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Comparative genomics

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https://www.readbyqxmd.com/read/29346588/genome-sequencing-of-museum-specimens-reveals-rapid-changes-in-the-genetic-composition-of-honey-bees-in-california
#1
Julie M Cridland, Santiago R Ramirez, Cheryl A Dean, Amber Sciligo, Neil D Tsutsui
The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years...
January 15, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#2
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346530/bacterioplankton-composition-in-tropical-high-elevation-lakes-of-the-andean-plateau
#3
Pablo Aguilar, Cristina Dorador, Irma Vila, Ruben Sommaruga
High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbour a unique genomic repertoire, but their composition and diversity are largely unknown. Here we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (???4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. OTUs composition was significantly different among lakes and between seasons...
January 16, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29346449/within-host-selection-for-faster-replicating-bacterial-symbionts
#4
Ewa Chrostek, Luis Teixeira
Wolbachia is a widespread, intracellular symbiont of arthropods, able to induce reproductive distortions and antiviral protection in insects. Wolbachia can also be pathogenic, as is the case with wMelPop, a virulent variant of the endosymbiont of Drosophila melanogaster. An extensive genomic amplification of the 20kb region encompassing eight Wolbachia genes, called Octomom, is responsible for wMelPop virulence. The Octomom copy number in wMelPop can be highly variable between individual D. melanogaster flies, even when comparing siblings arising from a single female...
2018: PloS One
https://www.readbyqxmd.com/read/29346437/tissue-specific-transcriptome-analyses-provide-new-insights-into-gpcr-signalling-in-adult-schistosoma-mansoni
#5
REVIEW
Steffen Hahnel, Nic Wheeler, Zhigang Lu, Arporn Wangwiwatsin, Paul McVeigh, Aaron Maule, Matthew Berriman, Timothy Day, Paula Ribeiro, Christoph G Grevelding
Schistosomes are blood-dwelling trematodes with global impact on human and animal health. Because medical treatment is currently based on a single drug, praziquantel, there is urgent need for the development of alternative control strategies. The Schistosoma mansoni genome project provides a platform to study and connect the genetic repertoire of schistosomes to specific biological functions essential for successful parasitism. G protein-coupled receptors (GPCRs) form the largest superfamily of transmembrane receptors throughout the Eumetazoan phyla, including platyhelminths...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29346379/a-putative-lateral-flagella-of-the-cystic-fibrosis-pathogen-burkholderia-dolosa-regulates-swimming-motility-and-host-cytokine-production
#6
Damien Roux, Matthew Schaefers, Bradley S Clark, Molly Weatherholt, Diane Renaud, David Scott, John J LiPuma, Gregory Priebe, Craig Gerard, Deborah R Yoder-Himes
Burkholderia dolosa caused an outbreak in the cystic fibrosis clinic at Boston Children's Hospital and was associated with high mortality in these patients. This species is part of a larger complex of opportunistic pathogens known as the Burkholderia cepacia complex (Bcc). Compared to other species in the Bcc, B. dolosa is highly transmissible; thus understanding its virulence mechanisms is important for preventing future outbreaks. The genome of one of the outbreak strains, AU0158, revealed a homolog of the lafA gene encoding a putative lateral flagellin, which, in other non-Bcc species, is used for movement on solid surfaces, attachment to host cells, or movement inside host cells...
2018: PloS One
https://www.readbyqxmd.com/read/29346103/wavedec-a-wavelet-approach-to-identify-both-shared-and-individual-patterns-of-copy-number-variations
#7
Hongmin Cai, Peihua Chen, Jiazhou Chen, Jiulun Cai, Yan Song, Guoqiang Han
Copy-number variations (CNVs) are associated with complex diseases and particular tumor types. Array-based comparative genomic hybridization (aCGH) is a common approach for the detection of CNVs. Traditional CNV detection methods for multiple aCGH samples mainly use batch samples to find common variations, not accounting for the individual characteristics of each sample. Accurately differentiating both the commonly shared and the individual CNV patterns is pivotal to identify cell populations, or to distinguish cell growth (as in cancer) from invasion of new cells...
February 2018: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/29345800/haplotype-based-genotyping-by-sequencing-in-oat-genome-research
#8
Wubishet A Bekele, Charlene P Wight, Shiaoman Chao, Catherine J Howarth, Nicholas A Tinker
In a de-novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker-density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel...
