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https://www.readbyqxmd.com/read/29774012/a-novel-enzyme-portfolio-for-red-algal-polysaccharide-degradation-in-the-marine-bacterium-paraglaciecola-hydrolytica-s66-t-encoded-in-a-sizeable-polysaccharide-utilization-locus
#1
Mikkel Schultz-Johansen, Pernille K Bech, Rosanna C Hennessy, Mikkel A Glaring, Tristan Barbeyron, Mirjam Czjzek, Peter Stougaard
Marine microbes are a rich source of enzymes for the degradation of diverse polysaccharides. Paraglaciecola hydrolytica S66T is a marine bacterium capable of hydrolyzing polysaccharides found in the cell wall of red macroalgae. In this study, we applied an approach combining genomic mining with functional analysis to uncover the potential of this bacterium to produce enzymes for the hydrolysis of complex marine polysaccharides. A special feature of P. hydrolytica S66T is the presence of a large genomic region harboring an array of carbohydrate-active enzymes (CAZymes) notably agarases and carrageenases...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29771380/dbcan2-a-meta-server-for-automated-carbohydrate-active-enzyme-annotation
#2
Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin
Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for complex carbohydrate metabolism. With an increasing number of plant and plant-associated microbial genomes and metagenomes being sequenced, there is an urgent need of automatic tools for genomic data mining of CAZymes. We developed the dbCAN web server in 2012 to provide a public service for automated CAZyme annotation for newly sequenced genomes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769539/integrated-analysis-of-hepatic-mrna-and-mirna-profiles-identified-molecular-networks-and-potential-biomarkers-of-nafld
#3
Mingzhe Zhu, Qianlei Wang, Wenjun Zhou, Tao Liu, Lili Yang, Peiyong Zheng, Li Zhang, Guang Ji
To enhance our understanding of molecular mechanisms and mine novel biomarkers of non-alcoholic fatty liver disease (NAFLD), RNA sequencing was performed to gain hepatic expression profiles of mRNAs and miRNAs in NAFLD and normal rats. Using DESeq with thresholds of a two-fold change and a false discovery rate (FDR) less than 0.05, 336 mRNAs and 21 miRNAs were identified as differentially expressed. Among those, 17 miRNAs (e.g., miR-144-3p, miR-99a-3p, miR-200b-3p, miR-200b-5p, miR-200c-3p, etc.) might serve as novel biomarkers of NAFLD...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29768440/transcriptome-analysis-reveals-a-stress-response-of-shewanella-oneidensis-deprived-of-background-levels-of-ionizing-radiation
#4
Hugo Castillo, Xiaoping Li, Faye Schilkey, Geoffrey B Smith
Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72...
2018: PloS One
https://www.readbyqxmd.com/read/29766351/comparative-whole-genome-re-sequencing-analysis-in-upland-new-rice-for-africa-insights-into-the-breeding-history-and-respective-genome-compositions
#5
Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad, Ajay Kohli
BACKGROUND: Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties...
May 15, 2018: Rice
https://www.readbyqxmd.com/read/29764514/integrative-analysis-of-gene-expression-profiles-reveals-specific-signaling-pathways-associated-with-pancreatic-duct-adenocarcinoma
#6
Jun Li, Wenle Tan, Linna Peng, Jialiang Zhang, Xudong Huang, Qionghua Cui, Jian Zheng, Wen Tan, Chen Wu, Dongxin Lin
BACKGROUND: Pancreatic duct adenocarcinoma (PDAC) remains a major health problem because conventional cancer treatments are relatively ineffective against it. Microarray studies have linked many genes to pancreatic cancer, but the available data have not been extensively mined for potential insights into PDAC. This study attempted to identify PDAC-associated genes and signaling pathways based on six microarray-based profiles of gene expression in pancreatic cancer deposited in the gene expression omnibus database...
April 27, 2018: Cancer communications
https://www.readbyqxmd.com/read/29762787/litvar-a-semantic-search-engine-for-linking-genomic-variant-data-in-pubmed-and-pmc
#7
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu
The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29761859/systematic-analyses-of-a-novel-lncrna-associated-signature-as-the-prognostic-biomarker-for-hepatocellular-carcinoma
#8
Jing Sui, Yan Miao, Jiali Han, Hongmei Nan, Bo Shen, Xiaomei Zhang, Yan Zhang, Yuan Wu, Wenjuan Wu, Tong Liu, Siyi Xu, Sheng Yang, Lihong Yin, Yuepu Pu, Geyu Liang
Accumulating evidence implies that long noncoding RNAs (lncRNAs) play a crucial role in predicting survival for Hepatocellular carcinoma (HCC) patients. This study aims to capture the current research hotspots of HCC, based on the analysis of publications related to HCC research from 2013 to 2017, and to identify a novel lncRNA signature for HCC prognosis through the data mining in The Cancer Genome Atlas (TCGA). "Prognosis" and "biomarker" were located in the core of the HCC research hotspot...
