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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/28314727/transcriptomic-analyses-elucidate-adaptive-differences-of-closely-related-strains-of-p-aeruginosa-in-fuel
#1
Thusitha S Gunasekera, Loryn L Bowen, Carol E Zhou, Susan C Howard-Byerly, William S Foley, Richard C Striebich, Larry C Dugan, Oscar N Ruiz
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28299517/characterization-and-complete-genome-sequence-analysis-of-a-novel-virulent-siphoviridae-phage-against-staphylococcus-aureus-isolated-from-bovine-mastitis-in-xinjiang-china
#2
Qian Zhang, Shaozhen Xing, Qiang Sun, Guangqian Pei, Shi Cheng, Yannan Liu, Xiaoping An, Xianglilan Zhang, Yonggang Qu, Yigang Tong
Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where Staphylococcus aureus is the most frequently isolated and a major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance. Using phage for pathogen control is a promising tool in the fight against antibiotic resistance. Mainly using high-throughput sequencing, bioinformatics and our proposed phage termini identification method, we have isolated and characterized a novel virulent phage, designated as vB_SauS_IMEP5, from manure collected from dairy farms in Shihezi, Xinjiang, China, for use as a biocontrol agent against Staphylococcus aureus infections...
March 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/28297664/coupling-between-protein-stability-and-catalytic-activity-determines-pathogenicity-of-g6pd-variants
#3
Anna D Cunningham, Alexandre Colavin, Kerwyn Casey Huang, Daria Mochly-Rosen
G6PD deficiency, an enzymopathy affecting 7% of the world population, is caused by over 160 identified amino acid variants in glucose-6-phosphate dehydrogenase (G6PD). The clinical presentation of G6PD deficiency is diverse, likely due to the broad distribution of variants across the protein and the potential for multidimensional biochemical effects. In this study, we use bioinformatic and biochemical analyses to interpret the relationship between G6PD variants and their clinical phenotype. Using structural information and statistical analyses of known G6PD variants, we predict the molecular phenotype of five uncharacterized variants from a reference population database...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28288890/abdominal-aortic-aneurysm-associated-microrna-516a-5p-regulates-expressions-of-methylenetetrahydrofolate-reductase-matrix-metalloproteinase-2-and-tissue-inhibitor-of-matrix-metalloproteinase-1-in-human-abdominal-aortic-vascular-smooth-muscle-cells
#4
Crystal Yin Tung Chan, Bernice Lai Yee Cheuk, Stephen Wing Keung Cheng
OBJECTIVE: MicroRNAs (miRNAs or miRs) have been highlighted to be involved in abdominal aortic aneurysm (AAA) with the emergence of recent miRNA microarray profiling studies. miR-516a-5p has been shown to be significantly overexpressed in vascular smooth muscle cells (VSMCs) from human AAA tissues from our previous microarray study, suggesting its crucial association with AAA. In addition, further bioinformatics analysis predicted methylenetetrahydrofolate reductase (MTHFR), which regulates homocysteine (Hcy) metabolism and is proposed to be a risk gene for AAA formation, to be the down-regulation target of miR-516a-5p...
March 10, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28284182/the-prediction-of-a-pathogenesis-related-secretome-of-puccinia-helianthi-through-high-throughput-transcriptome-analysis
#5
Lan Jing, Dandan Guo, Wenjie Hu, Xiaofan Niu
BACKGROUND: Many plant pathogen secretory proteins are known to be elicitors or pathogenic factors,which play an important role in the host-pathogen interaction process. Bioinformatics approaches make possible the large scale prediction and analysis of secretory proteins from the Puccinia helianthi transcriptome. The internet-based software SignalP v4.1, TargetP v1.01, Big-PI predictor, TMHMM v2.0 and ProtComp v9.0 were utilized to predict the signal peptides and the signal peptide-dependent secreted proteins among the 35,286 ORFs of the P...
March 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28280605/next-generation-sequencing-identifies-interactome-signatures-in-relapsed-and-refractory-metastatic-colorectal-cancer
#6
Benny Johnson, Laurence Cooke, Daruka Mahadevan
BACKGROUND: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. METHODS: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28260060/bioinformatics-analysis-on-the-differentiation-of-bone-mesenchymal-stem-cells-into-osteoblasts-and-adipocytes
#7
Xiaoyuan Xu, He Jiang, Xingnuan Li, Ping Wu, Jianyun Liu, Tao Wang, Xiaoou Zhou, Jianjun Xiong, Weidong Li
The present study aimed to screen several differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) for two types of mesenchymal stem cell (MSC) differentiation. Bone morphogenetic protein 6 (BMP‑6) and dexamethasone were used to induce MSCs towards osteoblastic differentiation or adipocytic differentiation. The t‑test in the Bioconductor bioinformatics software tool was used to screen DEGs and differentially expressed miRNAs in the two samples. Subsequent gene ontology (GO) and pathway analyses on the DEGs were performed using the GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively; potential target genes for the screened miRNAs were predicted using the TargetScan database...
