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An analysis of the mechanism underlying photocatalytic disinfection based on integrated metabolic networks and transcriptional data

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Journal of Environmental Sciences 2020年第6期32卷 28-37页

作者： Xiao-Long Liang Zhan-Min Liang Shuo Wang Xiao-Hui Chen Yao Ruan Qing-Ye Zhang Hong-Yu Zhang Hubei Key Laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan430070PR China

Photocatalytic disinfection has long been used to combat pathogenic ***,the specific mechanism underlying photocatalytic disinfection and its corresponding targets remain *** this study,an analysis of the potential mechanism underlying photocatalytic disinfection was performed based on integrated metabolic networks and transcriptional *** sets of rna-seq data(wild type and a photocatalysis-resistant mutant mediated by titanium dioxide(TiO2))were processed to constrain the genome scale metabolic models(GSMM)of *** analyzing the metabolic network,the differential metabolic flux of every reaction was computed in constrained GSMM,and several significantly differential metabolic fluxes in reactions were extracted and *** of these reactions were involved in the transmembrane transport of substances and occurred on the inner membrane or were an important component of the cell *** results,which are consistent with the reported information,validated our analysis *** addition,our work also identified other new and valuable metabolic pathways,such as the reaction ALCD2x,which has a great effect on the energy production process under bacterial anaerobic *** DHAK reaction is also related to the metabolic process of *** reactions with large differential metabolic fluxes merit further ***,to provide a strategy to address photocatalysis-resistant mutant bacteria,a metabolic compensation analysis was also *** metabolic compensation analysis results provided suggestions for a combined method that can effectively combat resistant *** method could also be used to explore the mechanisms of drug resistance in other microorganisms.

关键词： Photocatalytic disinfection Genome scale metabolic models(GSMM) rna-seq analysis Mechanism Metabolic compensation

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Comparative transcriptome profiling of two maize near-isogenic lines differing in the allelic state for bacterial brown spot disease resistance

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Journal of Integrative Agriculture 2015年第4期14卷 610-621页

作者： WU Xiao-jun Xu Li ZHAO Pan-feng LI Na WU Lei HE Yan WANG Shou-cai National Maize Improvement Center of China/Key Laboratory of Crop Genomics and Genetic of Maize China Agricultural University

The bacterial brown spot disease（BBS）, caused primarily by Pseudomonas syringae pv. syringae van Hall（Pss）, reduces plant vigor, yield and quality in maize. To reveal the nature of the defense mechanisms and identify genes involved in the effective host resistance, the dynamic changes of defense transcriptome triggered by the infection of Pss were investigated and compared between two maize near-isogenic lines（NILs）. We found that Pss infection resulted in a sophisticated transcriptional reprogramming of several biological processes and the resistant NIL employed much faster defense responses than the susceptible NIL. Numerous genes encoding essential components of plant basal resistance would be able to be activated in the susceptible NIL, such as PEN1, PEN2, PEN3, and EDR1, however, in a basic manner, such resistance might not be sufficient for suppressing Pss pathogenesis. In addition, the expressions of a large number of PTI-, ETI-, PR-, and WRKY-related genes were pronouncedly activated in the resistant NIL, suggesting that maize employ a multitude of defense pathways to defend Pss infection. Six R-gene homologs were identified to have significantly higher expression levels in the resistant NIL at early time point, indicating that a robust surveillance system（gene-to-gene model） might operate in maize during Pss attacks, and these homolog genes are likely to be potential candidate resistance genes involved in BBS disease resistance. Furthermore, a holistic group of novel pathogen-responsive genes were defined, providing the repertoire of candidate genes for further functional characterization and identification of their regulation patterns during pathogen infection.

关键词： maize(Zea mays L.) bacterial brown spot disease rna-seq analysis disease resistance

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Tissue-specific Gene Expression Changes Are Associated with Aging in Mice

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Genomics, Proteomics & Bioinformatics 2020年第4期18卷 430-442页

作者： Akash Srivastava Emanuel Barth Maria A.Ermolaeva Madlen Guenther Christiane Frahm Manja Marz Otto W.Witte Hans-Berger Department of Neurology University Hospital JenaFriedrich Schiller University Jena07747 JenaGermany Bioinformatics/High Throughput analysis Friedrich Schiller University Jena07743 JenaGermany FLI Leibniz Institute for Age Research 07745 JenaGermany

Aging is a complex process that can be characterized by functional and cognitive decline in an individual. Aging can be assessed based on the functional capacity of vital organs and their intricate interactions with one another. Thus, the nature of aging can be described by focusing on a specific organ and an individual itself. However, to fully understand the complexity of aging,one must investigate not only a single tissue or biological process but also its complex interplay and interdependencies with other biological processes. Here, using rna-seq, we monitored changes in the transcriptome during aging in four tissues(including brain, blood, skin and liver) in mice at9 months, 15 months, and 24 months, with a final evaluation at the very old age of 30 *** identified several genes and processes that were differentially regulated during aging in both tissue-dependent and tissue-independent manners. Most importantly, we found that the electron transport chain(ETC) of mitochondria was similarly affected at the transcriptome level in the four tissues during the aging process. We also identified the liver as the tissue showing the largest variety of differentially expressed genes(DEGs) over time. Lcn2(Lipocalin-2) was found to be similarly regulated among all tissues, and its effect on longevity and survival was validated using its orthologue in Caenorhabditis elegans. Our study demonstrated that the molecular processes of aging are relatively subtle in their progress, and the aging process of every tissue depends on the tissue’s specialized function and environment. Hence, individual gene or process alone cannot be described as the key of aging in the whole organism.

关键词： Aging rna-seq analysis Inflammaging Electron transport chain Tissue aging

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Challenges Analyzing rna-seq Gene Expression Data

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Open Journal of Statistics 2016年第4期6卷 628-636页

作者： Liliana López-Kleine Cristian González-Prieto Department of Statistics Universidad Nacional de Colombia—Sede Bogotá Bogotá Colombia

The analysis of messenger Ribonucleic acid obtained through sequencing techniques (rna-se- quencing) data is very challenging. Once technical difficulties have been sorted, an important choice has to be made during pre-processing: Two different paths can be chosen: Transform rna- sequencing count data to a continuous variable or continue to work with count data. For each data type, analysis tools have been developed and seem appropriate at first sight, but a deeper analysis of data distribution and structure, are a discussion worth. In this review, open questions regarding rna-sequencing data nature are discussed and highlighted, indicating important future research topics in statistics that should be addressed for a better analysis of already available and new appearing gene expression data. Moreover, a comparative analysis of rnaseq count and transformed data is presented. This comparison indicates that transforming rna-seq count data seems appropriate, at least for differential expression detection.

关键词： rna-seq analysis Count Data Preprocessing Differential Expression Gene Co-Expression Network

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The maize glossy26 gene encodes an enoyl-CoA reductase involved in the biosynthesis of epicuticular waxes

The maize glossy26 gene encodes an enoyl-CoA reductase invol...

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第十四届全国植物基因组学大会

作者： Xiaoli Ma Li Fan Sanzhen Liu Li Li Charles R Dietrich An-Ping Hsia Jun Zheng Guoying Wang Patrick S.Schnable Dept.of Plant Genetics & Breeding China Agricultural University

Epicuticular waxes coat the surfaces of aerial portions of plants where they play roles in resistance to biotic and abiotic *** affecting the biosynthesis or deposition epicuticular waxes present a "glossy" phenotype.... 详细信息

关键词： gl26 candidate gene approach ECR rna-seq analysis

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