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https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#1
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28101936/quantitative-itraq-based-proteomic-analysis-of-rice-grains-to-assess-high-night-temperature-stress
#2
Hong-Yu Zhang, Gang Lei, Hui-Wen Zhou, Chao He, Jiang-Lin Liao, Ying-Jin Huang
Rice yield and quality are adversely affected by increasing global surface temperature, and are strongly attributed to high night temperature (HNT) than high daytime temperature. However, the molecular mechanism underlying the heat-tolerant characteristics of rice remains unclear. In the present study, we compared the proteomes of heat-tolerant and -sensitive lines of rice at early milky stage using an iTRAQ method. We have identified 38 differentially expressed proteins between the two lines, of which 32 proteins have been functionally annotated in NCBI and/or the UniProt database...
January 19, 2017: Proteomics
https://www.readbyqxmd.com/read/28099838/osteoarthritis-year-in-review-2016-biomarkers-biochemical-markers
#3
REVIEW
A Mobasheri, A-C Bay-Jensen, W E van Spil, J Larkin, M C Levesque
PURPOSE: The aim of this "Year in Review" article is to summarize and discuss the implications of biochemical marker related articles published between the Osteoarthritis Research Society International (OARSI) 2015 Congress in Seattle and the OARSI 2016 Congress in Amsterdam. METHODS: The PubMed/MEDLINE bibliographic database was searched using the combined keywords: 'biomarker' and 'osteoarthritis'. The PubMed/MEDLINE literature search was conducted using the Advanced Search Builder function (http://www...
January 2, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28097169/molecular-characterization-of-argulus-bengalensis-and-argulus-siamensis-crustacea-argulidae-infecting-the-cultured-carps-in-west-bengal-india-using-18s-rrna-gene-sequences
#4
Avijit Patra, Anjan Mondal, Sayani Banerjee, Harresh Adikesavalu, Siddhartha Narayan Joardar, Thangapalam Jawahar Abraham
The present study characterized Argulus spp. infecting the cultured carps using 18S rRNA gene sequences, estimated the genetic similarity among Argulus spp. and established their phylogenetic relationship. Of the 320 fish samples screened, 34 fish (10.6%) had Argulus infection. The parasitic frequency index (PFI) was observed to be high (20%) in Hypophthalmichthys molitrix and Labeo bata. The frequency of infection was high in September (PFI: 17%) and October (PFI: 12.9%). The 18S rRNA sequences of five A. bengalensis (KF583878, KF192316, KM016968, KM016969, and KM016970) and one A...
September 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28096900/ms_histonedb-a-manually-curated-resource-for-proteomic-analysis-of-human-and-mouse-histones
#5
Sara El Kennani, Annie Adrait, Alexey K Shaytan, Saadi Khochbin, Christophe Bruley, Anna R Panchenko, David Landsman, Delphine Pflieger, Jérôme Govin
BACKGROUND: Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28094579/expression-profile-of-the-integrin-receptor-subunits-in-the-guinea-pig-sclera
#6
Kevin K Wang, Ravikanth Metlapally, Christine F Wildsoet
PURPOSE: The ocular dimensional changes in myopia reflect increased scleral remodeling, and in high myopia, loss of scleral integrity leads to biomechanical weakening and continued scleral creep. As integrins, a type of cell surface receptors, have been linked to scleral remodeling, they represent potential targets for myopia therapies. As a first step, this study aimed to characterize the integrin subunits at the messenger RNA level in the sclera of the guinea pig, a more recently added but increasingly used animal model for myopia research...
January 17, 2017: Current Eye Research
https://www.readbyqxmd.com/read/28093673/metagenomic-insights-into-effects-of-spent-engine-oil-perturbation-on-the-microbial-community-composition-and-function-in-a-tropical-agricultural-soil
#7
Lateef B Salam, Sunday O Obayori, Francisca O Nwaokorie, Aisha Suleiman, Raheemat Mustapha
Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23...
