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https://www.readbyqxmd.com/read/28633391/kmerpyramid-an-interactive-visualization-tool-for-nucleobase-and-k-mer-frequencies
#1
Jochen Kruppa, Erhard van der Vries, Wendy K Jo, Alexander Postel, Paul Becher, Albert Osterhaus, Klaus Jung
Summary: Bioinformatics methods often incorporate the frequency distribution of nulecobases or k -mers in DNA or RNA sequences, for example as part of metagenomic or phylogenetic analysis. Because the frequency matrix with sequences in the rows and nucleobases in the columns is multi-dimensional it is hard to visualize. We present the R-package 'kmerPyramid' that allows to display each sequence, based on its nucleobase or k -mer distribution projected to the space of principal components, as a point within a 3-dimensional, interactive pyramid...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632398/the-mitochondrial-protein-atlas-a-database-of-experimentally-verified-information-on-the-human-mitochondrial-proteome
#2
Noa Godin, Jerry Eichler
Given its central role in various biological systems, as well as its involvement in numerous pathologies, the mitochondrion is one of the best-studied organelles. However, although the mitochondrial genome has been extensively investigated, protein-level information remains partial, and in many cases, hypothetical. The Mitochondrial Protein Atlas (MPA; URL: lifeserv.bgu.ac.il/wb/jeichler/MPA ) is a database that provides a complete, manually curated inventory of only experimentally validated human mitochondrial proteins...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28627467/time-to-review-the-gold-standard-for-genotyping-vancomycin-resistant-enterococci-in-epidemiology-comparing-whole-genome-sequencing-with-pfge-and-mlst-in-three-suspected-outbreaks-in-sweden-during-2013-2015
#3
Birgitta Lytsy, Lars Engstrand, Åke Gustafsson, Rene Kaden
Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed. The aim of this study was to investigate the applicability of whole genome sequencing based analysis compared to Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) in epidemiological investigations as well as the development of a user friendly method for daily laboratory use...
June 13, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28626638/transcriptome-of-barley-under-three-different-heavy-metal-stress-reaction
#4
Martina Kintlová, Nicolas Blavet, Radim Cegan, Roman Hobza
In the present study, we used Illumina sequencing technology (HiSeq 2000) to sequence the transcriptome of barley (Hordeum vulgare L., cv. Morex) under three different heavy metal stress conditions: copper, zinc and cadmium. For each of those metals, the concentration causing a 50% inhibitory effect for root growth (EC50) was determined. We sequenced the total RNA of both roots and shoots from barley with and without heavy metal treatments in three replicates. Raw reads of the transcriptome project have been deposited in NCBI's BioProject accession number PRJNA382490...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28626637/transcriptome-analysis-of-reproductive-tissue-differentiation-in-jatropha-curcas-linn
#5
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Wickneswari Ratnam
Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28625989/rapid-high-throughput-identification-of-anthrax-causing-and-emetic-bacillus-cereus-group-genome-assemblies-using-btyper-a-computational-tool-for-virulence-based-classification-of-bacillus-cereus-group-isolates-using-nucleotide-sequencing-data
#6
Laura M Carroll, Jasna Kovac, Rachel A Miller, Martin Wiedmann
The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but can be particularly challenging due to the high genomic similarity of the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multi-locus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28625666/a-comparative-analysis-on-the-physicochemical-properties-of-tick-borne-encephalitis-virus-envelope-protein-residues-that-affect-its-antigenic-properties
#7
Yu S Bukin, Yu P Dzhioev, S E Tkachev, I V Kozlova, A I Paramonov, D Ruzek, Z Qu, V I Zlobin
This work is dedicated to the study of the variability of the main antigenic envelope protein E among different strains of tick-borne encephalitis virus at the level of physical and chemical properties of the amino acid residues. E protein variants were extracted from then NCBI database. Four amino acid residues properties in the polypeptide sequences were investigated: the average volume of the amino acid residue in the protein tertiary structure, the number of amino acid residue hydrogen bond donors, the charge of amino acid residue lateral radical and the dipole moment of the amino acid residue...
June 15, 2017: Virus Research
https://www.readbyqxmd.com/read/28622375/identification-of-benthic-diatoms-isolated-from-the-eastern-tidal-flats-of-the-yellow-sea-comparison-between-morphological-and-molecular-approaches
#8
Sung Min An, Dong Han Choi, Jung Ho Lee, Howon Lee, Jae Hoon Noh
Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene...
