clark, Natalie M. AU - Haque, Samiul AU - Williams, Cranos M. AU - Sozzani, Rosangela AU - Long, Terri A. T2 - PLANT PHYSIOLOGY AB - Plants must tightly regulate iron (Fe) sensing, acquisition, transport, mobilization, and storage to ensure sufficient levels of this essential micronutrient. POPEYE (PYE) is an iron responsive transcription factor that positively regulates the iron deficiency response, while also repressing genes essential for maintaining iron homeostasis. However, little is known about how PYE plays such contradictory roles. Under iron-deficient conditions, pPYE:GFP accumulates in the root pericycle while pPYE:PYE-GFP is localized to the nucleus in all Arabidopsis (Arabidopsis thaliana) root cells, suggesting that PYE may have cell-specific dynamics and functions. Using scanning fluorescence correlation spectroscopy and cell-specific promoters, we found that PYE-GFP moves between different cells and that the tendency for movement corresponds with transcript abundance. While localization to the cortex, endodermis, and vasculature is required to manage changes in iron availability, vasculature and endodermis localization of PYE-GFP protein exacerbated pye-1 defects and elicited a host of transcriptional changes that are detrimental to iron mobilization. Our findings indicate that PYE acts as a positive regulator of iron deficiency response by regulating iron bioavailability differentially across cells, which may trigger iron uptake from the surrounding rhizosphere and impact root energy metabolism. DA - 2022/8/3/ PY - 2022/8/3/ DO - 10.1093/plphys/kiac357 VL - 8 SP - SN - 1532-2548 UR - https://doi.org/10.1093/plphys/kiac357 ER - TY - JOUR TI - Application of raw industrial sweetpotato hydrolysates for butanol production by Clostridium beijerinckii NCIMB 8052 AU - Zuleta-Correa, Ana AU - Chinn, Mari S. AU - Bruno-Barcena, Jose M. T2 - BIOMASS CONVERSION AND BIOREFINERY DA - 2022/8/1/ PY - 2022/8/1/ DO - 10.1007/s13399-022-03101-z VL - 8 SP - SN - 2190-6823 UR - https://doi.org/10.1007/s13399-022-03101-z KW - Ipomoea batatas KW - ABE fermentation KW - Consolidated bioprocessing KW - Anthocyanin KW - Phenolics KW - Flour ER - TY - JOUR TI - Live-cell fluorescence spectral imaging as a data science challenge AU - Acuña-Rodriguez, Jessy Pamela AU - Mena-Vega, Jean Paul AU - Argüello-Miranda, Orlando T2 - Biophysical Reviews AB - Live-cell fluorescence spectral imaging is an evolving modality of microscopy that uses specific properties of fluorophores, such as excitation or emission spectra, to detect multiple molecules and structures in intact cells. The main challenge of analyzing live-cell fluorescence spectral imaging data is the precise quantification of fluorescent molecules despite the weak signals and high noise found when imaging living cells under non-phototoxic conditions. Beyond the optimization of fluorophores and microscopy setups, quantifying multiple fluorophores requires algorithms that separate or unmix the contributions of the numerous fluorescent signals recorded at the single pixel level. This review aims to provide both the experimental scientist and the data analyst with a straightforward description of the evolution of spectral unmixing algorithms for fluorescence live-cell imaging. We show how the initial systems of linear equations used to determine the concentration of fluorophores in a pixel progressively evolved into matrix factorization, clustering, and deep learning approaches. We outline potential future trends on combining fluorescence spectral imaging with label-free detection methods, fluorescence lifetime imaging, and deep learning image analysis. DA - 2022/4// PY - 2022/4// DO - 10.1007/s12551-022-00941-x UR - https://doi.org/10.1007/s12551-022-00941-x ER - TY - JOUR TI - Cell cycle–independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry AU - Argüello-Miranda, Orlando AU - Marchand, Ashley J. AU - Kennedy, Taylor AU - Russo, Marielle A.X. AU - Noh, Jungsik T2 - Journal of Cell Biology AB - Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0. DA - 2022/1/3/ PY - 2022/1/3/ DO - 10.1083/jcb.202103171 VL - 221 IS - 1 UR - https://doi.org/10.1083/jcb.202103171 ER - TY - JOUR TI - Cdc14 spatiotemporally dephosphorylates Atg13 to activate autophagy during meiotic divisions AU - Feng, Wenzhi AU - Arguello-Miranda, Orlando AU - Qian, Suhong AU - Wang, Fei T2 - JOURNAL OF CELL BIOLOGY AB - Autophagy is a conserved eukaryotic lysosomal degradation pathway that responds to environmental and cellular cues. Autophagy is essential for the meiotic exit and sporulation in budding yeast, but the underlying molecular mechanisms remain unknown. Here, we show that autophagy is maintained during meiosis and stimulated in anaphase I and II. Cells with higher levels of autophagy complete meiosis faster, and genetically enhanced autophagy increases meiotic kinetics and sporulation efficiency. Strikingly, our data reveal that the conserved phosphatase Cdc14 regulates meiosis-specific autophagy. Cdc14 is activated in anaphase I and II, accompanying its subcellular relocation from the nucleolus to the cytoplasm, where it dephosphorylates Atg13 to stimulate Atg1 kinase activity and thus autophagy. Together, our findings reveal a meiosis-tailored mechanism that spatiotemporally controls meiotic autophagy activity to ensure meiosis progression, exit, and sporulation. DA - 2022/3/3/ PY - 2022/3/3/ DO - 10.1083/jcb.202107151 VL - 221 IS - 5 SP - SN - 1540-8140 UR - https://doi.org/10.1083/jcb.202107151 ER - TY - JOUR TI - Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites AU - Sandy, Moriah AU - Bui, Tina I. AU - Aba, Kenia Segura AU - Ruiz, Nestor AU - Paszalek, John AU - Connor, Elise W. AU - Hawkes, Christine V. T2 - MICROBIAL ECOLOGY DA - 2022/6/17/ PY - 2022/6/17/ DO - 10.1007/s00248-022-02057-x VL - 6 SP - SN - 1432-184X UR - https://doi.org/10.1007/s00248-022-02057-x KW - Endophyte KW - Leaf KW - Metabolomics KW - Panicum virgatum KW - Switchgrass ER - TY - JOUR TI - Deciphering the molecular basis of tissue-specific gene expression in plants: Can synthetic biology help? AU - Yaschenko, Anna E. AU - Fenech, Mario AU - Mazzoni-Putman, Serina AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - CURRENT OPINION IN PLANT BIOLOGY AB - Gene expression differences between distinct cell types are orchestrated by specific sets of transcription factors and epigenetic regulators acting upon the genome. In plants, the mechanisms underlying tissue-specific gene activity remain largely unexplored. Although transcriptional and epigenetic profiling of individual organs, tissues, and more recently, of single cells can easily detect the molecular signatures of different biological samples, how these unique cell identities are established at the mechanistic level is only beginning to be decoded. Computational methods, including machine learning, used in combination with experimental approaches, enable the identification and validation of candidate cis-regulatory elements driving cell-specific expression. Synthetic biology shows great promise not only as a means of testing candidate DNA motifs but also for establishing the general rules of nature driving promoter architecture and for the rational design of genetic circuits in research and agriculture to confer tissue-specific expression to genes or molecular pathways of interest. DA - 2022/8// PY - 2022/8// DO - 10.1016/j.pbi.2022.102241 VL - 68 SP - SN - 1879-0356 UR - https://doi.org/10.1016/j.pbi.2022.102241 KW - Tissue specificity KW - Gene expression KW - Synthetic biology KW - Transcription KW - factor KW - Epigenetics KW - Single cell KW - Transcriptomics KW - Logic gate KW - Promoter KW - Cis-regulatory element ER - TY - JOUR TI - Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus AU - Zhao, Yu AU - Yuan, Zhibo AU - Wang, Shuang AU - Wang, Haoyu AU - Chao, Yanjie AU - Sederoff, Ronald R. AU - Sederoff, Heike AU - Yan, He AU - Pan, Jialiang AU - Peng, Mu AU - Wu, Di AU - Borriss, Rainer AU - Niu, Ben T2 - FRONTIERS IN MICROBIOLOGY AB - Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus. DA - 2022/// PY - 2022/// DO - 10.3389/fmicb.2022.870519 VL - 5 KW - sdaB KW - L-serine dehydratase KW - Enterobacter ludwigii KW - nematocidal activity KW - Bursaphelenchus xylophilus KW - pine wilt disease KW - methuosis ER - TY - JOUR TI - Cdc14 plans autophagy for meiotic cell divisions AU - Feng, Wenzhi AU - Arguello-Miranda, Orlando AU - Qian, Suhong AU - Wang, Fei T2 - AUTOPHAGY AB - The role of meiotic proteasome-mediated degradation has been extensively studied. At the same time, macroautophagy/autophagy only emerged recently as an essential regulator for meiosis progression. Our recent publication showed that autophagy in meiotic cells exhibits a temporal pattern distinct from that in quiescent cells or mitotic cells under prolonged starvation. Importantly, autophagic activity oscillates during meiotic cell divisions, i.e., meiosis I and meiosis II, which can accelerate meiotic progression and increase sporulation efficiency. Our in vitro and in vivo assays revealed that the conserved phosphatase Cdc14 stimulates autophagy initiation during meiotic divisions, specifically in anaphase I and II, when a subpopulation of active Cdc14 relocates to the cytosol and interacts with phagophore assembly sites (PAS) triggering the dephosphorylation of Atg13 to stimulate Atg1 kinase activity and autophagy. Together, our findings reveal a mechanism for the coordination of autophagy activity in the context of meiosis progression. DA - 2022/5/28/ PY - 2022/5/28/ DO - 10.1080/15548627.2022.2080956 VL - 18 IS - 6 SP - SN - 1554-8635 