January 16, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28087515/h-blast-a-fast-protein-sequence-alignment-toolkit-on-heterogeneous-computers-with-gpus
#8
Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
MOTIVATION: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. RESULTS: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
January 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28078751/cardiac-remodelling-during-normotensive-and-hypertensive-complicated-pregnancies-a-systematic-review-and-meta-analysis
#9
REVIEW
Sander de Haas, Chahinda Ghossein-Doha, Lauren Geerts, Sander Mj van Kuijk, Joris van Drongelen, Marc Ea Spaanderman
OBJECTIVE: The aim of this systematic review and meta-analyses was to comprehensively describe the normotensive pattern of cardiac remodelling during human singleton pregnancies and compared to that during hypertensive complicated pregnancies. METHODS: We performed a meta-analysis of the current literature on cardiac remodelling during normotensive and complicated pregnancies. Literature was retrieved from PubMed (NCBI) and Embase (Ovid) databases. Included studies needed to report a reference measurement (matched non-pregnant control group, pre-pregnancy, or post-partum) and measurements during a predetermined gestational interval...
January 12, 2017: Ultrasound in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28077563/the-bioc-biogrid-corpus-full-text-articles-annotated-for-curation-of-protein-protein-and-genetic-interactions
#10
Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-Aryamontri, Christie S Chang, Rose Oughtred, Jennifer Rust, W John Wilbur, Donald C Comeau, Kara Dolinski, Mike Tyers
A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28073829/dutpase-dut-is-mutated-in-a-novel-monogenic-syndrome-with-diabetes-and-bone-marrow-failure
#11
Reinaldo Sousa Dos Santos, Mathilde Daures, Anne Philippi, Sophie Romero, Lorella Marselli, Piero Marchetti, Valérie Senée, Delphine Bacq, Céline Besse, Baz Baz, Laura Marroquí, Sarah Ivanoff, Julien Masliah-Planchon, Marc Nicolino, Jean Soulier, Gérard Socié, Decio L Eizirik, Jean-François Gautier, Cécile Julier
We describe a new syndrome characterized by early onset diabetes mellitus, associated with bone marrow failure affecting mostly the erythrocytic lineage. Using whole exome sequencing in a remotely consanguineous patient from a family with two affected siblings, we identified a single homozygous missense mutation (chr15.hg19:g.48,626,619A>G) located in the dUTPase (DUT) gene (NCBI Gene ID: 1854), affecting both the mitochondrial (DUT-M p.Y142C) and the nuclear (DUT-N p.Y54C) isoforms. We found the same homozygous mutation in an unrelated consanguineous patient with diabetes and bone marrow aplasia from a family with two affected siblings, while none of the >60,000 subjects from the Exome Aggregation Consortium (ExAC) was homozygous for this mutation...
January 10, 2017: Diabetes
https://www.readbyqxmd.com/read/28073756/feature-selection-using-a-one-dimensional-na%C3%A3-ve-bayes-classifier-increases-the-accuracy-of-support-vector-machine-classification-of-cdr3-repertoires
#12
Mattia Cinelli, Yuxin Sun, Katharine Best, James M Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain
MOTIVATION: Somatic DNA recombination, the hallmark of vertebrate adaptive immunity, has the potential to generate a vast diversity of antigen receptor sequences. How this diversity captures antigen specificity remains incompletely understood. In this study we use high throughput sequencing to compare the global changes in T cell receptor β chain complementarity determining region 3 (CDR3β) sequences following immunization with ovalbumin administered with complete Freund's adjuvant (CFA) or CFA alone...
January 10, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28073082/vibrio-parahaemolyticus-o4-k8-forms-a-potential-predominant-clone-in-southern-china-as-detected-by-whole-genome-sequence-analysis
#13
Baisheng Li, Xingfen Yang, Hailing Tan, Bixia Ke, Dongmei He, Changwen Ke, Yonghui Zhang
Vibrio parahaemolyticus has been the most common food-borne pathogen in southern China, especially the O3:K6 pandemic clone and its serovariants. Recently, the serotype O4:K8 became more and more prevalent in southern China, which was different from the O3:K6 pandemic clone. Thus, the aim of the present work was to elucidate the molecular characteristics of the O4:K8. Some O3:K6 pandemic clone and its serovariants isolated in the same period were selected for comparative analysis, which were still dominant clone locally...
