Publications

Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

Posted by on Jul 2, 2020 in Publications | Comments Off on Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models

Susan J Robertson, Paul Lemire, Heather Maughan, Ashleigh Goethel, Williams Turpin, Larbi Bedrani, David S Guttman, Kenneth Croitoru, Stephen E Girardin, Dana J Philpott Cell Rep. 2019 May 7;27(6):1910-1919.e2. doi: 10.1016/j.celrep.2019.04.023 PMID: 31067473
Abstract: The intestinal microbiota is a fundamental factor that broadly influences physiology. Thus, studies using transgenic animals should be designed to limit the confounding effects of microbiota variation between strains. Here, we report the impact on intestinal microbiota of co-housed versus F2-generation littermates,...

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Entropy and Information within Intrinsically Disordered Protein Regions

Posted by on Apr 27, 2020 in Publications | Comments Off on Entropy and Information within Intrinsically Disordered Protein Regions

Iva Pritišanac, Robert M. Vernon, Alan M. Moses, Julie D. Forman Kay Entropy 2019 21(7):622. 10.3390/e21070662
Abstract: Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-structure-function paradigm to IDRs and motivates the development of new methods to extract information from IDR sequences. We argue that the information in IDR sequences cannot be fully revealed through positional...

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Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer.

Posted by on Apr 27, 2020 in Publications | Comments Off on Limiting oxidative DNA damage reduces microbe-induced colitis-associated colorectal cancer.

Irrazabal T, Thakur BK, Kang M, Malaise Y, Streutker C, Wong EOY, Copeland J, Gryfe R, Guttman DS, Navarre WW, Martin A Nature Communications 2020 11(1):1802. 10.1038/s41467-020-15549-6 PMID:32286276
Abstract: Inflammatory bowel disease patients have a greatly increased risk of developing colitis-associated colon cancer (CAC); however, the basis for inflammation-induced genetic damage requisite for neoplasia is unclear. Using three models of CAC, we find that sustained inflammation triggers 8-oxoguanine DNA lesions. Strikingly, antioxidants or iNOS inhibitors reduce 8-oxoguanine...

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Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.

Posted by on Apr 27, 2020 in Publications | Comments Off on Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production.

Zhang L, Liu M, Long H, Dong W, Pasha A, Esteban E, Li W, Yang X, Li Z, Song A, Ran D, Zhao G, Zeng Y, Chen H, Zou M, Li J, Liang F, Xie M, Hu J, Wang D, Cao H, Provart NJ, Zhang L, Tan X. Genomics Proteomics Bioinformatics 2020 S1672-0229(18):30216. 10.1016/j.gpb.2019.03.006 PMID:32224189
Abstract: Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific...

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An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Posted by on Apr 27, 2020 in Publications | Comments Off on An abscisic acid-responsive protein interaction network for sucrose non-fermenting related kinase1 in abiotic stress response

Carina Steliana Carianopol, Aaron Lorheed Chan, Shaowei Dong, Nicholas J. Provart, Shelley Lumba & Sonia Gazzarrini   Nature Communications Biology 2020 3(1):145. 10.1038/s42003-020-0866-8 PMID:32218501
Abstract: Yeast Snf1 (Sucrose non-fermenting1), mammalian AMPK (5′ AMP-activated protein kinase) and plant SnRK1 (Snf1-Related Kinase1) are conserved heterotrimeric kinase complexes that re-establish energy homeostasis following stress. The hormone abscisic acid (ABA) plays a crucial role in plant stress response. Activation of SnRK1 or ABA signaling results in...

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QuiC2 represents a functionally distinct class of dehydroshikimate dehydratases identified in Listeria species including Listeria monocytogenes

Posted by on Apr 27, 2020 in Publications | Comments Off on QuiC2 represents a functionally distinct class of dehydroshikimate dehydratases identified in Listeria species including Listeria monocytogenes

Kevin Xue, Stephanie M. Prezioso, Dinesh Christendat Environmental Microbiology 2020 ():. 10.1111/1462-2920.14987 PMID:32190965
Abstract: Many Listeria species including L. monocytogenes contain the pathway for the biosynthesis of protocatechuate from shikimate and quinate. The qui1 and qui2 operons within these Listeria spp. encode enzymes for this pathway. The diversion of shikimate pathway intermediates in some Listeria species to produce protocatechuate suggests an important biological role for this compound to these organisms. A total of seven ORFs, including quiC2, were...

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Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Posted by on Apr 27, 2020 in Publications | Comments Off on Light-responsive expression atlas reveals the effects of light quality and intensity in Kalanchoë fedtschenkoi, a plant with crassulacean acid metabolism

Jin Zhang, Rongbin Hu, Avinash Sreedasyam, Travis M Garcia, Anna Lipzen, Mei Wang, Pradeep Yerramsetty, Degao Liu, Vivian Ng, Jeremy Schmutz, John C Cushman, Anne M Borland, Asher Pasha, Nicholas J Provart, Jin-Gui Chen, Wellington Muchero, Gerald A Tuskan, Xiaohan Yang GigaScience 2020 9(3):giaa018. 10.1093/gigascience/giaa018 PMID:32135007
Abstract: Background: Crassulacean acid metabolism (CAM), a specialized mode of photosynthesis, enables plant adaptation to water-limited environments and improves photosynthetic efficiency via an inorganic carbon-concentrating mechanism....

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Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum.

Posted by on Apr 27, 2020 in Publications | Comments Off on Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum.

Doll NM, Just J, Brunaud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T Plant Cell 2020 32(4):833-852. 10.1105/tpc.19.00756 PMID:32086366
Abstract: Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm, and maternal tissues). However, the complexity of the kernel makes it difficult to understand intercompartment interactions without access to spatially accurate information. Here, we took advantage of the large size of the maize (Zea mays) kernel to...

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The pan-genome effector-triggered immunity landscape of a host-pathogen interaction

Posted by on Apr 27, 2020 in Publications | Comments Off on The pan-genome effector-triggered immunity landscape of a host-pathogen interaction

Bradley Laflamme, Marcus M. Dillon1, Alexandre Martel, Renan N. D. Almeida, Darrell Desveaux, David S. Guttman Science 2020 367(6479):763-768. 10.1126/science.aax4079 PMID:32054757
Abstract: Effector-triggered immunity (ETI), induced by host immune receptors in response to microbial effectors, protects plants against virulent pathogens. However, a systematic study of ETI prevalence against species-wide pathogen diversity is lacking. We constructed the Pseudomonas syringae Type III Effector Compendium (PsyTEC) to reduce the pan-genome complexity of 5127 unique effector...

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Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots.

Posted by on Apr 27, 2020 in Publications | Comments Off on Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots.

Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M. Plant Cell 2020 32(4):853-870. 10.1105/tpc.19.00780 PMID:31988262
Abstract: Selaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the...

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