2017: PloS One
https://www.readbyqxmd.com/read/28621814/identification-and-characterization-of-the-zebrafish-glutathione-s-transferase-pi-1
#9
Maryam S Abunnaja, Katsuhisa Kurogi, Yasir I Mohammed, Yoichi Sakakibara, Masahito Suiko, Ezdihar A Hassoun, Ming-Cheh Liu
Zebrafish has in recent years emerged as a popular vertebrate model for use in pharmacological and toxicological studies. While there have been sporadic studies on the zebrafish glutathione S-transferases (GSTs), the zebrafish GST gene superfamily still awaits to be fully elucidated. We report here the identification of 15 zebrafish cytosolic GST genes in NCBI GenBank database and the expression, purification, and enzymatic characterization of the zebrafish cytosolic GST Pi-1 (GSTP1). The cDNA encoding the zebrafish GSTP1 was cloned from a 3-month-old female zebrafish, expressed in Eschelichia coli host cells, and purified...
June 16, 2017: Journal of Biochemical and Molecular Toxicology
https://www.readbyqxmd.com/read/28619636/isolation-and-characterization-of-a-non-specific-lipid-transfer-protein-from-chelidonium-majus-l-latex
#10
Robert Nawrot, Damian Jozefiak, Anna Sip, Dorota Kuzma, Oskar Musidlak, Anna Gozdzicka-Jozefiak, Jakub Barylski
Plant non-specific lipid transfer proteins (nsLTPs) are small basic proteins, which mostly play a role in intracellular lipid transport and antimicrobial defense. Recently it was shown using shotgun proteomic approach that the whole plant extract of Chelidonium majus L. (Papaveraceae) contains relatively abundant nsLTPs. Therefore the aim of the work was to isolate and characterize nsLTP from C. majus latex. RESULTS: obtained using PCR approach with degenerate primers showed nsLTP protein from C...
June 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28617857/variability-in-citxet-expression-and-xet-activity-in-citrus-cultivar-huangguogan-seedlings-with-differed-degrees-of-etiolation
#11
Bo Xiong, Xianjie Gu, Xia Qiu, Zhixiang Dong, Shuang Ye, Guochao Sun, Shengjia Huang, Xinya Liu, Lijuan Xi, Zhihui Wang
Considering the known effects of xyloglucan endotransglycosylase (XET) on plant growth and development, we aimed to determine whether XETs help to regulate the growth and elongation of Huangguogan shoots and roots. We confirmed a possible role for XET during seedling etiolation. Our results revealed that the roots of etiolated seedlings (H-E) were longer than those of green seedlings (H-G). However, shoot length exhibited the opposite pattern. We also observed positive and negative effects on the xyloglucan-degrading activity of XET in the root sub-apical region and shoots of etiolated Huangguogan seedling, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28615886/first-record-on-the-occurrence-of-ryukyua-circularis-pillai-1954-a-parasitic-cymothoid-crustacean-isopoda-infesting-the-clupeid-fish-amblygaster-sirm-walbaum-from-andaman-islands-india
#12
J Praveenraj, K Saravanan, P Puneeth Kumar, S Ravichandran, Arunjyoti Baruah, S Monalisha Devi, R Kiruba Sankar, S Dam Roy
In the present study, occurrence of branchial parasitic cymothoid, Ryukyua circularis from the marine finfish, Amblygaster sirm is reported for the first time from Andaman Islands. Morphological characterization was carried out which confirmed the parasite as R. circularis. Molecular characterization using 28S rDNA revealed 443 bp sequence which has been submitted to NCBI GenBank under the accession no. KX090447. Ten female and one male parasite (R. circularis) were collected from the branchial cavity of the individual host fishes (A...