February 8, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28259674/assessment-of-the-potential-utility-of-different-regions-of-streptococcus-uberis-adhesion-molecule-suam-for-mastitis-subunit-vaccine-development
#8
Melina Soledad Perrig, Carolina Veaute, María Sol Renna, Nazarena Pujato, Luis Calvinho, Iván Marcipar, María Sol Barbagelata
Streptococcus uberis is one of the most prevalent pathogens causing clinical and subclinical mastitis worldwide. Among bacterial factors involved in intramammary infections caused by this organism, S. uberis adhesion molecule (SUAM) is one of the main virulence factors identified. This molecule is involved in S. uberis internalization to mammary epithelial cells through lactoferrin (Lf) binding. The objective of this study was to evaluate SUAM properties as a potential subunit vaccine component for prevention of S...
March 1, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28242707/oligomeric-lipoprotein-pelc-guides-pel-polysaccharide-export-across-the-outer-membrane-of-pseudomonas-aeruginosa
#9
Lindsey S Marmont, Jacquelyn D Rich, John C Whitney, Gregory B Whitfield, Henrik Almblad, Howard Robinson, Matthew R Parsek, Joe J Harrison, P Lynne Howell
Secreted polysaccharides are important functional and structural components of bacterial biofilms. The opportunistic pathogen Pseudomonas aeruginosa produces the cationic exopolysaccharide Pel, which protects bacteria from aminoglycoside antibiotics and contributes to biofilm architecture through ionic interactions with extracellular DNA. A bioinformatics analysis of genome databases suggests that gene clusters for Pel biosynthesis are present in >125 bacterial species, yet little is known about how this biofilm exopolysaccharide is synthesized and exported from the cell...
February 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28242650/multitasking-immune-sp185-333-protein-rsptransformer-e1-and-its-recombinant-fragments-undergo-secondary-structural-transformation-upon-binding-targets
#10
Cheng Man Lun, Barney M Bishop, L Courtney Smith
The purple sea urchin, Strongylocentrotus purpuratus, expresses a diverse immune response protein family called Sp185/333. A recombinant Sp185/333 protein, previously called rSp0032, shows multitasking antipathogen binding ability, suggesting that the protein family mediates a flexible and effective immune response to multiple foreign cells. Bioinformatic analysis predicts that rSp0032 is intrinsically disordered, and its multiple binding characteristic suggests structural flexibility to adopt different conformations depending on the characteristics of the target...
February 27, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28242451/characterisation-of-the-bordetella-pertussis-secretome-under-different-media
#11
Laurence Don Wai Luu, Sophie Octavia, Ling Zhong, Mark Raftery, Vitali Sintchenko, Ruiting Lan
Our understanding of the Bordetella pertussis secretome remains limited including the role of different growth conditions in the secretome. In this study the secretome of L1423, a clinical isolate from the 2008-2012 Australian epidemic, cultured on Stainer-Scholte (SS) and Thalen-IJssel (THIJS) media for 12h was characterised using liquid chromatography-mass spectrometry (LC-MS/MS). In the supernatant, LC-MS/MS identified 260 proteins with 143 bioinformatically predicted to be secreted. Eighty percent of proteins were identified in both media...
February 24, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28242426/in-silico-design-of-an-immunogen-against-acinetobacter-baumannii-based-on-a-novel-model-for-native-structure-of-outer-membrane-protein-a
#12
Abolfazl Jahangiri, Iraj Rasooli, Parviz Owlia, Abbas Ali Imani Fooladi, Jafar Salimian
Outer membrane protein A (OmpA) is the most promising vaccine candidate against one of the most successful nosocomial pathogens, A. baumannii. Despite advantages of the antigen, its cytotoxicity could be considered as a challenge in clinical trials. In order to improve this effective immunogen, rational vaccine design strategies such as structure-based vaccinology should be assessed. However, native structure of OmpA remains controversial. The present study is conducted to address the native structure of OmpA; then, a novel immunogen with lower toxicity and higher antigenicity was designed based on structural vaccinology...
