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Comparative genomics

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https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#1
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29775428/the-involvement-of-human-monogenic-cardiomyopathy-genes-in-experimental-polygenic-cardiac-hypertrophy
#2
Priscilla R Prestes, Francine Z Marques, Guillermo Lopez-Campos, Paul Lewandowski, Lea M D Delbridge, Fadi J Charchar, Stephen B Harrap
Hypertrophic cardiomyopathy thickens heart muscles reducing functionality and increasing risk of cardiac disease and morbidity. Genetic factors are involved, but their contribution is poorly understood. We used the hypertrophic heart rat (HHR), a unique normotensive polygenic model of cardiac hypertrophy and heart failure to investigate the role of genes associated with monogenic human cardiomyopathy. We selected 42 genes involved in monogenic human cardiomyopathies to study: 1) DNA variants, by sequencing the whole-genome of 13-week old HHR and age-matched normal heart rat (NHR), its genetic control strain; 2) mRNA expression, by targeted RNA-sequencing in left ventricles of HHR and NHR at five ages (2-days old, 4-, 13-, 33- and 50-weeks old) compared to human idiopathic dilated data; and 3) microRNA expression, with rat microRNA microarrays in left ventricles of 2-days old HHR and age-matched NHR...
May 18, 2018: Physiological Genomics
https://www.readbyqxmd.com/read/29775201/tacrolimus-population-pharmacokinetics-and-multiple-cyp3a5-genotypes-in-black-and-white-renal-transplant-recipients
#3
Olivia Campagne, Donald E Mager, Daniel Brazeau, Rocco C Venuto, Kathleen M Tornatore
Tacrolimus exhibits inter-patient pharmacokinetic variability attributed to CYP3A5 isoenzymes and the efflux transporter, P-glycoprotein. Most black renal transplant recipients require higher tacrolimus doses compared to whites to achieve similar troughs when race-adjusted recommendations are used. An established guideline provides tacrolimus genotype dosing recommendations based on CYP3A5*1(W/T) and loss of protein function variants: CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272), CYP3A5*7 (rs41303343) and may provide more comprehensive race-adjusted dosing recommendations...
May 18, 2018: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/29774872/a-signature-based-on-survival-related-genes-identifies-high-risk-glioblastomas-harboring-immunosuppressive-and-aggressive-ecm-characteristics
#4
Di Chen, Dikang Chen, Dongqing Cao, Jian Hu, Yu Yao
To seek survival-related genes in glioblastoma and establish a survival-gene signature for predicting prognoses of glioblastoma using public databases.
 Methods: Three independent glioma databases (GEO GSE53733, CGGA, TCGA) with whole genome expression data were included for analysis. Survival-related genes were obtained by comparing the long-term (>36 months) and short-term (<12 months) survivors in the database GSE53733. CGGA was used as the training set to develop the signature and TCGA was used as the validation set...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774830/frequent-implication-of-multistress-tolerant-campylobacter-jejuni-in-human-infections
#5
Euna Oh, Linda Chui, Junghee Bae, Vincent Li, Angela Ma, Steven K Mutschall, Eduardo N Taboada, Lynn M McMullen, Byeonghwa Jeon
Campylobacter jejuni, a major cause of bacterial foodborne illnesses, is considered highly susceptible to environmental stresses. In this study, we extensively investigated the stress tolerance of 121 clinical strains of C. jejuni against 5 stress conditions (aerobic stress, disinfectant exposure, freeze-thaw, heat treatment, and osmotic stress) that this pathogenic bacterium might encounter during foodborne transmission to humans. In contrast to our current perception about high stress sensitivity of C. jejuni, a number of clinical strains of C...
June 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29774533/analysis-of-type-2-diabetes-and-obesity-genetic-variants-in-mexican-pima-indians-marked-allelic-differentiation-among-amerindians-at-hla
#6
Wen-Chi Hsueh, Peter H Bennett, Julian Esparza-Romero, Rene Urquidez-Romero, Mauro E Valencia, Eric Ravussin, Robert C Williams, William C Knowler, Leslie J Baier, Leslie O Schulz, Robert L Hanson
Prevalence of diabetes and obesity in Mexican Pima Indians is low, while prevalence in US Pima Indians is high. Although lifestyle likely accounts for much of the difference, the role of genetic factors is not well explored. To examine this, we genotyped 359 single nucleotide polymorphisms, including established type 2 diabetes and obesity variants from genome-wide association studies (GWAS) and 96 random markers, in 342 Mexican Pimas. A multimarker risk score of obesity variants was associated with body mass index (BMI; β = 0...
