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https://www.readbyqxmd.com/read/27922124/convex-analysis-of-mixtures-for-separating-non-negative-well-grounded-sources
#1
Yitan Zhu, Niya Wang, David J Miller, Yue Wang
Blind Source Separation (BSS) is a powerful tool for analyzing composite data patterns in many areas, such as computational biology. We introduce a novel BSS method, Convex Analysis of Mixtures (CAM), for separating non-negative well-grounded sources, which learns the mixing matrix by identifying the lateral edges of the convex data scatter plot. We propose and prove a sufficient and necessary condition for identifying the mixing matrix through edge detection in the noise-free case, which enables CAM to identify the mixing matrix not only in the exact-determined and over-determined scenarios, but also in the under-determined scenario...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922118/mining-visualizing-and-comparing-multidimensional-biomolecular-data-using-the-genomics-data-miner-gmine-web-server
#2
Carla Proietti, Martha Zakrzewski, Thomas S Watkins, Bernard Berger, Shihab Hasan, Champa N Ratnatunga, Marie-Jo Brion, Peter D Crompton, John J Miles, Denise L Doolan, Lutz Krause
Genomics Data Miner (GMine) is a user-friendly online software that allows non-experts to mine, cluster and compare multidimensional biomolecular datasets. Various powerful visualization techniques are provided, generating high quality figures that can be directly incorporated into scientific publications. Robust and comprehensive analyses are provided via a broad range of data-mining techniques, including univariate and multivariate statistical analysis, supervised learning, correlation networks, clustering and multivariable regression...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922085/diversity-of-major-urinary-proteins-mups-in-wild-house-mice
#3
Michaela Thoß, Viktoria Enk, Hans Yu, Ingrid Miller, Kenneth C Luzynski, Boglarka Balint, Steve Smith, Ebrahim Razzazi-Fazeli, Dustin J Penn
Major urinary proteins (MUPs) are often suggested to be highly polymorphic, and thereby provide unique chemical signatures used for individual and genetic kin recognition; however, studies on MUP variability have been lacking. We surveyed populations of wild house mice (Mus musculus musculus), and examined variation of MUP genes and proteins. We sequenced several Mup genes (9 to 11 loci) and unexpectedly found no inter-individual variation. We also found that microsatellite markers inside the MUP cluster show remarkably low levels of allelic diversity, and significantly lower than the diversity of markers flanking the cluster or other markers in the genome...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921343/complete-genome-sequence-of-streptococcus-troglodytae-tku31-isolated-from-an-oral-cavity-of-chimpanzee-pan-troglodytes
#4
Masaaki Okamoto, Mariko Naito, Mayu Miyanohara, Susumu Imai, Yoshiaki Nomura, Wataru Saito, Yasuko Momoi, Kazuko Takada, Takako Miyabe-Nishiwaki, Masaki Tomonaga, Nobuhiro Hanada
Streptococcus troglodytae TKU31 was isolated from an oral cavity of chimpanzee (Pan troglodytes), and it is the most closely related species to Streptococcus mutans among the mutans group streptococci. The complete sequence of TKU31 genome consisted of a single circular chromosome that was 2,097,874 base pairs in length, with a G + C content of 37.18%. It possessed a total of 2,082 coding sequences (CDSs), 65 tRNAs and five rRNA operons (15 rRNAs). Two clustered regularly interspaced short palindromic repeats (CRISPRs), six insertion sequences (IS) and two predicted prophage elements were identified...
December 6, 2016: Microbiology and Immunology
https://www.readbyqxmd.com/read/27921136/penicillium-roqueforti-pr-toxin-gene-cluster-characterization
#5
Pedro I Hidalgo, Elisabeth Poirier, Ricardo V Ullán, Justine Piqueras, Laurence Meslet-Cladière, Emmanuel Coton, Monika Coton
PR toxin is a well-known isoprenoid mycotoxin almost solely produced by Penicillium roqueforti after growth on food or animal feed. This mycotoxin has been described as the most toxic produced by this species. In this study, an in silico analysis allowed identifying for the first time a 22.4-kb biosynthetic gene cluster involved in PR toxin biosynthesis in P. roqueforti. The pathway contains 11 open reading frames encoding for ten putative proteins including the major fungal terpene cyclase, aristolochene synthase, involved in the first farnesyl-diphosphate cyclization step as well as an oxidoreductase, an oxidase, two P450 monooxygenases, a transferase, and two dehydrogenase enzymes...