January 4, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28070539/data-on-genome-analysis-of-mycoplasmagallisepticum-during-intracellular-infection
#14
Daria Matyushkina, Olga Pobeguts, Irina Garanina, Vladislav Babenko, Maria Vakhitova, Gleb Fisunov, Vadim Govorun
The genus Mycoplasma relates to Gram-positive bacteria that lack a cell wall and are capable to cause chronic disease in humans and animals. Among the agents of infection and disease in domestic poultry and wild birds, Mycoplasma gallisepticum is the most important mycoplasma species, causing considerable losses in the poultry industry. In the present paper, we provide data on adaptation of M. gallisepticum to the eukaryotic host cells on the genomic level. The major changes were predominantly localized in the VlhA-hemagglutinin genes which are important components of pathogenesis...
February 2017: Data in Brief
https://www.readbyqxmd.com/read/28070488/transcriptome-profiling-of-elettaria-cardamomum-l-maton-small-cardamom
#15
F Nadiya, N Anjali, Jinu Thomas, A Gangaprasad, K K Sabu
Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28070487/unraveling-the-microbial-and-functional-diversity-of-coamo-thermal-spring-in-puerto-rico-using-metagenomic-library-generation-and-shotgun-sequencing
#16
Ricky Padilla-Del Valle, Luis R Morales-Vale, Carlos Ríos-Velázquez
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28068515/comparative-analysis-of-amino-acid-composition-in-the-active-site-of-nirk-gene-encoding-copper-containing-nitrite-reductase-cunir-in-bacterial-spp
#17
Utpal Kumar Adhikari, M Mizanur Rahman
The nirk gene encoding the copper-containing nitrite reductase (CuNiR), a key catalytic enzyme in the environmental denitrification process that helps to produce nitric oxide from nitrite. The molecular mechanism of denitrification process is definitely complex and in this case a theoretical investigation has been conducted to know the sequence information and amino acid composition of the active site of CuNiR enzyme using various Bioinformatics tools. 10 Fasta formatted sequences were retrieved from the NCBI database and the domain and disordered regions identification and phylogenetic analyses were done on these sequences...
December 31, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28068324/role-of-akt2-in-regulation-of-metastasis-suppressor-1-expression-and-colorectal-cancer-metastasis
#18
E Agarwal, C M Robb, L M Smith, M G Brattain, J Wang, J D Black, S Chowdhury
Survival signaling is critical for the metastatic program of cancer cells. The current study investigated the role of Akt survival proteins in colorectal cancer (CRC) metastasis and explored potential mechanisms of Akt-mediated metastasis regulation. Using an orthotopic implantation model in mice, which uniquely recapitulates the entire multistep process of CRC metastasis, combined with an inducible system of short hairpin RNA-mediated Akt isoform knockdown in human CRC cells, our studies confirm a role of Akt2 in CRC cell dissemination to distant organs in vivo...
January 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28066713/sequencing-and-de-novo-transcriptome-assembly-of-anthopleura-dowii-verrill-1869-from-mexico
#19
Jorge-Tonatiuh Ayala-Sumuano, Alexei Licea-Navarro, Enrique Rudiño-Piñera, Estefanía Rodríguez, Claudia Rodríguez-Almazán
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Moreover, the development of tools for big data set analysis has allowed the identification of molecules and networks involved in metabolism, evolution or behavior. By natural habitats aquatic organisms have implemented molecular strategies for survival, including the production and secretion of toxic compounds for their predators; therefore these organisms are possible sources of proteins or peptides with potential biotechnological application...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28066712/de-novo-transcriptome-assembly-of-shrimp-palaemon-serratus
#20
Alejandra Perina, Ana M González-Tizón, Iago F Meilán, Andrés Martínez-Lage
: The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769...
March 2017: Genomics Data
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