UR - https://doi.org/10.1080/15548627.2022.2080956 KW - Atg1 KW - Atg13 KW - autophagy KW - Cdc14 KW - meiosis KW - phosphatase KW - sporulation ER - TY - JOUR TI - Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere AU - Liu, Bin-Bin AU - Ren, Chen AU - Kwak, Myounghai AU - Hodel, Richard G. J. AU - Xu, Chao AU - He, Jian AU - Zhou, Wen-Bin AU - Huang, Chien-Hsun AU - Ma, Hong AU - Qian, Guan-Ze AU - Hong, De-Yuan AU - Wen, Jun T2 - JOURNAL OF INTEGRATIVE PLANT BIOLOGY AB - Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets. DA - 2022/5// PY - 2022/5// DO - 10.1111/jipb.13246 VL - 64 IS - 5 SP - 1020-1043 SN - 1744-7909 KW - deep genome skimming KW - genomic discordance KW - historical biogeography KW - massive extinction KW - reticulate evolution KW - single-copy nuclear genes ER - TY - JOUR TI - Lessons for a SECURE Future: Evaluating Diversity in Crop Biotechnology Across Regulatory Regimes AU - George, Dalton R. AU - Hornstein, Eli D. AU - Clower, Carrie A. AU - Coomber, Allison L. AU - Dillard, DeShae AU - Mugwanya, Nassib AU - Pezzini, Daniela T. AU - Rozowski, Casey T2 - FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY AB - Regulation of next-generation crops in the United States under the newly implemented "SECURE" rule promises to diversify innovation in agricultural biotechnology. Specifically, SECURE promises to expand the number of products eligible for regulatory exemption, which proponents theorize will increase the variety of traits, genes, organisms, and developers involved in developing crop biotechnology. However, few data-driven studies have looked back at the history of crop biotechnology to understand how specific regulatory pathways have affected diversity in crop biotechnology and how those patterns might change over time. In this article, we draw upon 30 years of regulatory submission data to 1) understand historical diversification trends across the landscape and history of past crop biotechnology regulatory pathways and 2) forecast how the new SECURE regulations might affect future diversification trends. Our goal is to apply an empirical approach to exploring the relationship between regulation and diversity in crop biotechnology and provide a basis for future data-driven analysis of regulatory outcomes. Based on our analysis, we suggest that diversity in crop biotechnology does not follow a single trajectory dictated by the shifts in regulation, and outcomes of SECURE might be more varied and restrictive despite the revamped exemption categories. In addition, the concept of confidential business information and its relationship to past and future biotechnology regulation is reviewed in light of our analysis. DA - 2022/5/2/ PY - 2022/5/2/ DO - 10.3389/fbioe.2022.886765 VL - 10 SP - SN - 2296-4185 KW - crop biotechnology KW - SECURE rule KW - regulation KW - diversity trends KW - innovation KW - United States ER - TY - JOUR TI - Enhancing HR Frequency for Precise Genome Editing in Plants AU - Chen, Hao AU - Neubauer, Matthew AU - Wang, Jack P. T2 - FRONTIERS IN PLANT SCIENCE AB - Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems. DA - 2022/5/3/ PY - 2022/5/3/ DO - 10.3389/fpls.2022.883421 VL - 13 SP - SN - 1664-462X KW - homologous recombination KW - homology-directed repair KW - gene targeting KW - donor template KW - programmable nucleases ER - TY - JOUR TI - A viewpoint on ecological and evolutionary study of plant thermal performance curves in a warming world AU - Wooliver, Rachel AU - Vtipilthorpe, Emma E. AU - Wiegmann, Amelia M. AU - Sheth, Seema N. T2 - AOB PLANTS AB - We can understand the ecology and evolution of plant thermal niches through thermal performance curves (TPCs), which are unimodal, continuous reaction norms of performance across a temperature gradient. Though there are numerous plant TPC studies, plants remain under-represented in syntheses of TPCs. Further, few studies quantify plant TPCs from fitness-based measurements (i.e. growth, survival and reproduction at the individual level and above), limiting our ability to draw conclusions from the existing literature about plant thermal adaptation. We describe recent plant studies that use a fitness-based TPC approach to test fundamental ecological and evolutionary hypotheses, some of which have uncovered key drivers of climate change responses. Then, we outline three conceptual questions in ecology and evolutionary biology for future plant TPC studies: (i) Do populations and species harbour genetic variation for TPCs? (ii) Do plant TPCs exhibit plastic responses to abiotic and biotic factors? (iii) Do fitness-based TPCs scale up to population-level thermal niches? Moving forward, plant ecologists and evolutionary biologists can capitalize on TPCs to understand how plasticity and adaptation will influence plant responses to climate change. DA - 2022/5/23/ PY - 2022/5/23/ DO - 10.1093/aobpla/plac016 VL - 14 IS - 3 SP - SN - 2041-2851 KW - Climate change KW - evolutionary ecology KW - genetic variation KW - plasticity KW - thermal adaptation KW - thermal niche KW - thermal performance curve KW - trade-off ER - TY - JOUR TI -

Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E

AU - Zhu, Yue AU - Scholle, Frank AU - Kisthardt, Samantha C. AU - Xie, De-Yu T2 - VIROLOGY AB - Since December 2019, the deadly novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the current COVID-19 pandemic. To date, vaccines are available in the developed countries to prevent the infection of this virus; however, medicines are necessary to help control COVID-19. Human coronavirus 229E (HCoV-229E) causes the common cold. The main protease (Mpro) is an essential enzyme required for the multiplication of these two viruses in the host cells, and thus is an appropriate candidate to screen potential medicinal compounds. Flavonols and dihydroflavonols are two groups of plant flavonoids. In this study, we report docking simulation with two Mpro enzymes and five flavonols and three dihydroflavonols, in vitro inhibition of the SARS-CoV-2 Mpro, and in vitro inhibition of the HCoV 229E replication. The docking simulation results predicted that (+)-dihydrokaempferol, (+)- dihydroquercetin, (+)-dihydromyricetin, kaempferol, quercetin, myricentin, isoquercitrin, and rutin could bind to at least two subsites (S1, S1', S2, and S4) in the binding pocket and inhibit the activity of SARS-CoV-2 Mpro. Their affinity scores ranged from -8.8 to -7.4 (kcal/mol). Likewise, these compounds were predicted to bind and inhibit the HCoV-229E Mpro activity with affinity scores ranging from -7.1 to -7.8 (kcal/mol). In vitro inhibition assays showed that seven available compounds effectively inhibited the SARS-CoV-2 Mpro activity and their IC50 values ranged from 0.125 to 12.9 μM. Five compounds inhibited the replication of HCoV-229E in Huh-7 cells. These findings indicate that these antioxidative flavonols and dihydroflavonols are promising candidates for curbing the two viruses. DA - 2022/6// PY - 2022/6// DO - 10.1016/j.virol.2022.04.005 VL - 571 SP - 21-33 SN - 1089-862X KW - (+)-dihydrokaempferol KW -

(+)-dihydroquercetin (taxifolin)

KW - (+)-dihydromyricetin KW - Kaempferol KW - Quercetin KW - Myricentin KW - Isoquercitrin KW - Rutin KW - Flavan-3-ols ER - TY - JOUR TI - Single-well push-pull tests evaluating isobutane as a primary substrate for promoting in situ cometabolic biotransformation reactions AU - Rolston, Hannah AU - Hyman, Michael AU - Semprini, Lewis T2 - BIODEGRADATION DA - 2022/5/12/ PY - 2022/5/12/ DO - 10.1007/s10532-022-09987-w VL - 5 SP - SN - 1572-9729 UR - https://doi.org/10.1007/s10532-022-09987-w KW - Cometabolism KW - Push-pull tests KW - Isobutane KW - Isobutene KW - 1 KW - 1-Dichloroethene KW - 1 KW - 4-Dioxane ER - TY - JOUR TI - De novo phytosterol synthesis in animals AU - Michellod, Dolma AU - Bien, Tanja AU - Birgel, Daniel AU - Jensen, Marlene AU - Kleiner, Manuel AU - Fearn, Sarah AU - Zeidler, Caroline AU - Gruber-Vodicka, Harald R AU - Dubilier, Nicole AU - Liebeke, Manuel AB - Abstract Sterols are lipids that regulate multiple processes in eukaryotic cells, and are essential components of cellular membranes. Sterols are currently assumed to be kingdom specific, with phytosterol synthesis restricted to plants while animals are only able to synthesize cholesterol. Here, we challenge this assumption by demonstrating that the marine annelids Olavius and Inanidrilus synthesize the phytosterol sitosterol de novo . Using multi-omics, high-resolution metabolite imaging, heterologous gene expression and enzyme assays, we show that sitosterol is the most abundant (60%) sterol in these animals and characterize its biosynthetic pathway. We show that phytosterol synthesis partially overlaps with cholesterol synthesis and involves a non-canonical C-24 sterol methyltransferase (C 24 -SMT). C 24 -SMT is an essential enzyme for sitosterol synthesis in plants, but not known from animals with bilateral symmetry (bilaterians). Our comparative phylogenetic analyses of C 24 -SMT homologs revealed that these are widely distributed across annelids and other animal phyla, including sponges and rotifers. Our findings show that phytosterol synthesis and use is not restricted to the plant kingdom, and indicate that the evolution of sterols in animals is more complex than previously assumed. DA - 2022/4/22/ PY - 2022/4/22/ DO - 10.1101/2022.04.22.489198 VL - 4 UR - https://doi.org/10.1101/2022.04.22.489198 ER - TY - JOUR TI - We Can Dance If We Want To (with Safety Measures) AU - Carson, Susan T2 - MBIO AB - This work considers the spread of SARS-CoV-2 during a multiday intensive dance camp occurring from 26 December 2021 to 1 January 2022 in Asheville, North Carolina. Approximately 370 dancers and performers were in attendance, and the data presented are the result of an anonymous survey distributed 10 days following the event. DA - 2022/4/26/ PY - 2022/4/26/ DO - 10.1128/mbio.00295-22 VL - 13 IS - 2 SP - SN - 2150-7511 UR - https://doi.org/10.1128/mbio.00295-22 KW - COVID-19 KW - SARS-CoV-2 KW - Lindy Hop KW - public health KW - social gatherings KW - viral transmission ER - TY - JOUR TI - Protist Predation Influences the Temperature Response of Bacterial Communities AU - Rocca, Jennifer D. AU - Yammine, Andrea AU - Simonin, Marie AU - Gibert, Jean P. T2 - FRONTIERS IN MICROBIOLOGY AB - Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer-protists-influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species-Tetrahymena thermophila and Colpidium sp.