May 15, 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29761469/hymenoptera-genome-database-using-hymenopteramine-to-enhance-genomic-studies-of-hymenopteran-insects
#9
Christine G Elsik, Aditi Tayal, Deepak R Unni, Gregory W Burns, Darren E Hagen
The Hymenoptera Genome Database (HGD; http://hymenopteragenome.org ) is a genome informatics resource for insects of the order Hymenoptera, which includes bees, ants and wasps. HGD provides genome browsers with manual annotation tools (JBrowse/Apollo), BLAST, bulk data download, and a data mining warehouse (HymenopteraMine). This chapter focuses on the use of HymenopteraMine to create annotation data sets that can be exported for use in downstream analyses. HymenopteraMine leverages the InterMine platform to combine genome assemblies and official gene sets with data from OrthoDB, RefSeq, FlyBase, Gene Ontology, UniProt, InterPro, KEGG, Reactome, dbSNP, PubMed, and BioGrid, as well as precomputed gene expression information based on publicly available RNAseq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761466/using-wormbase-a-genome-biology-resource-for-caenorhabditis-elegans-and-related-nematodes
#10
Christian Grove, Scott Cain, Wen J Chen, Paul Davis, Todd Harris, Kevin L Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken, Gary Williams
WormBase ( www.wormbase.org ) provides the nematode research community with a centralized database for information pertaining to nematode genes and genomes. As more nematode genome sequences are becoming available and as richer data sets are published, WormBase strives to maintain updated information, displays, and services to facilitate efficient access to and understanding of the knowledge generated by the published nematode genetics literature. This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761461/bovine-genome-database-tools-for-mining-the-bos-taurus-genome
#11
Darren E Hagen, Deepak R Unni, Aditi Tayal, Gregory W Burns, Christine G Elsik
The Bovine Genome Database (BGD; http://bovinegenome.org ) is a web-accessible resource that supports bovine genomics research by providing genome annotation and data mining tools. BovineMine is a tool within BGD that integrates BGD data, including the genome, genes, precomputed gene expression levels and variant consequences, with external data sources that include quantitative trait loci (QTL), orthologues, Gene Ontology, gene interactions, and pathways. BovineMine enables researchers without programming skills to create custom integrated datasets for use in downstream analyses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29761457/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#12
Susanne Warrenfeltz, Evelina Y Basenko, Kathryn Crouch, Omar S Harb, Jessica C Kissinger, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco
Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen's biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources ( http://eupathdb.org ) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpathogenic species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760905/roads-to-isolation-similar-genomic-history-patterns-in-two-species-of-freshwater-crabs-with-contrasting-environmental-tolerances-and-range-sizes
#13
Ywee Chieh Tay, Daniel Jia Jun Ng, Jun Bin Loo, Danwei Huang, Yixiong Cai, Darren Chong Jinn Yeo, Rudolf Meier
Freshwater species often show high levels of endemism and risk of extinction owing to their limited dispersal abilities. This is exemplified by the stenotopic freshwater crab, Johora singaporensis which is one of the world's 100 most threatened species, and currently inhabits less than 0.01 km2 of five low order hill streams within the highly urbanized island city-state of Singapore. We compared populations of J. singaporensis with that of the non-threatened, widespread, abundant, and eurytopic freshwater crab, Parathelphusa maculata , and found surprisingly high congruence between their population genomic histories...
May 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29760061/methylglucosylation-of-aromatic-amino-and-phenolic-moieties-of-drug-like-biosynthons-by-combinatorial-biosynthesis
#14
Linan Xie, Liwen Zhang, Chen Wang, Xiaojing Wang, Ya-Ming Xu, Hefen Yu, Ping Wu, Shenglan Li, Lida Han, A A Leslie Gunatilaka, Xiaoyi Wei, Min Lin, István Molnár, Yuquan Xu
Glycosylation is a prominent strategy to optimize the pharmacokinetic and pharmacodynamic properties of drug-like small-molecule scaffolds by modulating their solubility, stability, bioavailability, and bioactivity. Glycosyltransferases applicable for "sugarcoating" various small-molecule acceptors have been isolated and characterized from plants and bacteria, but remained cryptic from filamentous fungi until recently, despite the frequent use of some fungi for whole-cell biocatalytic glycosylations...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29753486/functional-analysis-and-heterologous-expression-of-bifunctional-glutathione-synthetase-from-lactobacillus
#15
Zhi-Qiang Xiong, Ling-Hui Kong, Guang-Qiang Wang, Yong-Jun Xia, Hui Zhang, Bo-Xing Yin, Lian-Zhong Ai
Bifunctional glutathione synthetase (GshF) has recently been reported to simultaneously catalyze the 2-step ATP-dependent biosynthesis of reduced glutathione (GSH). In this work, 19 putative gshF were mined from the complete sequenced genome of 20 representative Lactobacillus species. To functionally analyze these putative GshF, GshF from Lactobacillus plantarum and Lactobacillus casei were selected and successfully expressed in Escherichia coli. Compared with the control without expressing GshF, GSH titers were enhanced significantly in E...