December 5, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27921008/age-related-differences-in-the-luminal-and-mucosa-associated-gut-microbiome-of-broiler-chickens-and-shifts-associated-with-campylobacter-jejuni-infection
#6
Wageha A Awad, Evelyne Mann, Monika Dzieciol, Claudia Hess, Stephan Schmitz-Esser, Martin Wagner, Michael Hess
Despite the importance of gut microbiota for broiler performance and health little is known about the composition of this ecosystem, its development and response towards bacterial infections. Therefore, the current study was conducted to address the composition and structure of the microbial community in broiler chickens in a longitudinal study from day 1 to day 28 of age in the gut content and on the mucosa. Additionally, the consequences of a Campylobacter (C.) jejuni infection on the microbial community were assessed...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27920300/the-role-of-the-nifb1-and-nifb2-promoters-in-cell-type-specific-expression-of-two-mo-nitrogenases-in-the-cyanobacterium-anabaena-variabilis-atcc-29413
#7
Susan Vernon, Brenda S Pratte, Teresa Thiel
: Anabaena variabilis ATCC 29413 has one Mo-nitrogenase that is made under oxic growth conditions in specialized cells called heterocysts and a second Mo-nitrogenase that is made only under anoxic conditions in vegetative cells. The two large nif gene clusters responsible for these two nitrogenases are under the control of the promoter of the first gene, nifB1 or nifB2, in the operon. Despite differences in expression patterns of nifB1 and nifB2 related to oxygen and cell type, the regions upstream of their transcription start sites (tss) show striking homology, including three highly conserved sequences (CS)...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27919956/expression-patterns-of-growth-and-survival-genes-with-prognostic-implications-in-advanced-pancreatic-cancer
#8
Dimitrios Pectasides, Vasiliki Kotoula, George Papaxoinis, Zoi Alexopoulou, Christos Dervenis, Epaminontas Samantas, Kleo Papaparaskeva, Elpida Charalambous, Chrysoula Gkakou, Christos Agalianos, Konstantine T Kalogeras, George Pentheroudakis, George Fountzilas
AIM: The aim of this study was to evaluate the mRNA expression pattern of growth- and survival-related genes and assess their prognostic significance in patients with advanced pancreatic cancer. PATIENTS AND METHODS: In total, 98 patients were included in this retrospective translational research study and were evaluated for Kirsten rat sarcoma viral oncogene homolog (KRAS) mutational status, and v-akt murine thymoma viral oncogene homolog 1 (AKT1), AKT serine/threonine kinase 2 (AKT2), AKT serine/threonine kinase 3 (AKT3), cyclin D1 (CCND1), epidermal growth factor receptor (EGFR), mitogen-activated protein kinase 1 (MAPK1), hepatocellular growth factor receptor (MET), avian myelomatosis viral oncogene homolog (MYC), nuclear factor kappa B subunit 1 (NFKb1), phosphatase and tensin homolog (PTEN) and mechanistic target of rapamycin (FRAP1) genes mRNA expression...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919802/integrative-view-of-2-oxoglutarate-fe-ii-dependent-oxygenase-diversity-and-functions-in-bacteria
#9
Baolei Jia, Xiaomeng Jia, Kyung Hyun Kim, Che Ok Jeon
BACKGROUND: The 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily is extremely diverse and includes enzymes responsible for protein modification, DNA and mRNA repair, and synthesis of secondary metabolites. METHODS: To investigate the evolutionary relationship and make functional inferences within this remarkably diverse superfamily in bacteria, we used a protein sequence similarity network and other bioinformatics tools to analyze the bacterial proteins in the superfamily...
December 2, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27919203/current-trends-in-molecular-diagnostics-of-chronic-myeloid-leukemia
#10
Raquel Vinhas, Milton Cordeiro, Pedro Pedrosa, Alexandra R Fernandes, Pedro V Baptista
Nearly 1.5 million people worldwide suffer from chronic myeloid leukemia (CML), characterized by the genetic translocation t(9;22)(q34;q11.2), involving the fusion of the Abelson oncogene (ABL1) with the breakpoint cluster region (BCR) gene. Early onset diagnosis coupled to current therapeutics allow for a treatment success rate of 90, which has focused research on the development of novel diagnostics approaches. In this review, we present a critical perspective on current strategies for CML diagnostics, comparing to gold standard methodologies and with an eye on the future trends on nanotheranostics...