January 18, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#9
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29345613/comparative-transcriptomics-of-aspergillus-fumigatus-strains-upon-exposure-to-human-airway-epithelial-cells
#10
Tonya N Watkins, Hong Liu, Matthew Chung, Tracy H Hazen, Julie C Dunning Hotopp, Scott G Filler, Vincent M Bruno
Aspergillus fumigatus is an opportunistic, ubiquitous, saprophytic mould that can cause severe allergic responses in atopic individuals as well as life-threatening infections in immunocompromised patients. A critical step in the establishment of infection is the invasion of airway epithelial cells by the inhaled fungi. Understanding how A. fumigatus senses and responds to airway cells is important to understand the pathogenesis of invasive pulmonary aspergillosis. Here, we analysed the transcriptomes of two commonly used clinical isolates, Af293 and CEA10, during infection of the A549 type II pneumocyte cell line in vitro...
January 18, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29345414/molecular-characterization-of-a-series-of-990-index-patients-with-albinism
#11
E Lasseaux, C Plaisant, V Michaud, P Pennamen, A Trimouille, L Gaston, S Monfermé, D Lacombe, C Rooryck, F Morice-Picard, B Arveiler
Albinism is a clinically and genetically heterogeneous disease characterized by variable degrees of hypopigmentation and by nystagmus, foveal hypoplasia, and chiasmatic misrouting of the optic nerves. The wide phenotypic heterogeneity impedes the establishment of phenotype-genotype correlations. In order to obtain a precise diagnosis we screened the 19 known albinism genes in 990 index patients using targeted next generation sequencing (NGS) and high resolution comparative genomic hybridization. A molecular diagnosis was obtained in 72...
January 18, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29345073/improving-accuracy-of-genomic-prediction-in-brangus-cattle-by-adding-animals-with-imputed-low-density-snp-genotypes
#12
F B Lopes, X-L Wu, H Li, J Xu, T Perkins, J Genho, R Ferretti, R G Tait, S Bauck, G J M Rosa
Reliable genomic prediction of breeding values for quantitative traits requires the availability of sufficient number of animals with genotypes and phenotypes in the training set. As of 31 October 2016, there were 3,797 Brangus animals with genotypes and phenotypes. These Brangus animals were genotyped using different commercial SNP chips. Of them, the largest group consisted of 1,535 animals genotyped by the GGP-LDV4 SNP chip. The remaining 2,262 genotypes were imputed to the SNP content of the GGP-LDV4 chip, so that the number of animals available for training the genomic prediction models was more than doubled...
February 2018: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/29345010/genetic-variation-in-the-shape-of-cold-survival-curves-in-a-single-fly-population-suggests-potential-for-selection-from-climate-variability
#13
Nicholas M Teets, Daniel A Hahn
Temperature variation is one of the primary challenges facing ectotherms, and the ability to tolerate a range of thermal environments is critical for setting current and future species distributions. Low temperature is particularly challenging for ectotherms because winter conditions have strong latitudinal and temporal variation. Lower lethal temperature (LLT) is a common metric of cold tolerance used in studies of local adaptation and plasticity. Comparisons of LLT across groups typically assume parallel S-shaped survival curves, but genetic variation in the shape of survival vs...
January 18, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29344954/mixed-ductal-lobular-carcinomas-evidence-for-progression-from-ductal-to-lobular-morphology
#14
Amy E McCart Reed, Jamie R Kutasovic, Katia Nones, Jodi M Saunus, Leonard Da Silva, Felicity Newell, Stephen Kazakoff, Lewis Melville, Janani Jayanthan, Ana Cristina Vargas, Lynne E Reid, Jonathan Beesley, Xiao Qing Chen, Anne Marie Patch, D David Clouston, Alan Porter, Elizabeth Evans, John V Pearson, Georgia Chenevix-Trench, Margaret C Cummings, Nic Waddell, Sunil R Lakhani, Peter T Simpson
Mixed ductal-lobular carcinomas (MDL) display both ductal and lobular morphology, and are an archetypal example of intra-tumour morphological heterogeneity. The mechanisms underlying coexistence of these different morphologic entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinico-pathological analysis of a cohort of 82 MDLs and found: i) MDLs more frequently co-exist with ductal carcinoma in situ (DCIS) than lobular carcinoma in situ (LCIS); ii) the E-cadherin-catenin complex was normal in the ductal component in 77...