February 27, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28242392/two-novel-mutations-in-the-ppib-gene-cause-a-rare-pedigree-of-osteogenesis-imperfecta-type-ix
#13
Yu Jiang, Jingxin Pan, Dongwei Guo, Wei Zhang, Jie Xie, Zishui Fang, Chunmiao Guo, Qun Fang, Weiying Jiang, Yibin Guo
BACKGROUND: Osteogenesis imperfecta (OI) is a rare genetic skeletal disorder characterized by increased bone fragility and vulnerability to fractures. PPIB is identified as a candidate gene for OI-IX, here we detect two pathogenic mutations in PPIB and analyze the genotype-phenotype correlation in a Chinese family with OI. METHODS: Next-generation sequencing (NGS) was used to screen the whole exome of the parents of proband. Screening of variation frequency, evolutionary conservation comparisons, pathogenicity evaluation, and protein structure prediction were conducted to assess the pathogenicity of the novel mutations...
February 24, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28224923/high-throughput-sequencing-reveals-modulation-of-micrornas-in-vigna-mungo-upon-mungbean-yellow-mosaic-india-virus-inoculation-highlighting-stress-regulation
#14
Anirban Kundu, Sujay Paul, Avishek Dey, Amita Pal
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing...
April 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28221970/genomic-tools-for-customized-recovery-and-detection-of-foodborne-shiga-toxigenic-escherichia-coli
#15
Michael Knowles, Sara Stinson, Dominic Lambert, Catherine Carrillo, Adam Koziol, Martine Gauthier, Burton Blais
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e...
December 2016: Journal of Food Protection
https://www.readbyqxmd.com/read/28206987/id2-promotes-survival-of-glioblastoma-cells-during-metabolic-stress-by-regulating-mitochondrial-function
#16
Zhonghua Zhang, Gilbert J Rahme, Pranam D Chatterjee, Matthew C Havrda, Mark A Israel
Tumor cells proliferate in cellular environments characterized by a lack of optimal tissue organization resulting oftentimes in compromised cellular metabolism affecting nutrition, respiration, and energetics. The response of tumor cells to adverse environmental conditions is a key feature affecting their pathogenicity. We found that inhibitor of DNA binding 2 (ID2) expression levels significantly correlate with the ability of glioblastoma (GBM)-derived cell lines to survive glucose deprivation. ID2 suppressed mitochondrial oxidative respiration and mitochondrial ATP production by regulating the function of mitochondrial electron transport chain (mETC) complexes, resulting in reduced superoxide and reactive oxygen species (ROS) production from mitochondria...
February 16, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28193166/vacsol-a-high-throughput-in-silico-pipeline-to-predict-potential-therapeutic-targets-in-prokaryotic-pathogens-using-subtractive-reverse-vaccinology
#17
Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali
BACKGROUND: With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28193117/exome-sequencing-identifies-de-novo-dync1h1-mutations-associated-with-distal-spinal-muscular-atrophy-and-malformations-of-cortical-development
#18
Yulin Chen, Yufei Xu, Guoqiang Li, Niu Li, Tingting Yu, Ru-En Yao, Xiumin Wang, Yiping Shen, Jian Wang
Exome sequencing has become a formidable tool for identifying potential de novo variants in causative genes of human diseases, such as neurodegenerative disorders. This article describes a 16-month-old girl with spinal muscular atrophy with lower extremity predominance and a 13-month-old girl with malformations of cortical development. Exome sequencing identified a novel de novo heterozygous missense mutation c.3395G>A (p.Gly1132Glu) and a previously reported de novo heterozygous missense mutation c.10151G>A (p...
March 2017: Journal of Child Neurology
https://www.readbyqxmd.com/read/28185569/a-comprehensive-collection-of-annotations-to-interpret-sequence-variation-in-human-mitochondrial-transfer-rnas
#19
Maria Angela Diroma, Paolo Lubisco, Marcella Attimonelli
BACKGROUND: The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically about the variability of the 22 human mitochondrial transfer RNA (tRNA) genes and their involvement in diseases. The complex enrichment and isolation of tRNAs in vitro leads to an incomplete knowledge of their post-transcriptional modifications and three-dimensional folding, essential for correct tRNA functioning...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28158222/comparative-analysis-of-nbs-lrr-genes-and-their-response-to-aspergillus-flavus-in-arachis
#20
Hui Song, Pengfei Wang, Changsheng Li, Suoyi Han, Chuanzhi Zhao, Han Xia, Yuping Bi, Baozhu Guo, Xinyou Zhang, Xingjun Wang
Studies have demonstrated that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes respond to pathogen attack in plants. Characterization of NBS-LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS-LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches...
2017: PloS One
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