-at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming. DA - 2022/4/7/ PY - 2022/4/7/ DO - 10.3389/fmicb.2022.847964 VL - 13 SP - SN - 1664-302X KW - predation KW - temperature KW - protistan bacterivory KW - bacterivores KW - aquatic microbiome KW - microbial respiration ER - TY - JOUR TI - Insights into acylation mechanisms: co-expression of serine carboxypeptidase-like acyltransferases and their non-catalytic companion paralogs AU - Yao, Shengbo AU - Liu, Yajun AU - Zhuang, Juhua AU - Zhao, Yue AU - Dai, Xinlong AU - Jiang, Changjuan AU - Wang, Zhihui AU - Jiang, Xiaolan AU - Zhang, Shuxiang AU - Qian, Yumei AU - Tai, Yuling AU - Wang, Yunsheng AU - Wang, Haiyan AU - Xie, De-Yu AU - Gao, Liping AU - Xia, Tao T2 - PLANT JOURNAL AB - Serine carboxypeptidase-like acyltransferases (SCPL-ATs) play a vital role in the diversification of plant metabolites. Galloylated flavan-3-ols highly accumulate in tea (Camellia sinensis), grape (Vitis vinifera), and persimmon (Diospyros kaki). To date, the biosynthetic mechanism of these compounds remains unknown. Herein, we report that two SCPL-AT paralogs are involved in galloylation of flavan-3-ols: CsSCPL4, which contains the conserved catalytic triad S-D-H, and CsSCPL5, which has the alternative triad T-D-Y. Integrated data from transgenic plants, recombinant enzymes, and gene mutations showed that CsSCPL4 is a catalytic acyltransferase, while CsSCPL5 is a non-catalytic companion paralog (NCCP). Co-expression of CsSCPL4 and CsSCPL5 is likely responsible for the galloylation. Furthermore, pull-down and co-immunoprecipitation assays showed that CsSCPL4 and CsSCPL5 interact, increasing protein stability and promoting post-translational processing. Moreover, phylogenetic analyses revealed that their homologs co-exist in galloylated flavan-3-ol- or hydrolyzable tannin-rich plant species. Enzymatic assays further revealed the necessity of co-expression of those homologs for acyltransferase activity. Evolution analysis revealed that the mutations of the CsSCPL5 catalytic residues may have taken place about 10 million years ago. These findings show that the co-expression of SCPL-ATs and their NCCPs contributes to the acylation of flavan-3-ols in the plant kingdom. DA - 2022/5/7/ PY - 2022/5/7/ DO - 10.1111/tpj.15782 VL - 5 SP - SN - 1365-313X KW - tea KW - serine carboxypeptidase-like acyltransferase KW - flavan-3-ol gallates KW - co-expression KW - galloylation KW - non-catalytic companion paralog ER - TY - JOUR TI - Anthocyanins from muscadine (Vitis rotundifolia) grape fruit AU - Yuzuak, Seyit AU - Xie, De-Yu T2 - CURRENT PLANT BIOLOGY AB - Muscadine grapes (Vitis rotundifolia) have multiple health benefits to human health. The high nutritional values of muscadine berries result from antioxidative anthocyanins and other phenolic compounds. Since the middle of the 18th century, muscadine grapes have been cropped in the southeastern United States. Early cultivars were selected from wild vines. To date, the breeding efforts have created more than 100 cultivars featured by different fruit pigmentations for wine, juice, or fresh market industries. Herein, we review features of anthocyanin profiles in muscadine berries and different final products. Main anthocyanidins include cyanidin, delphinidin, petunidin, peonidin, and malvidin. Pelargonidin has been also reported in certain types of varieties. Main anthocyanins are comprised of cyanin and delphinin, which derive from non-acylated 3,5-O-diglucosides of the main five anthocyanidins. In addition, minor pelargonin such as pelargonidin 3, 5-diglucoside and other minor anthocyanins have been identified in some cultivars. Moreover, we discussed biosynthesis of anthocyanins, color instability and intensity of anthocyanins, and effects of copigments such as proanthocyanidins on color stability and intensity of muscadine products. DA - 2022/4// PY - 2022/4// DO - 10.1016/j.cpb.2022.100243 VL - 30 SP - SN - 2214-6628 KW - Vitis rotundifolia KW - Muscadine KW - Grape KW - Polyphenols KW - Anthocyanins KW - Cyanin KW - Delphinin KW - Pelargonin ER - TY - JOUR TI - Molecular and biochemical characterization of two 4-coumarate: CoA ligase genes in tea plant (Camellia sinensis) AU - Li, Mingzhuo AU - Guo, Lili AU - Wang, Yeru AU - Li, Yanzhi AU - Jiang, Xiaolan AU - Liu, Yajun AU - Xie, De-Yu AU - Gao, Liping AU - Xia, Tao T2 - PLANT MOLECULAR BIOLOGY AB - Two 4-coumarate: CoA ligase genes in tea plant involved in phenylpropanoids biosynthesis and response to environmental stresses. Tea plant is rich in flavonoids benefiting human health. Lignin is essential for tea plant growth. Both flavonoids and lignin defend plants from stresses. The biosynthesis of lignin and flavonoids shares a key intermediate, 4-coumaroyl-CoA, which is formed from 4-coumaric acid catalyzed by 4-coumaric acid: CoA ligase (4CL). Herein, we report two 4CL paralogs from tea plant, Cs4CL1 and Cs4CL2, which are a member of class I and II of this gene family, respectively. Cs4CL1 was mainly expressed in roots and stems, while Cs4CL2 was mainly expressed in leaves. The promoter of Cs4CL1 had AC, nine types of light sensitive (LSE), four types of stress-inducible (SIE), and two types of meristem-specific elements (MSE). The promoter of Cs4CL2 also had AC and nine types of LSEs, but only had two types of SIEs and did not have MSEs. In addition, the LSEs varied in the two promoters. Based on the different features of regulatory elements, three stress treatments were tested to understand their expression responses to different conditions. The resulting data indicated that the expression of Cs4CL1 was sensitive to mechanical wounding, while the expression of Cs4CL2 was UV-B-inducible. Enzymatic assays showed that both recombinant Cs4CL1 and Cs4CL2 transformed 4-coumaric acid (CM), ferulic acid (FR), and caffeic acid (CF) to their corresponding CoA ethers. Kinetic analysis indicated that the recombinant Cs4CL1 preferred to catalyze CF, while the recombinant Cs4CL2 favored to catalyze CM. The overexpression of both Cs4CL1 and Cs4CL2 increased the levels of chlorogenic acid and total lignin in transgenic tobacco seedlings. In addition, the overexpression of Cs4CL2 consistently increased the levels of three flavonoid compounds. These findings indicate the differences of Cs4CL1 and Cs4CL2 in the phenylpropanoid metabolism. DA - 2022/5/12/ PY - 2022/5/12/ DO - 10.1007/s11103-022-01269-6 VL - 109 IS - 4-5 SP - SN - 1573-5028 UR - https://doi.org/10.1007/s11103-022-01269-6 KW - 4-Coumaric acid KW - CoA ligase KW - Flavonoids KW - Lignin KW - Metabolic engineering of phenylpropanoid KW - Stress ER - TY - JOUR TI - Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae AU - Shin, Hosub AU - Park, Jeong Eun AU - Park, Hye Rang AU - Choi, Woo Lee AU - Yu, Seung Hwa AU - Koh, Wonjun AU - Kim, Seungill AU - Soh, Hye Yeon AU - Waminal, Nomar Espinosa AU - Belandres, Hadassah Roa AU - Lim, Joo Young AU - Yi, Gibum AU - Ahn, Jong Hwa AU - Kim, June-Sik AU - Kim, Yong-Min AU - Koo, Namjin AU - Kim, Kyunghee AU - Perumal, Sampath AU - Kang, Taegu AU - Kim, Junghyo AU - Jang, Hosung AU - Kang, Dong Hyun AU - Kim, Ye Seul AU - Jeong, Hyeon-Min AU - Yang, Junwoo AU - Song, Somin AU - Park, Suhyoung AU - Kim, Jin A. AU - Lim, Yong Pyo AU - Park, Beom-Seok AU - Hsieh, Tzung-Fu AU - Yang, Tae-Jin AU - Choi, Doil AU - Kim, Hyun Hee AU - Lee, Soo-Seong AU - Huh, Jin Hoe T2 - NEW PHYTOLOGIST AB - Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species are rare in nature due to reproductive barriers but how such hurdles can be overcome is largely unknown. Here we report the hybrid genome structure of xBrassicoraphanus, a synthetic allotetraploid of Brassica rapa and Raphanus sativus. We performed cytogenetic analysis and de novo genome assembly to examine chromosome behaviors and genome integrity in the hybrid. Transcriptome analysis was conducted to investigate expression of duplicated genes in conjunction with epigenome analysis to address whether genome admixture entails epigenetic reconfiguration. Allotetraploid xBrassicoraphanus retains both parental chromosomes without genome rearrangement. Meiotic synapsis formation and chromosome exchange are avoided between nonhomologous progenitor chromosomes. Reconfiguration of transcription network occurs, and less divergent cis-elements of duplicated genes are associated with convergent expression. Genome-wide DNA methylation asymmetry between progenitors is largely maintained but, notably, B. rapa-originated transposable elements are transcriptionally silenced in xBrassicoraphanus through gain of DNA methylation. Our results demonstrate that hybrid genome stabilization and transcription compatibility necessitate epigenome landscape adjustment and rewiring of cis-trans