January 18, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344851/the-evolution-of-crispr-cas9-and-their-cousins-hope-or-hype
#15
REVIEW
Kulbhushan Chaudhary, Anirudha Chattopadhyay, Dharmendra Pratap
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system allows biologists to edit genomic DNA of any cell in precise and specific way, entailing great potential for crop improvement, drug development and gene therapy. The system involves a nuclease (Cas9) and a designed guide RNA that are involved in wide range of applications such as genome modification, transcriptional modulation, genomic loci marking and RNA tracking. The limitation of the technique, in view of resistance of thymidine-rich genome to Cas9 cleavage, has now been overcome by the use of Cpf1 nuclease...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29344811/metabolic-evolution-and-a-comparative-omics-analysis-of-corynebacterium-glutamicum-for-putrescine-production
#16
Zhen Li, Yu-Ping Shen, Xuan-Long Jiang, Li-Shen Feng, Jian-Zhong Liu
Putrescine is widely used in the industrial production of bioplastics, pharmaceuticals, agrochemicals, and surfactants. Because the highest titer of putrescine is much lower than that of its precursor L-ornithine reported in microorganisms to date, further work is needed to increase putrescine production in Corynebacterium glutamicum. We first compared 7 ornithine decarboxylase genes and found that the Enterobacter cloacae ornithine decarboxylase gene speC1 was most suitable for putrescine production in C. glutamicum...
January 17, 2018: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29344651/identification-of-genes-and-pathways-in-the-synovia-of-women-with-osteoarthritis-by-bioinformatics-analysis
#17
Bobin Mi, Guohui Liu, Wu Zhou, Huijuan Lv, Yi Liu, Jing Liu
Osteoarthritis (OA) has a high prevalence in female patients and sex may be a key factor affecting the progression of OA. The aim of the present study was to identify genetic signatures in the synovial membranes of female patients with OA and to elucidate the potential associated molecular mechanisms. The gene expression profiles of the GSE55457 and GSE55584 datasets were obtained from the Gene Expression Omnibus database. Data of two synovial membranes from normal female individuals (GSM1337306 and GSM1337310) and two synovial membranes from female patients affected by OA (GSM1337327 and GSM1337330) were obtained from the dataset GSE55457, and those of three synovial membranes from female patients affected by OA (GSM1339628, GSM1339629 and GSM1339632) were obtained from the dataset GSE55584...
January 15, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29344158/construction-of-the-pot1-promoter-report-gene-vector-and-the-effect-and-underlying-mechanism-of-the-pot1-promoter-in-regulating-telomerase-and-telomere-length
#18
Liang Zeng, Yue-Li Wang, Fa Wang, Shi-Quan Cui, Liang Hu, Di-Nan Huang, Gan Hou
By using human genomic DNA as a template to clone protection of telomere 1 (POT1) promoter gene segments and construct the POT1 promoter luciferase report gene vector (pGL3-Control-POT1-promoter), the association between POT1, and the regulation of telomerase and telomere length was investigated. In the present study, two recombinant luciferase report gene vectors were constructed, which included different regions of the POT1 promoter. The plasmids were transformed into DH5α and the positive clones were obtained...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344121/a-five-gene-based-risk-score-with-high-prognostic-value-in-colorectal-cancer
#19
Yida Pan, Hongyang Zhang, Mingming Zhang, Jie Zhu, Jianghong Yu, Bangting Wang, Jigang Qiu, Jun Zhang
Colorectal cancer (CRC) is one of the most frequently occurring malignancies worldwide. The outcomes of patients with similar clinical symptoms or at similar pathological stages remain unpredictable. This inherent clinical diversity is most likely due to the genetic heterogeneity. The present study aimed to create a predicting tool to evaluate patient survival based on genetic profile. Firstly, three Gene Expression Omnibus (GEO) datasets (GSE9348, GSE44076 and GSE44861) were utilized to identify and validate differentially expressed genes (DEGs) in CRC...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29343788/multiple-losses-of-photosynthesis-and-convergent-reductive-genome-evolution-in-the-colourless-green-algae-prototheca
#20
Shigekatsu Suzuki, Rikiya Endoh, Ri-Ichiroh Manabe, Moriya Ohkuma, Yoshihisa Hirakawa
Autotrophic eukaryotes have evolved by the endosymbiotic uptake of photosynthetic organisms. Interestingly, many algae and plants have secondarily lost the photosynthetic activity despite its great advantages. Prototheca and Helicosporidium are non-photosynthetic green algae possessing colourless plastids. The plastid genomes of Prototheca wickerhamii and Helicosporidium sp. are highly reduced owing to the elimination of genes related to photosynthesis. To gain further insight into the reductive genome evolution during the shift from a photosynthetic to a heterotrophic lifestyle, we sequenced the plastid and nuclear genomes of two Prototheca species, P...
January 17, 2018: Scientific Reports
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