May 17, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29774528/slc40a1-and-cp-single-nucleotide-polymorphisms-in-porphyria-cutanea-tarda-patients-of-mixed-ancestry
#7
Isabella Brasil Succi, Luís Cristóvão Pôrto, Dayse Silva, Adriana Nascimento, Ronald Costa Neto, João Carlos Fonseca
Porphyria cutanea tarda (PCT) is a multifactorial disease; clinical expression depends on both genetic and acquired factors. Few studies have examined the connection between PCT and the regulation of iron metabolism genes other than the HFE gene. We selected five polymorphisms in the CYBRD1, CP, SLC40A1, and HAMP genes to determine whether these polymorphisms can act as genetic modulators in patients with sporadic PCT. None of the 29 patients carried the C282Y mutation. Genomic DNA from 29 PCT patients was isolated...
May 17, 2018: Annals of Human Genetics
https://www.readbyqxmd.com/read/29774473/genomic-and-probiotic-characterization-of-sjp-snu-strain-of-pichia-kudriavzevii
#8
Seung-Min Hong, Hyuk-Joon Kwon, Se-Joon Park, Won-Jin Seong, Ilhwan Kim, Jae-Hong Kim
The yeast strain SJP-SNU was investigated as a probiotic and was characterized with respect to growth temperature, bile salt resistance, hydrogen sulfide reducing activity, intestinal survival ability and chicken embryo pathogenicity. In addition, we determined the complete genomic and mitochondrial sequences of SJP-SNU and conducted comparative genomics analyses. SJP-SNU grew rapidly at 37 °C and formed colonies on MacConkey agar containing bile salt. SJP-SNU reduced hydrogen sulfide produced by Salmonella serotype Enteritidis and, after being fed to 4-week-old chickens, could be isolated from cecal feces...
May 17, 2018: AMB Express
https://www.readbyqxmd.com/read/29774245/evaluation-of-phylogenetic-reconstruction-methods-using-bacterial-whole-genomes-a-simulation-based-study
#9
John A Lees, Michelle Kendall, Julian Parkhill, Caroline Colijn, Stephen D Bentley, Simon R Harris
Background : Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods : We simulated data from a defined "true tree" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29774238/chitinase-genes-chia-s-provide-genomic-footprints-of-a-post-cretaceous-dietary-radiation-in-placental-mammals
#10
Christopher A Emerling, Frédéric Delsuc, Michael W Nachman
The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals...
May 2018: Science Advances
https://www.readbyqxmd.com/read/29774079/long-non-coding-rnas-ac026904-1-and-uca1-a-one-two-punch-for-tgf-%C3%AE-induced-snai2-activation-and-epithelial-mesenchymal-transition-in-breast-cancer
#11
Guo-Yin Li, Wei Wang, Jian-Yong Sun, Bo Xin, Xiang Zhang, Ting Wang, Qian-Feng Zhang, Li-Bo Yao, Hua Han, Dai-Ming Fan, An-Gang Yang, Lin-Tao Jia, Lei Wang
Transforming growth factor-β (TGF-β) has received much attention as a major inducer of epithelial-mesenchymal transition (EMT) during cancer progression, mainly by activating a set of pleiotropic transcription factors including SNAI2/Slug. However, the involvement of long non-coding RNAs (lncRNAs) in TGF-β-induced Slug activation and EMT remains largely unknown. Methods: In this study, we used microarray analysis to compare lncRNA expression profiles between TGF-β treated and untreated breast cancer cells...
2018: Theranostics
https://www.readbyqxmd.com/read/29774075/plectin-targeted-liposomes-enhance-the-therapeutic-efficacy-of-a-parp-inhibitor-in-the-treatment-of-ovarian-cancer
#12
Siva Sai Krishna Dasa, Galina Diakova, Ryo Suzuki, Anne M Mills, Michael F Gutknecht, Alexander L Klibanov, Jill K Slack-Davis, Kimberly A Kelly
Advances in genomics and proteomics drive precision medicine by providing actionable genetic alterations and molecularly targeted therapies, respectively. While genomic analysis and medicinal chemistry have advanced patient stratification with treatments tailored to the genetic profile of a patient's tumor, proteomic targeting has the potential to enhance the therapeutic index of drugs like poly(ADP-ribose) polymerase (PARP) inhibitors. PARP inhibitors in breast and ovarian cancer patients with BRCA1/2 mutations have shown promise...
2018: Theranostics
https://www.readbyqxmd.com/read/29774049/bioreactor-microbial-ecosystems-with-differentiated-methanogenic-phenol-biodegradation-and-competitive-metabolic-pathways-unraveled-with-genome-resolved-metagenomics
#13
Feng Ju, Yubo Wang, Tong Zhang
Background: Methanogenic biodegradation of aromatic compounds depends on syntrophic metabolism. However, metabolic enzymes and pathways of uncultured microorganisms and their ecological interactions with methanogenic consortia are unknown because of their resistance to isolation and limited genomic information. Results: Genome-resolved metagenomics approaches were used to reconstruct and dissect 23 prokaryotic genomes from 37 and 20 °C methanogenic phenol-degrading reactors...