interactions. Overall, this study suggests that a certain extent of genome divergence facilitates hybridization across species, which may explain the great diversification and expansion of angiosperms during evolution. DA - 2022/4/28/ PY - 2022/4/28/ DO - 10.1111/nph.18155 VL - 4 SP - SN - 1469-8137 KW - allopolyploidy KW - Brassicaceae KW - DNA methylation KW - epigenome KW - genome divergence KW - hybrid KW - xBrassicoraphanus ER - TY - JOUR TI - A de novo regulation design shows an effectiveness in altering plant secondary metabolism AU - Li, Mingzhuo AU - He, Xianzhi AU - La Hovary, Christophe AU - Zhu, Yue AU - Dong, Yilun AU - Liu, Shibiao AU - Xing, Hucheng AU - Liu, Yajun AU - Jie, Yucheng AU - Ma, Dongming AU - Yuzuak, Seyit AU - Xie, De-Yu T2 - JOURNAL OF ADVANCED RESEARCH AB - Transcription factors (TFs) and cis-regulatory elements (CREs) control gene transcripts involved in various biological processes. We hypothesize that TFs and CREs can be effective molecular tools for De Novo regulation designs to engineer plants. We selected two Arabidopsis TF types and two tobacco CRE types to design a De Novo regulation and evaluated its effectiveness in plant engineering. G-box and MYB recognition elements (MREs) were identified in four Nicotiana tabacum JAZs (NtJAZs) promoters. MRE-like and G-box like elements were identified in one nicotine pathway gene promoter. TF screening led to select Arabidopsis Production of Anthocyanin Pigment 1 (PAP1/MYB) and Transparent Testa 8 (TT8/bHLH). Two NtJAZ and two nicotine pathway gene promoters were cloned from commercial Narrow Leaf Madole (NL) and KY171 (KY) tobacco cultivars. Electrophoretic mobility shift assay (EMSA), cross-linked chromatin immunoprecipitation (ChIP), and dual-luciferase assays were performed to test the promoter binding and activation by PAP1 (P), TT8 (T), PAP1/TT8 together, and the PAP1/TT8/Transparent Testa Glabra 1 (TTG1) complex. A DNA cassette was designed and then synthesized for stacking and expressing PAP1 and TT8 together. Three years of field trials were performed by following industrial and GMO protocols. Gene expression and metabolic profiling were completed to characterize plant secondary metabolism. PAP1, TT8, PAP1/TT8, and the PAP1/TT8/TTG1 complex bound to and activated NtJAZ promoters but did not bind to nicotine pathway gene promoters. The engineered red P + T plants significantly upregulated four NtJAZs but downregulated the tobacco alkaloid biosynthesis. Field trials showed significant reduction of five tobacco alkaloids and four carcinogenic tobacco specific nitrosamines in most or all cured leaves of engineered P + T and PAP1 genotypes. G-boxes, MREs, and two TF types are appropriate molecular tools for a De Novo regulation design to create a novel distant-pathway cross regulation for altering plant secondary metabolism. DA - 2022/3// PY - 2022/3// DO - 10.1016/j.jare.2021.06.017 VL - 37 SP - 43-60 SN - 2090-1224 KW - Arabidopsis KW - Alkaloid KW - Anthocyanin KW - Molecular tools KW - Tobacco KW - Transcription factor ER - TY - JOUR TI - Diversity and Structure of Bacterial Communities in Different Rhizocompartments (Rhizoplane, Rhizosphere, and Bulk) at Flag Leaf Emergence in Four Winter Wheat Varieties AU - Zervas, Athanasios AU - Ellegaard-Jensen, Lea AU - Hennessy, Rosanna C. AU - Bak, Frederik AU - Guan, Ying AU - Horn Herms, Courtney AU - Molina Zamudio, Kitzia Yashvelt AU - Thybo Ganzhorn, Dorthe AU - Muller-Stover, Dorette Sophie AU - Ahmad, Jabeen AU - Grunden, Amy AU - Jacobsen, Carsten S. AU - Nicolaisen, Mette Haubjerg T2 - MICROBIOLOGY RESOURCE ANNOUNCEMENTS AB - Understanding basic interactions at the plant-soil interphase is critical if we are to exploit natural microbial communities for improved crop resilience. We report here 16S amplicon sequencing data from 3 rhizocompartments of 4 wheat cultivars grown under controlled greenhouse conditions. We observed that rhizocompartments and cultivar affect the community composition. DA - 2022/4/13/ PY - 2022/4/13/ DO - 10.1128/mra.00222-22 VL - 4 SP - SN - 2576-098X ER - TY - JOUR TI - Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs AU - Tong, Haonan AU - Chen, Hao AU - Williams, Cranos M. T2 - VIRUSES-BASEL AB - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that caused the coronavirus disease 2019 (COVID-19) pandemic. Though previous studies have suggested that SARS-CoV-2 cellular tropism depends on the host-cell-expressed proteins, whether transcriptional regulation controls SARS-CoV-2 tropism factors in human lung cells remains unclear. In this study, we used computational approaches to identify transcription factors (TFs) regulating SARS-CoV-2 tropism for different types of lung cells. We constructed transcriptional regulatory networks (TRNs) controlling SARS-CoV-2 tropism factors for healthy donors and COVID-19 patients using lung single-cell RNA-sequencing (scRNA-seq) data. Through differential network analysis, we found that the altered regulatory role of TFs in the same cell types of healthy and SARS-CoV-2-infected networks may be partially responsible for differential tropism factor expression. In addition, we identified the TFs with high centralities from each cell type and proposed currently available drugs that target these TFs as potential candidates for the treatment of SARS-CoV-2 infection. Altogether, our work provides valuable cell-type-specific TRN models for understanding the transcriptional regulation and gene expression of SARS-CoV-2 tropism factors. DA - 2022/4// PY - 2022/4// DO - 10.3390/v14040837 VL - 14 IS - 4 SP - SN - 1999-4915 KW - SARS-CoV-2 KW - single-cell RNA-seq KW - differential network analysis ER - TY - JOUR TI - RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry AU - Adhikari, Tika B. AU - Aryal, Rishi AU - Redpath, Lauren E. AU - Broeck, Lisa AU - Ashrafi, Hamid AU - Philbrick, Ashley N. AU - Jacobs, Raymond L. AU - Sozzani, Rosangela AU - Louws, Frank J. T2 - FRONTIERS IN GENETICS AB - Two hemibiotrophic pathogens, Colletotrichum acutatum (Ca) and C . gloeosporioides (Cg), cause anthracnose fruit rot and anthracnose crown rot in strawberry ( Fragaria × ananassa Duchesne), respectively. Both Ca and Cg can initially infect through a brief biotrophic phase, which is associated with the production of intracellular primary hyphae that can infect host cells without causing cell death and establishing hemibiotrophic infection (HBI) or quiescent (latent infections) in leaf tissues. The Ca and Cg HBI in nurseries and subsequent distribution of asymptomatic infected transplants to fruit production fields is the major source of anthracnose epidemics in North Carolina. In the absence of complete resistance, strawberry varieties with good fruit quality showing rate-reducing resistance have frequently been used as a source of resistance to Ca and Cg. However, the molecular mechanisms underlying the rate-reducing resistance or susceptibility to Ca and Cg are still unknown. We performed comparative transcriptome analyses to examine how rate-reducing resistant genotype NCS 10-147 and susceptible genotype ‘Chandler’ respond to Ca and Cg and identify molecular events between 0 and 48 h after the pathogen-inoculated and mock-inoculated leaf tissues. Although plant response to both Ca and Cg at the same timepoint was not similar, more genes in the resistant interaction were upregulated at 24 hpi with Ca compared with those at 48 hpi. In contrast, a few genes were upregulated in the resistant interaction at 48 hpi with Cg. Resistance response to both Ca and Cg was associated with upregulation of MLP-like protein 44, LRR receptor-like serine/threonine-protein kinase, and auxin signaling pathway, whereas susceptibility was linked to modulation of the phenylpropanoid pathway. Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions. Our results provide valuable insights into transcriptional changes during resistant and susceptible interactions, which can further facilitate assessing candidate genes necessary for resistance to two hemibiotrophic Colletotrichum spp. in strawberry. DA - 2022/3/10/ PY - 2022/3/10/ DO - 10.3389/fgene.2021.805771 VL - 12 SP - SN - 1664-8021 KW - Colletotrichum acutatum KW - Colletotrichum gloeosporioides KW - Fragaria x ananassa KW - rate-reducing resistance KW - gene regulatory network ER - TY - JOUR TI - Considerations for constructing a protein sequence database for metaproteomics AU - Blakeley-Ruiz, J. Alfredo AU - Kleiner, Manuel T2 - COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL AB - Mass spectrometry-based metaproteomics has emerged as a prominent technique for interrogating the functions of specific organisms in microbial communities, in addition to total community function. Identifying proteins by mass spectrometry requires matching mass spectra of fragmented peptide ions to a database of protein sequences corresponding to the proteins in the sample. This sequence database determines which protein sequences can be identified from the measurement, and as such the taxonomic and functional information that can be inferred from a metaproteomics measurement. Thus, the construction of the protein sequence database directly impacts the outcome of any metaproteomics study. Several factors, such as source of sequence information and database curation, need to be considered during database construction to maximize accurate protein identifications traceable to the species of origin. In this review, we provide an overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies. Based on this review of the literature and our experience we provide a decision tree and best practices for choosing and implementing database construction strategies. DA - 2022/// PY - 2022/// DO - 10.1016/j.csbj.2022.01.018 VL - 20 SP - 937-952 SN - 2001-0370 UR - http://dx.doi.org/10.1016/j.csbj.2022.01.018 KW - Metaproteome KW - Metagenomics KW - Microbiome KW - Microbial community KW - Multi-omics KW - Microbiota KW - Microbial ecology ER - TY - JOUR TI - BTS Is a Negative Regulator for the Cellular Energy Level and the Expression of Energy Metabolism-Related Genes Encoded by Two Organellar Genomes in Leaf Tissues AU - Choi, Bongsoo AU - Hyeon, Do Young AU - Lee, Juhun AU - Long, Terri A. AU - Hwang, Daehee AU - Hwang, Inhwan T2 - MOLECULES AND CELLS AB - E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana. The role of BTS in root tissues has been well established. However, its role in shoot tissues has been scarcely studied. Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. Moreover, in shoot tissues of bts-1 plants, levels of ADP and ATP and the ratio of ADP/ATP were greatly increased with a concomitant decrease in levels of soluble sugar and starch. The decreased starch level in bts-1 shoot tissues was restored to the level of shoot tissues of wild-type plants upon vanadate treatment. Through this study, we expand the role of BTS to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots. DA - 2022/4/15/ PY - 2022/4/15/ DO - 10.14348/molcells.2022.2029 VL - 4 SP - SN - 0219-1032 UR - https://doi.org/10.14348/molcells.2022.2029 KW - Arabidopsis thaliana KW - BRUTUS KW - energy metabolism KW - shoot tissues ER - TY - JOUR TI - Tandem C2 domains mediate dynamic organelle targeting of a DOCK family guanine nucleotide exchange factor AU - Mallery, Eileen L. AU - Yanagisawa, Makoto AU - Zhang, Chunhua AU - Lee, Youngwoo AU - Robles, Linda M. AU - Alonso, Jose M. AU - Szymanski, Daniel B. T2 - JOURNAL OF CELL SCIENCE AB - ABSTRACT Multicellular organisms use dedicator of cytokinesis (DOCK) family guanine nucleotide exchange factors (GEFs) to activate Rac/Rho-of-plants small GTPases and coordinate cell shape change. In developing tissues, DOCK signals integrate cell-cell interactions with cytoskeleton remodeling, and the GEFs cluster reversibly at specific organelle surfaces to orchestrate cytoskeletal reorganization. The domain organizations among DOCK orthologs are diverse, and the mechanisms of localization control are poorly understood. Here, we use combinations of transgene complementation and live-cell imaging assays to uncover an evolutionarily conserved and essential localization determinant in the DOCK-GEF named SPIKE1. The SPIKE1-DHR3 domain is sufficient for organelle association in vivo, and displays a complicated lipid-binding selectivity for both phospholipid head groups and fatty acid chain saturation. SPIKE1-DHR3 is predicted to adopt a C2-domain structure and functions as part of a tandem C2 array that enables reversible clustering at the cell apex. This work provides mechanistic insight into how DOCK GEFs sense compositional and biophysical membrane properties at the interface of two organelle systems. DA - 2022/4// PY - 2022/4// DO - 10.1242/jcs.259825 VL - 135 IS - 7 SP - SN - 1477-9137 UR - https://doi.org/10.1242/jcs.259825 KW - DOCK KW - Rac/Rho-of-plants KW - Lipid binding KW - Organelle association KW - Small GTPases ER - TY - JOUR TI - Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka AU - Noar, Roslyn D. AU - Thomas, Elizabeth AU - Daub, Margaret E. T2 - PLANTS-BASEL AB - The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease. DA - 2022/4// PY - 2022/4// DO - 10.3390/plants11070948 VL - 11 IS - 7 SP - SN - 2223-7747 UR - https://www.mdpi.com/2223-7747/11/7/948 KW - black Sigatoka KW - cell wall KW - dispensable chromosomes KW - Dothideomycetes KW - effectors KW - genomics KW - host resistance KW - pathogenicity KW - secondary metabolism ER - TY - JOUR TI - Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka AU - Noar, R.D. AU - Thomas, E. T2 - Plants AB - The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease. DA - 2022/3/31/ PY - 2022/3/31/ DO - https://doi.org/10.3390/plants11070948 UR - https://www.mdpi.com/2223-7747/11/7/948/htm ER - TY - JOUR TI - Metabolomic characterization of 5 native Peruvian chili peppers (Capsicum spp.) as a tool for species discrimination AU - Espichán, F. AU - Rojas, R. AU - Quispe, F. AU - Cabanac, G. AU - Marti, G. T2 - Food Chemistry AB - Many species of chili peppers have overlapping morphological characters and delimitation by visual descriptors in many cases fails to differentiate one species from another. In Peru, there are 413 accessions of native chili pepper and 296 accessions of rocotos conserved in the Germplasm Collections of the National Institute of Agrarian Innovation (INIA), of which five accessions (three species from three locations) were selected for the present metabolomic study. The Discrimination of the three species of native chili peppers and identification of biomarkers was performed using untargeted metabolomic approach based on profiling by UHPLC-HRMS and multivariate data analysis. The samples of fresh chili peppers (whole fruit) from Chincha area were used to construct an OPLS-DA model. To validate the biomarkers (identified 15 biomarkers, mainly flavonoids), an external validation set of the OPLS-DA model was constructed using Chiclayo and Huaral collection datasets. Consequently, the OPLS-DA based on Chincha samples model has a high predictive capacity demonstrating that the biomarkers have a high probability of continuity in any culture space, being successful in discriminating the species by untargeted metabolomics. DA - 2022/8/30/ PY - 2022/8/30/ DO - 10.1016/j.foodchem.2022.132704 VL - 386, 30 SP - 13274 UR - http://dx.doi.org/10.1016/j.foodchem.2022.132704 KW - Metabolomic KW - Capsicum KW - OPLS-DA KW - SUS-plot KW - Biomarkers KW - Peruvian native chili peppers ER - TY - JOUR TI - Microbes, memory and moisture: Predicting microbial moisture responses and their impact on carbon cycling AU - Evans, Sarah AU - Allison, Steven AU - Hawkes, Christine T2 - FUNCTIONAL ECOLOGY AB - Abstract Soil moisture is a major driver of microbial activity and thus, of the release of carbon (C) into the Earth's atmosphere. Yet, there is no consensus on the relationship between soil moisture and microbial respiration, and as a result, moisture response functions are a poorly constrained aspect of C models. In addition, models assume that the response of microbial respiration to moisture is the same for all ecosystems, regardless of climate history, an assumption that many empirical studies have challenged. These gaps in understanding of the microbial respiration response to moisture contribute to uncertainty in model predictions. We review our understanding of what drives microbial moisture response, highlighting evidence that historical precipitation can influence both responses to moisture and sensitivity to drought. We present two hypotheses, the ‘climate history hypothesis’, where we predict that baseline moisture response functions change as a function of precipitation history, and the ‘drought legacy hypothesis’, in which we suggest that the intensity and frequency of historical drought have shaped microbial communities in ways that will control moisture responses to contemporary drought. Underlying mechanisms include biological selection and filtering of the microbial community by rainfall regimes, which result in microbial traits and trade‐offs that shape function. We present an integrated modelling and empirical approach for understanding microbial moisture responses and improving models. Standardized measures of moisture response (respiration rate across a range of moistures) and accompanying microbial properties are needed across sites. These data can be incorporated into trait‐based models to produce generalized moisture response functions, which can then be validated and incorporated into conventional and microbially explicit ecosystem models of soil C cycling. Future studies should strive to analyse realistic moisture conditions and consider the role of environmental factors and soil structure in microbial response. Microbes are the engines that drive C storage and are sensitive to changes in rainfall. A greater understanding of the factors that govern this sensitivity could be a key part of improving predictions of soil C dynamics, climate change and C‐climate feedbacks. Read the free Plain Language Summary for this article on the Journal blog. DA - 2022/3/20/ PY - 2022/3/20/ DO - 10.1111/1365-2435.14034 VL - 3 SP - SN - 1365-2435 UR - https://doi.org/10.1111/1365-2435.14034 KW - carbon KW - drought KW - legacy KW - microbial communities KW - modelling KW - rainfall KW - respiration KW - soil ER - TY - JOUR TI - Early detection of plant virus infection using multispectral imaging and spatial-spectral machine learning AU - Peng, Yao AU - Dallas, Mary M. AU - Ascencio-Ibanez, Jose T. AU - Hoyer, J. Steen AU - Legg, James AU - Hanley-Bowdoin, Linda AU - Grieve, Bruce AU - Yin, Hujun T2 - SCIENTIFIC REPORTS AB - Abstract Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers’ access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses. DA - 2022/2/24/ PY - 2022/2/24/ DO - 10.1038/s41598-022-06372-8 VL - 12 IS - 1 SP - SN - 2045-2322 ER - TY - JOUR TI - Organic solar powered greenhouse performance optimization and global economic opportunity AU - Ravishankar, Eshwar AU - Booth, Ronald E. AU - Hollingsworth, Joseph A. AU - Ade, Harald AU - Sederoff, Heike AU - DeCarolis, Joseph F. AU - Brendan T. O'Connor, T2 - ENERGY & ENVIRONMENTAL SCIENCE AB - This work integrates greenhouse