December 6, 2016: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/27918597/seqplots-interactive-software-for-exploratory-data-analyses-pattern-discovery-and-visualization-in-genomics
#11
Przemyslaw Stempor, Julie Ahringer
Experiments involving high-throughput sequencing are widely used for analyses of chromatin function and gene expression. Common examples are the use of chromatin immunoprecipitation for the analysis of chromatin modifications or factor binding, enzymatic digestions for chromatin structure assays, and RNA sequencing to assess gene expression changes after biological perturbations. To investigate the pattern and abundance of coverage signals across regions of interest, data are often visualized as profile plots of average signal or stacked rows of signal in the form of heatmaps...
2016: Wellcome Open Res
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#12
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27918193/dna-barcodes-identify-medically-important-tick-species-in-canada
#13
Danielle A Ondrejicka, Kevin C Morey, Robert H Hanner
Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5' region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species...
July 19, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27917342/genomic-studies-of-envelope-gene-sequences-from-mosquito-and-human-samples-from-bangkok-thailand
#14
Pannamthip Pitaksajjakul, Surachet Benjathummarak, Hyun Ngoc Son, Supatra Thongrungkiat, Pongrama Ramasoota
Dengue virus (DENV) is an RNA virus showing a high degree of genetic variation as a consequence of its proofreading inability. This variation plays an important role in virus evolution and pathogenesis. Although levels of within-host genetic variation are similar following equilibrium, variation among different hosts is frequently different. To identify dengue quasispecies present among two hosts, we collected patient samples from six acute DENV cases and two pools of Aedes aegypti mosquitoes and analyzed the genetic variation of regions of the viral envelope gene...
2016: SpringerPlus
https://www.readbyqxmd.com/read/27917292/deep-resequencing-of-cftr-in-762-f508del-homozygotes-reveals-clusters-of-non-coding-variants-associated-with-cystic-fibrosis-disease-traits
#15
Briana Vecchio-Pagán, Scott M Blackman, Melissa Lee, Melis Atalar, Matthew J Pellicore, Rhonda G Pace, Arianna L Franca, Karen S Raraigh, Neeraj Sharma, Michael R Knowles, Garry R Cutting
Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5' and 5 kb 3' of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration...
2016: Human Genome Variation
https://www.readbyqxmd.com/read/27917194/a-network-approach-of-gene-co-expression-in-the-zea-mays-aspergillus-flavus-pathosystem-to-map-host-pathogen-interaction-pathways
#16
Bryan M Musungu, Deepak Bhatnagar, Robert L Brown, Gary A Payne, Greg OBrian, Ahmad M Fakhoury, Matt Geisler
A gene co-expression network (GEN) was generated using a dual RNA-seq study with the fungal pathogen Aspergillus flavus and its plant host Zea mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27917188/crispr-cas9-tool-for-qualitative-and-quantitative-plant-genome-editing
#17
REVIEW
Ali Noman, Muhammad Aqeel, Shuilin He
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#18
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27917159/predominately-uncultured-microbes-as-sources-of-bioactive-agents
#19
REVIEW
David J Newman
In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving "state of the art" genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916987/weight-loss-induced-cellular-stress-in-subcutaneous-adipose-tissue-and-the-risk-for-weight-regain-in-overweight-and-obese-adults
#20
N J T Roumans, R G Vink, F G Bouwman, P Fazelzadeh, M A van Baak, E C M Mariman
BACKGROUND/OBJECTIVE: Weight loss is often followed by weight regain after the dietary intervention (DI). Cellular stress is increased in adipose tissue of obese individuals. However, the relation between cellular stress and weight regain is unclear. Previously, we observed increased adipose tissue cellular stress of participants regaining weight compared to participants maintaining weight loss. In the current study, we further investigated the relation between weight regain and changes in the expression of stress-related genes and stress protein levels to determine possible predictors of weight regain...
December 5, 2016: International Journal of Obesity: Journal of the International Association for the Study of Obesity
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