2018: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/29774017/identifying-group-specific-sequences-for-microbial-communities-using-long-k-mer-sequence-signatures
#14
Ying Wang, Lei Fu, Jie Ren, Zhaoxia Yu, Ting Chen, Fengzhu Sun
Comparing metagenomic samples is crucial for understanding microbial communities. For different groups of microbial communities, such as human gut metagenomic samples from patients with a certain disease and healthy controls, identifying group-specific sequences offers essential information for potential biomarker discovery. A sequence that is present, or rich, in one group, but absent, or scarce, in another group is considered " group-specific " in our study. Our main purpose is to discover group-specific sequence regions between control and case groups as disease-associated markers...
2018: Frontiers in Microbiology
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
#15
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/29773867/novel-haloarchaeon-natrinema-thermophila-having-the-highest-growth-temperature-among-haloarchaea-with-a-large-genome-size
#16
Yeon Bee Kim, Joon Yong Kim, Hye Seon Song, Changsu Lee, Seung Woo Ahn, Se Hee Lee, Min Young Jung, Jin-Kyu Rhee, Juseok Kim, Dong-Wook Hyun, Jin-Woo Bae, Seong Woon Roh
Environmental temperature is one of the most important factors for the growth and survival of microorganisms. Here we describe a novel extremely halophilic archaeon (haloarchaea) designated as strain CBA1119T isolated from solar salt. Strain CBA1119T had the highest maximum and optimal growth temperatures (66 °C and 55 °C, respectively) and one of the largest genome sizes among haloarchaea (5.1 Mb). It also had the largest number of strain-specific pan-genome orthologous groups and unique pathways among members of the genus Natrinema in the class Halobacteria...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773850/comparative-genomic-analysis-of-acinetobacter-spp-plasmids-originating-from-clinical-settings-and-environmental-habitats
#17
Ileana P Salto, Gonzalo Torres Tejerizo, Daniel Wibberg, Alfred Pühler, Andreas Schlüter, Mariano Pistorio
Bacteria belonging to the genus Acinetobacter have become of clinical importance over the last decade due to the development of a multi-resistant phenotype and their ability to survive under multiple environmental conditions. The development of these traits among Acinetobacter strains occurs frequently as a result of plasmid-mediated horizontal gene transfer. In this work, plasmids from nosocomial and environmental Acinetobacter spp. collections were separately sequenced and characterized. Assembly of the sequenced data resulted in 19 complete replicons in the nosocomial collection and 77 plasmid contigs in the environmental collection...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773659/modeling-leaderless-transcription-and-atypical-genes-results-in-more-accurate-gene-prediction-in-prokaryotes
#18
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang, Mark Borodovsky
In a conventional view of the prokaryotic genome organization, promoters precede operons and RBS sites with Shine-Dalgarno consensus precede genes. However, recent experimental research suggesting a more diverse view motivated us to develop an algorithm with improved gene-finding accuracy. We describe GeneMarkS 2, an ab initio algorithm that uses a model derived by self-training for finding species-specific (native) genes, along with an array of pre-computed "heuristic" models designed to identify harder-to-detect genes (likely horizontally transferred)...
May 17, 2018: Genome Research
https://www.readbyqxmd.com/read/29773624/complete-genome-sequence-of-mycobacterium-marinum-atcc-927-t-obtained-using-nanopore-and-illumina-sequencing-technologies
#19
Mitsunori Yoshida, Hanako Fukano, Yuji Miyamoto, Keigo Shibayama, Masato Suzuki, Yoshihiko Hoshino
Mycobacterium marinum is a slowly growing, broad-host-range mycobacterial species. Here, we report the complete genome sequence of a Mycobacterium marinum type strain that was isolated from tubercles of diseased fish. This sequence will provide essential information for future taxonomic and comparative genome studies of its relatives.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29773553/intratumoral-androgen-levels-are-linked-to-tmprss2-erg-fusion-in-prostate-cancer
#20
Matias Knuuttila, Arfa Mehmood, Jenni Mäki-Jouppila, Henrik Ryberg, Pekka Taimen, Juha Knaapila, Otto Ettala, Peter J Bostrom, Claes Ohlsson, Mikko S Venäläinen, Asta Laiho, Laura L Elo, Petra Sipilä, Sari Makela, Matti Poutanen
Intratumoral androgen biosynthesis is one of the mechanisms involved in the progression of prostate cancer, and an important target for novel prostate cancer therapies. Using gas chromatography-tandem mass spectrometry and genome-wide RNA sequencing, we have analyzed androgen concentrations and androgen-regulated gene expression in cancerous and morphologically benign prostate tissue specimens and serum samples obtained from 48 primary prostate cancer patients. Intratumoral DHT concentrations were significantly higher in the cancerous tissues compared to benign prostate (p<0...
May 17, 2018: Endocrine-related Cancer
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