May 9, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29752270/the-discovery-of-two-native-baeyer-villiger-monooxygenases-for-asymmetric-synthesis-of-bulky-chiral-sulfoxides
#16
Yan Zhang, Feng Liu, Na Xu, Yin-Qi Wu, Yu-Cong Zheng, Qian Zhao, Guoqiang Lin, Hui-Lei Yu, Jian-He Xu
Two Baeyer-Villiger monooxygenases (BVMOs) designated Bo BVMO and Am BVMO were discovered from Bradyrhizobium oligotrophicum and Aeromicrobium marinum , respectively. Both monooxygenases displayed novel features for catalyzing the asymmetric sulfoxidation of bulky and pharmaceutically relevant thioethers. Evolutionary relationship and sequence analysis revealed that the two BVMOs belong to the family of typical type I BVMO and the subtype ethionamide monooxygenase. Both BVMOs are active toward medium- and long-chain aliphatic ketones as well as various thioether substrates, but ineffective toward cyclohexanone, aromatic ketones and other typical BVMO substrates...
May 11, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29750165/how-artificial-intelligence-can-improve-our-understanding-of-the-genes-associated-with-endometriosis-natural-language-processing-of-the-pubmed-database
#17
REVIEW
J Bouaziz, R Mashiach, S Cohen, A Kedem, A Baron, M Zajicek, I Feldman, D Seidman, D Soriano
Endometriosis is a disease characterized by the development of endometrial tissue outside the uterus, but its cause remains largely unknown. Numerous genes have been studied and proposed to help explain its pathogenesis. However, the large number of these candidate genes has made functional validation through experimental methodologies nearly impossible. Computational methods could provide a useful alternative for prioritizing those most likely to be susceptibility genes. Using artificial intelligence applied to text mining, this study analyzed the genes involved in the pathogenesis, development, and progression of endometriosis...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29749535/oncogenic-role-of-mir%C3%A2-183%C3%A2-5p-in-lung-adenocarcinoma-a-comprehensive-study-of-qpcr-in-vitro-experiments-and-bioinformatic-analysis
#18
Rong-Quan He, Li Gao, Jie Ma, Zu-Yun Li, Xiao-Hua Hu, Gang Chen
Despite the fact that previous studies have reported the aberrant expression of miR‑183‑5p in lung adenocarcinoma (LUAD), the oncogenic role of miR‑183‑5p in LUAD and its underlying mechanisms have remained elusive. Hence, we attempted to elucidate the clinicopathological significance of miR‑183‑5p expression in LUAD and identify the biological function of miR‑183‑5p in LUAD in this study. Meta‑analysis of Gene Expression Omnibus (GEO) data, data mining of The Cancer Genome Atlas (TCGA) and real‑time quantitative polymerase chain reaction (qPCR) were performed to evaluate the clinicopathological significance of miR‑183‑5p in LUAD...
May 9, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29749470/overexpression-of-plin2-is-a-prognostic-marker-and-attenuates-tumor-progression-in-clear-cell-renal-cell-carcinoma
#19
Qi Cao, Hailong Ruan, Keshan Wang, Zhengshuai Song, Lin Bao, Tianbo Xu, Haibing Xiao, Cheng Wang, Gong Cheng, Junwei Tong, Xiangui Meng, Di Liu, Hongmei Yang, Ke Chen, Xiaoping Zhang
Clear cell renal cell carcinoma (ccRCC) is the most common renal malignancy in adults, the incidence of which continues to increase. The lipid droplet protein perilipin 2 (PLIN2), which was originally considered an RNA transcript, is markedly expressed during adipocyte differentiation. In addition, it has been observed to be elevated in numerous types of cancer, including ccRCC; however, its essential function remains unclear in ccRCC. The present study examined the expression of PLIN2 in ccRCC, and aimed to determine the association between PLIN2 expression and patient survival...
April 26, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29748902/a-thiotrophic-microbial-community-in-an-acidic-brine-lake-in-northern-chile
#20
Lorena Escudero, Nia Oetiker, Karem Gallardo, Cinthya Tebes-Cayo, Mariela Guajardo, Claudia Nuñez, Carol Davis-Belmar, J J Pueyo, Guillermo Chong Díaz, Cecilia Demergasso
The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies...
May 10, 2018: Antonie Van Leeuwenhoek
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