energy demand, solar power production, and plant growth modeling to assess the economic opportunity of organic solar powered greenhouses. Results show these systems have positive economic outlook across broad climates. DA - 2022/3/10/ PY - 2022/3/10/ DO - 10.1039/D1EE03474J VL - 15 IS - 4 SP - SN - 1754-5706 UR - https://doi.org/10.1039/D1EE03474J ER - TY - JOUR TI - Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development AU - Ortiz, Anna C. AU - De Smet, Ive AU - Sozzani, Rosangela AU - Locke, Anna M. T2 - ENVIRONMENTAL AND EXPERIMENTAL BOTANY AB - An average temperature increase between 2.6 and 4.8 °C, along with more frequent extreme temperatures, will challenge crop productivity by the end of the century. To investigate genotypic variation in soybean response to elevated temperature, six soybean (Glycine max) genotypes were subjected to elevated air temperature of + 4.5 °C above ambient for 28 days in open-top field chambers. Gas exchange and chlorophyll fluorescence were measured before and during heating and yield as well as seed composition were evaluated at maturity. Results show that long-term elevated air temperature increased nighttime respiration, increased the maximum velocity of carboxylation by Rubisco, impacted seed protein concentration, and reduced seed oil concentration across genotypes. The genotypes in this study varied in temperature responses for photosynthetic CO2 assimilation, stomatal conductance, photosystem II operating efficiency, quantum efficiency of CO2 assimilation, and seed protein concentration at maturity. These diverse responses among genotypes to elevated air temperature during seed development in the field, reveal the potential for soybean heat tolerance to be improved through breeding and underlines the importance of identifying efficient selection strategies for stress-tolerant crops. DA - 2022/3// PY - 2022/3// DO - 10.1016/j.envexpbot.2021.104768 VL - 195 SP - SN - 1873-7307 KW - Photosynthesis KW - V-cmax KW - Respiration KW - Yield KW - Seed composition ER - TY - JOUR TI - A New Pipeline for Removing Paralogs in Target Enrichment Data AU - Zhou, Wenbin AU - Soghigian, John AU - Xiang, Qiu-Yun Jenny T2 - SYSTEMATIC BIOLOGY AB - Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperms353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of data sets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene data sets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperms353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. [Angiosperms353; Castanea; divergence time; Hamamelis; Hyb-Seq, paralogs, phylogenomics.]. DA - 2022/2/10/ PY - 2022/2/10/ DO - 10.1093/sysbio/syab044 VL - 71 IS - 2 SP - 410-425 SN - 1076-836X ER - TY - JOUR TI - An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing AU - Aimone, Catherine D. AU - Hoyer, J. Steen AU - Dye, Anna E. AU - Deppong, David O. AU - Duffy, Siobain AU - Carbone, Ignazio AU - Hanley-Bowdoin, Linda T2 - JOURNAL OF VIROLOGICAL METHODS AB - The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses. DA - 2022/2// PY - 2022/2// DO - 10.1016/j.jviromet.2021.114405 VL - 300 SP - SN - 1879-0984 UR - http://dx.doi.org/10.1016/j.jviromet.2021.114405 KW - Phi29 KW - EquiPhi29 KW - MiSeq KW - Whiteflies KW - Viral DNA sequencing ER - TY - JOUR TI - Next Steps in Integrative Biology: Mapping Interactive Processes Across Levels of Biological Organization AU - Cavigelli, Sonia AU - Leips, Jeff AU - Xiang, Qiu-Yun AU - Lemke, Dawn AU - Konow, Nicolai T2 - INTEGRATIVE AND COMPARATIVE BIOLOGY AB - Emergent biological processes result from complex interactions within and across levels of biological organization, ranging from molecular to environmental dynamics. Powerful theories, database tools, and modeling methods have been designed to characterize network connections within levels, such as those among genes, proteins, biochemicals, cells, organisms, and species. Here, we propose that developing integrative models of organismal function in complex environments can be facilitated by taking advantage of these methods to identify key nodes of communication across levels of organization. Mapping key drivers or connections among levels of organization will provide data and leverage to model potential rule-sets by which organisms respond and adjust to perturbations at any level of biological organization. DA - 2022/2/5/ PY - 2022/2/5/ DO - 10.1093/icb/icab161 VL - 61 IS - 6 SP - 2066-2074 SN - 1557-7023 ER - TY - JOUR TI - Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques AU - Walsh, Evan S. AU - Tollison, Tammy S. AU - Brochu, Hayden N. AU - Shaw, Brian I AU - Diveley, Kayleigh R. AU - Chou, Hsuan AU - Law, Lynn AU - Kirk, Allan D. AU - Gale, Michael, Jr. AU - Peng, Xinxia T2 - JOURNAL OF IMMUNOLOGY AB - Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level. DA - 2022/2/1/ PY - 2022/2/1/ DO - 10.4049/jimmunol.2100824 VL - 208 IS - 3 SP - 762-771 SN - 1550-6606 ER - TY - JOUR TI - The evolution of thermal performance in native and invasive populations of Mimulus guttatus AU - Querns, Aleah AU - Wooliver, Rachel AU - Vallejo-Marin, Mario AU - Sheth, Seema Nayan T2 - EVOLUTION LETTERS AB - The rise of globalization has spread organisms beyond their natural range, allowing further opportunity for species to adapt to novel environments and potentially become invaders. Yet, the role of thermal niche evolution in promoting the success of invasive species remains poorly understood. Here, we use thermal performance curves (TPCs) to test hypotheses about thermal adaptation during the invasion process. First, we tested the hypothesis that if species largely conserve their thermal niche in the introduced range, invasive populations may not evolve distinct TPCs relative to native populations, against the alternative hypothesis that thermal niche and therefore TPC evolution has occurred in the invasive range. Second, we tested the hypothesis that clines of TPC parameters are shallower or absent in the invasive range, against the alternative hypothesis that with sufficient time, standing genetic variation, and temperature-mediated selection, invasive populations would re-establish clines found in the native range in response to temperature gradients. To test these hypotheses, we built TPCs for 18 native (United States) and 13 invasive (United Kingdom) populations of the yellow monkeyflower, Mimulus guttatus. We grew clones of multiple genotypes per population at six temperature regimes in growth chambers. We found that invasive populations have not evolved different thermal optima or performance breadths, providing evidence for evolutionary stasis of thermal performance between the native and invasive ranges after over 200 years post introduction. Thermal optimum increased with mean annual temperature in the native range, indicating some adaptive differentiation among native populations that was absent in the invasive range. Further, native and invasive populations did not exhibit adaptive clines in thermal performance breadth with latitude or temperature seasonality. These findings suggest that TPCs remained unaltered post invasion, and that invasion may proceed via broad thermal tolerance and establishment in already climatically suitable areas rather than rapid evolution upon introduction. DA - 2022/2/13/ PY - 2022/2/13/ DO - 10.1002/evl3.275 VL - 2 SP - SN - 2056-3744 UR - https://doi.org/10.1002/evl3.275 KW - Adaptive divergence KW - evolutionary ecology KW - invasion ecology KW - latitudinal gradient KW - niche conservatism KW - phenotypic cline KW - thermal performance curve KW - thermal tolerance ER - TY - JOUR TI - To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses AU - Chen, Hao AU - Bullock, David A., Jr. AU - Alonso, Jose M. AU - Stepanova, Anna N. T2 - PLANTS-BASEL AB - Plants often live in adverse environmental conditions and are exposed to various stresses, such as heat, cold, heavy metals, salt, radiation, poor lighting, nutrient deficiency, drought, or flooding. To adapt to unfavorable environments, plants have evolved specialized molecular mechanisms that serve to balance the trade-off between abiotic stress responses and growth. These mechanisms enable plants to continue to develop and reproduce even under adverse conditions. Ethylene, as a key growth regulator, is leveraged by plants to mitigate the negative effects of some of these stresses on plant development and growth. By cooperating with other hormones, such as jasmonic acid (JA), abscisic acid (ABA), brassinosteroids (BR), auxin, gibberellic acid (GA), salicylic acid (SA), and cytokinin (CK), ethylene triggers defense and survival mechanisms thereby coordinating plant growth and development in response to abiotic stresses. This review describes the crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses. DA - 2022/1// PY - 2022/1// DO - 10.3390/plants11010033 VL - 11 IS - 1 SP - SN - 2223-7747 KW - ethylene KW - abiotic stress KW - hormone crosstalk KW - growth and defense tradeoff ER - TY - JOUR TI - Phylogenomics and biogeography of Torreya (Taxaceae)-Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq AU - Zhou, Wenbin AU - Harris, A. J. AU - Xiang, Qiu-Yun T2 - JOURNAL OF SYSTEMATICS AND EVOLUTION AB - Abstract Restriction site‐associated DNA sequencing (RAD‐seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD‐seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RAD‐seq Allele Dropout Remedy in our study of the gymnosperm genus, Torreya , to mitigate ADO in outgroups by recovering missing loci from previously published transcriptomes. By using RADADOR to supplement Rad‐seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records, we reconstructed the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian‐North American floristic disjunction. Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya . Using the fossilized birth–death model and divergence–extinction–cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid‐Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the “out of NA” pattern common to gymnosperms and to the “out of EA” hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii , suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii . DA - 2022/5/30/ PY - 2022/5/30/ DO - 10.1111/jse.12838 VL - 2 SP - SN - 1759-6831 UR - https://doi.org/10.1111/jse.12838 KW - Angiosperms353 KW - eastern Asian-North American disjunction KW - fossilized birth-death model KW - phylogenetic discordance KW - plastid genome sequences ER - TY - JOUR TI - Not all trees can make a forest: Tree species composition and competition control forest encroachment in a tropical savanna AU - Flake, Samuel W. AU - Honda, Eliane A. AU - Pilon, Natashi A. L. AU - Hoffmann, William A. AU - Durigan, Giselda T2 - JOURNAL OF ECOLOGY AB - Abstract Forest encroachment into savannas is a widespread phenomenon, the rate of which may depend on soil conditions, species composition or changes in stand structure. As savanna specialist trees are replaced by generalist species, rates of stand development may increase. Because generalists can persist in forests, they are likely to grow more quickly and survive longer in dense stands, compared to savanna specialists. Furthermore, the faster growth rates of generalists may allow them to overtop and outcompete savanna specialists, causing rapid species turnover. We measured growth and survival of 6,147 individuals of 112 species of savanna and generalist tree species over a period of 10 years in an ecological reserve in Assis, São Paulo State, Brazil. We modelled growth and mortality as a function of soil texture and nutrients, tree size, competitive neighbourhood, and membership in savanna or generalist (species which can persist in forests and savannas) functional groups. Tree growth and survival was strongly influenced by competition, as estimated by the basal area of trees taller than a focal tree. At the stand level, savanna species are unable to contribute basal area growth in closed stands, while generalist species continue to increase in basal area even at high stand basal area. This phenomenon is driven by differences in growth and mortality. Generalists grew faster than savanna species, both in height and diameter. This difference in growth rates led to savanna species becoming suppressed more rapidly than generalists. When suppressed, savanna species were more than twice as likely to die than were generalists. Soils had inconsistent and mostly weak effects which were difficult to separate from gradients of stand structure. Synthesis . We demonstrate that the presence of generalist trees accelerates the rates of basal area accumulation due to their greater growth rates and tolerance of shading. Generalists outcompete savanna trees by growing faster in the open and overtopping savanna specialists. Due to the slow growth and high mortality of savanna species in the shade, they are unable to form closed‐canopy stands. Accounting for differences among functional types and development of vegetation structure is critical for modelling forest encroachment. DA - 2022/1/20/ PY - 2022/1/20/ DO - 10.1111/1365-2745.13820 SP - SN - 1365-2745 KW - Cerrado KW - competition KW - forest encroachment KW - stand development KW - tree growth KW - tree mortality KW - woody encroachment ER - TY - JOUR TI - Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation AU - Thomas, Hannah AU - Broeck, Lisa AU - Spurney, Ryan AU - Sozzani, Rosangela AU - Frank, Margaret T2 - PLANT CELL AB - Grafting has been adopted for a wide range of crops to enhance productivity and resilience; for example, grafting of Solanaceous crops couples disease-resistant rootstocks with scions that produce high-quality fruit. However, incompatibility severely limits the application of grafting and graft incompatibility remains poorly understood. In grafts, immediate incompatibility results in rapid death, but delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system using heterografting of tomato (Solanum lycopersicum) and pepper (Capsicum annuum). These grafted plants express signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation, we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we inferred gene regulatory networks for compatible self-grafts and incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we examined the role of vascular development in graft formation and uncovered SlWOX4 as a potential regulator of graft compatibility. Following this predicted regulator up with functional analysis, we show that Slwox4 homografts fail to form xylem bridges across the junction, demonstrating that indeed, SlWOX4 is essential for vascular reconnection during grafting, and may function as an early indicator of graft failure. DA - 2022/1// PY - 2022/1// DO - 10.1093/plcell/koab246 VL - 34 IS - 1 SP - 535-556 SN - 1532-298X UR - https://doi.org/10.1093/plcell/koab246 ER - TY - JOUR TI - Plasma-driven biocatalysis: In situ hydrogen peroxide production with an atmospheric pressure plasma jet increases the performance of OleT(JE) when compared to adding the same molar amount of hydrogen peroxide in bolus AU - Wapshott-Stehli, Hannah L. AU - Myers, Brayden G. AU - Quesada, Maria J. Herrera AU - Grunden, Amy AU - Stapelmann, Katharina T2 - PLASMA PROCESSES AND POLYMERS AB - Abstract Enzymes like fatty acid peroxygenase OleT JE are desirable enzymes for the industry. While they require inexpensive hydrogen peroxide for activity, the same hydrogen peroxide also causes overoxidation of their reactive heme center. Here, we generate hydrogen peroxide slowly in situ using the Cooperation in Science and Technology (COST)‐Jet, an atmospheric pressure plasma jet, to avoid overoxidizing OleT JE . The COST‐Jet was operated in helium with a water admixture to provide hydrogen peroxide for OleT JE activity. This helium/water admixture produced the highest enzyme turnover numbers after 2 min of treatment. These turnover numbers were even superior to using an equimolar amount of hydrogen peroxide to treat the enzymes exogenously, showing that this plasma source can provide a reliable amount of reaction mediator to support OleT JE activity. DA - 2022/2/3/ PY - 2022/2/3/ DO - 10.1002/ppap.202100160 VL - 2 SP - SN - 1612-8869 UR - https://doi.org/10.1002/ppap.202100160 KW - atmospheric pressure plasma jet KW - biocatalysis KW - cytochrome P450 enzymes KW - hydrogen peroxide KW - plasma liquid chemistry ER - TY - JOUR TI - Rcompadre and Rage-Two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life-history traits from matrix population models AU - Jones, Owen R. AU - Barks, Patrick AU - Stott, Iain AU - James, Tamora D. AU - Levin, Sam AU - Petry, William K. AU - Capdevila, Pol AU - Che-Castaldo, Judy AU - Jackson, John AU - Romer, Gesa AU - Schuette, Caroline AU - Thomas, Chelsea C. AU - Salguero-Gomez, Roberto T2 - METHODS IN ECOLOGY AND EVOLUTION AB - Abstract Matrix population models (MPMs) are an important tool for biologists seeking to understand the causes and consequences of variation in vital rates (e.g. survival, reproduction) across life cycles. Empirical MPMs describe the age‐ or stage‐structured demography of organisms and usually represent the life history of a population during a particular time frame at a specific geographical location. The COMPADRE Plant Matrix Database and COMADRE Animal Matrix Database are the most extensive resources for MPM data, collectively containing >12,000 individual projection matrices for >1,100 species globally. Although these databases represent an unparalleled resource for researchers, land managers and educators, the current computational tools available to answer questions with MPMs impose significant barriers to potential COM(P)ADRE database users by requiring advanced knowledge to handle diverse data structures and program custom analysis functions. To close this knowledge gap, we present two interrelated R packages designed to (a) facilitate the use of these databases by providing functions to acquire, quality control and manage both the MPM data contained in COMPADRE and COMADRE, and a user's own MPM data ( Rcompadre ) and (b) present a range of functions to calculate life‐history traits from MPMs in support of ecological and evolutionary analyses ( Rage ) . We provide examples to illustrate the use of both. Rcompadre and Rage will facilitate demographic analyses using MPM data and contribute to the improved replicability of studies using these data. We hope that this new functionality will allow researchers, land managers and educators to unlock the potential behind the thousands of MPMs and ancillary metadata stored in the COMPADRE and COMADRE matrix databases, and in their own MPM data. DA - 2022/1/20/ PY - 2022/1/20/ DO - 10.1111/2041-210X.13792 VL - 1 SP - SN - 2041-2096 KW - ageing KW - age-structured population model KW - life-history strategy KW - matrix population model KW - population dynamics KW - population projection model KW - stage-structured population model ER - TY - JOUR TI - Alternative splicing of CsJAZ1 negatively regulates flavan-3-ol biosynthesis in tea plants AU - Zhu, Junyan AU - Yan, Xiaomei AU - Liu, Shengrui AU - Xia, Xiaobo AU - An, Yanlin AU - Xu, Qingshan AU - Zhao, Shiqi AU - Liu, Lu AU - Guo, Rui AU - Zhang, Zhaoliang AU - Xie, De-Yu AU - Wei, Chaoling T2 - PLANT JOURNAL AB - Flavan-3-ols are abundant in the tea plant (Camellia sinensis) and confer tea with flavor and health benefits. We recently found that alternative splicing of genes is likely involved in the regulation of flavan-3-ol biosynthesis; however, the underlying regulatory mechanisms remain unknown. Here, we integrated metabolomics and transcriptomics to construct metabolite-gene networks in tea leaves, collected over five different months and from five spatial positions, and found positive correlations between endogenous jasmonic acid (JA), flavan-3-ols, and numerous transcripts. Transcriptome mining further identified CsJAZ1, which is negatively associated with flavan-3-ols formation and has three CsJAZ1 transcripts, one full-length (CsJAZ1-1), and two splice variants (CsJAZ1-2 and -3) that lacked 3' coding sequences, with CsJAZ1-3 also lacking the coding region for the Jas domain. Confocal microscopy showed that CsJAZ1-1 was localized to the nucleus, while CsJAZ1-2 and CsJAZ1-3 were present in both the nucleus and the cytosol. In the absence of JA, CsJAZ1-1 was bound to CsMYC2, a positive regulator of flavan-3-ol biosynthesis; CsJAZ1-2 functioned as an alternative enhancer of CsJAZ1-1 and an antagonist of CsJAZ1-1 in binding to CsMYC2; and CsJAZ1-3 did not interact with CsMYC2. In the presence of JA, CsJAZ1-3 interacted with CsJAZ1-1 and CsJAZ1-2 to form heterodimers that stabilized the CsJAZ1-1-CsMYC2 and CsJAZ1-2-CsMYC2 complexes, thereby repressing the transcription of four genes that act late in the flavan-3-ol biosynthetic pathway. These data indicate that the alternative splicing variants of CsJAZ1 coordinately regulate flavan-3-ol biosynthesis in the tea plant and improve our understanding of JA-mediated flavan-3-ol biosynthesis. DA - 2022/3/4/ PY - 2022/3/4/ DO - 10.1111/tpj.15670 VL - 1 SP - SN - 1365-313X UR - http://dx.doi.org/10.1111/tpj.15670 KW - alternative splicing KW - JASMONATE ZIM-domain (JAZ) protein KW - flavan-3-ols KW - jasmonic acid KW - MYC2 transcription factor KW - protein-protein interaction KW - Camellia sinensis ER - TY - JOUR TI - Species distribution models rarely predict the biology of real populations AU - Lee‐Yaw, Julie A. AU - McCune, Jenny L. AU - Pironon, Samuel AU - Sheth, Seema N. T2 - Ecography AB - Species distribution models (SDMs) are widely used in ecology. In theory, SDMs capture (at least part of) species' ecological niches and can be used to make inferences about the distribution of suitable habitat for species of interest. Because habitat suitability is expected to influence population demography, SDMs have been used to estimate a variety of population parameters, from occurrence to genetic diversity. However, a critical look at the ability of SDMs to predict independent data across different aspects of population biology is lacking. Here, we systematically reviewed the literature, retrieving 201 studies that tested predictions from SDMs against independent assessments of occurrence, abundance, population performance, and genetic diversity. Although there is some support for the ability of SDMs to predict occurrence (~53% of studies depending on how support was assessed), the predictive performance of these models declines progressively from occurrence to abundance, to population mean fitness, to genetic diversity. At the same time, we observed higher success among studies that evaluated performance for single versus multiple species, pointing to a possible publication bias. Thus, the limited accuracy of SDMs reported here may reflect the best‐case scenario. We discuss the limitations of these models and provide specific recommendations for their use for different applications going forward. However, we emphasize that predictions from SDMs, especially when used to inform conservation decisions, should be treated as hypotheses to be tested with independent data rather than as stand‐ins for the population parameters we seek to know. DA - 2022/6// PY - 2022/6// DO - 10.1111/ecog.05877 UR - https://doi.org/10.1111/ecog.05877 KW - abundance KW - ecological niche KW - genetic diversity KW - habitat suitability KW - independent data KW - occurrence KW - performance KW - population growth ER - TY - JOUR TI - Spatial variation in high temperature‐regulated gene expression predicts evolution of plasticity with climate change in the scarlet monkeyflower AU - Preston, Jill C. AU - Wooliver, Rachel AU - Driscoll, Heather AU - Coughlin, Aeran AU - Sheth, Seema N. T2 - Molecular Ecology AB - Abstract A major way that organisms can adapt to changing environmental conditions is by evolving increased or decreased phenotypic plasticity. In the face of current global warming, more attention is being paid to the role of plasticity in maintaining fitness as abiotic conditions change over time. However, given that temporal data can be challenging to acquire, a major question is whether evolution in plasticity across space can predict adaptive plasticity across time. In growth chambers simulating two thermal regimes, we generated transcriptome data for western North American scarlet monkeyflowers ( Mimulus cardinalis ) collected from different latitudes and years (2010 and 2017) to test hypotheses about how plasticity in gene expression is responding to increases in temperature, and if this pattern is consistent across time and space. Supporting the genetic compensation hypothesis, individuals whose progenitors were collected from the warmer‐origin northern 2017 descendant cohort showed lower thermal plasticity in gene expression than their cooler‐origin northern 2010 ancestors. This was largely due to a change in response at the warmer (40°C) rather than cooler (20°C) treatment. A similar pattern of reduced plasticity, largely due to a change in response at 40°C, was also found for the cooler‐origin northern versus the warmer‐origin southern population from 2017. Our results demonstrate that reduced phenotypic plasticity can evolve with warming and that spatial and temporal changes in plasticity predict one another. DA - 2022/2// PY - 2022/2// DO - 10.1111/mec.16300 UR - https://doi.org/10.1111/mec.16300 KW - climate change KW - differential gene expression KW - Mimulus cardinalis KW - phenotypic plasticity KW - space by time substitution KW - thermal adaptation ER - TY - JOUR TI - Molecular mechanisms of endomembrane trafficking in plants AU - Aniento, Fernando AU - Medina Hernandez, Victor Sanchez AU - Dagdas, Yasin AU - Rojas-Pierce, Marcela AU - Russinova, Eugenia T2 - PLANT CELL AB - Endomembrane trafficking is essential for all eukaryotic cells. The best-characterized membrane trafficking organelles include the endoplasmic reticulum (ER), Golgi apparatus, early and recycling endosomes, multivesicular body, or late endosome, lysosome/vacuole, and plasma membrane. Although historically plants have given rise to cell biology, our understanding of membrane trafficking has mainly been shaped by the much more studied mammalian and yeast models. Whereas organelles and major protein families that regulate endomembrane trafficking are largely conserved across all eukaryotes, exciting variations are emerging from advances in plant cell biology research. In this review, we summarize the current state of knowledge on plant endomembrane trafficking, with a focus on four distinct trafficking pathways: ER-to-Golgi transport, endocytosis, trans-Golgi network-to-vacuole transport, and autophagy. We acknowledge the conservation and commonalities in the trafficking machinery across species, with emphasis on diversity and plant-specific features. Understanding the function of organelles and the trafficking machinery currently nonexistent in well-known model organisms will provide great opportunities to acquire new insights into the fundamental cellular process of membrane trafficking. DA - 2022/1// PY - 2022/1// DO - 10.1093/plcell/koab235 VL - 34 IS - 1 SP - 146-173 SN - 1532-298X UR - https://doi.org/10.1093/plcell/koab235 ER - TY - JOUR TI - Evaluating the Effects of the Circadian Clock and Time of Day on Plant Gravitropic Responses AU - Tolsma, Joseph S. AU - Torres, Jacob J. AU - Richards, Jeffrey T. AU - Perera, Imara Y. AU - Doherty, Colleen J. T2 - PLANT GRAVITROPISM AB - Circadian rhythms are regular oscillations of an organism's physiology with a period of approximately 24 h. In the model plant Arabidopsis thaliana, circadian rhythms regulate a suite of physiological processes, including transcription, photosynthesis, growth, and flowering. The circadian clock and external rhythmic factors have extensive control of the underlying biochemistry and physiology. Therefore, it is critical to consider the time of day when performing gravitropism experiments, even if the circadian clock is not a focus of study. We describe the critical factors and methods to be considered and methods to investigate the possible circadian regulation of gravitropic responses. DA - 2022/// PY - 2022/// DO - 10.1007/978-1-0716-1677-2_19 VL - 2368 SP - 301-319 SN - 1940-6029 UR - https://doi.org/10.1007/978-1-0716-1677-2_19 KW - Circadian KW - Gravistimulation KW - Time of day KW - Diel KW - Simulated microgravity ER - TY - JOUR TI - Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass AU - Whitaker, Briana K. AU - Giauque, Hannah AU - Timmerman, Corey AU - Birk, Nicolas AU - Hawkes, Christine V. T2 - Microbial Ecology DA - 2022/7// PY - 2022/7// DO - 10.1007/s00248-021-01836-2 VL - 8 UR - https://doi.org/10.1007/s00248-021-01836-2 KW - Source-sink dynamics KW - Microbiome KW - Dispersal limitation KW - Turnover KW - Nestedness KW - Precipitation gradient ER -