June 2017: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
https://www.readbyqxmd.com/read/28615636/autotransporter-domain-dependent-enzymatic-analysis-of-a-novel-extremely-thermostable-carboxylesterase-with-high-biodegradability-towards-pyrethroid-pesticides
#13
Xianghai Cai, Wei Wang, Lin Lin, Dannong He, Gang Huang, Yaling Shen, Wei Wei, Dongzhi Wei
The EstPS1 gene, which encodes a novel carboxylesterase of Pseudomonas synxantha PS1 isolated from oil well-produced water, was cloned and sequenced. EstPS1 has an open reading frame of 1923 bp and encodes the 640-amino acid carboxylesterase (EstPS1), which contains an autotransporter (AT) domain (357-640 amino acids). Homology analysis revealed that EstPS1 shared the highest identity (88%) with EstA from Pseudomonas fluorescens A506 (NCBI database) and belonged to the carboxylesterase family (EC 3.1.1.1). The optimum pH and temperature of recombinant EstPS1 were found to be 8...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614366/de-novo-transcriptomic-analysis-and-development-of-est-ssrs-for-sorbus-pohuashanensis-hance-hedl
#14
Congcong Liu, Ying Dou, Xuelian Guan, Qiang Fu, Ze Zhang, Zenghui Hu, Jian Zheng, Yizeng Lu, Wei Li
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species...
2017: PloS One
https://www.readbyqxmd.com/read/28612535/-prediction-and-analysis-of-epitopes-in-clpp2-of-mycobacterium-tuberculosis
#15
Si-Jing Liu, Ming-Juan Jiang, Qi-Kang Pu, Chen-Yan Ren, Lin Su, Xiang Zhang, Chuan Wang
OBJECTIVES: To predict and analyze the antigenic epitopes in Mycobacterium tuberculosis protein caseinolytic protease P2 (clpP2), and explore its possibility to be applied as a new tuberculosis (TB) vaccine and drug development target. METHODS: Secondary structure of clpP2 based on nucleic sequence was predicted by DNA Star software. The homologous sequence conformation were analyzed by Swiss-Model online software. T cells antigenic epitopes were predicted through VaxiPred, and B cell epitopes were predicted by combining use of several different prediction programs, such as ABCpred, COBEPro and BepiPredPred...
March 2017: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28612275/the-recent-importation-of-grapevine-pinot-gris-virus-into-australia
#16
Qi Wu, Nuredin Habili
A total of 575 commercial grapevine (Vitis vinifera) samples from Australia have been tested for a newly emerging virus, Grapevine Pinot gris virus (Trichovirus, Betaflexiviridae) during 2015-2017. Nine samples from two states tested positive. Six of these were from New South Wales and 3 from South Australia in a total of eight varieties. All these varieties were imported from Europe within the last 4-19 years. A fragment of 431 nucleotides on the coat protein gene of Grapevine Pinot gris virus was targeted for virus identification by RT-PCR...
June 13, 2017: Virus Genes
https://www.readbyqxmd.com/read/28611956/comparative-genomic-and-phylogenetic-analysis-of-a-shiga-toxin-producing-shigella-sonnei-stss-strain
#17
Domonkos Sváb, Balázs Bálint, Bálint Vásárhelyi, Gergely Maróti, István Tóth
Shigella strains are important agents of bacillary dysentery, and in recent years Shigella sonnei has emerged as the leading cause of shigellosis in industrialized and rapidly developing countries. More recently, several S. sonnei and Shigella flexneri strains producing Shiga toxin (Stx) have been reported from sporadic cases and from an outbreak in America. In the present study we aimed to shed light on the evolution of a recently identified Shiga toxin producing S. sonnei (STSS) isolated in Europe. Here we report the first completely assembled whole genome sequence of a multidrug resistant (MDR) Stx-producing S...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28609482/quickly-identifying-identical-and-closely-related-subjects-in-large-databases-using-genotype-data
#18
Yumi Jin, Alejandro A Schäffer, Stephen T Sherry, Michael Feolo
Genome-wide association studies (GWAS) usually rely on the assumption that different samples are not from closely related individuals. Detection of duplicates and close relatives becomes more difficult both statistically and computationally when one wants to combine datasets that may have been genotyped on different platforms. The dbGaP repository at the National Center of Biotechnology Information (NCBI) contains datasets from hundreds of studies with over one million samples. There are many duplicates and closely related individuals both within and across studies from different submitters...
2017: PloS One
https://www.readbyqxmd.com/read/28608322/long-evans-rat-spermatogonial-lines-are-effective-germline-vectors-for-transgenic-rat-production
#19
F Kent Hamra, Christopher T Richie, Brandon K Harvey
Long Evans rat strains are applied as research models in a broad spectrum of biomedical fields (>15,800 citations, NCBI PubMed). Here, we report an approach to genetically modify the Long Evans rat germline in donor spermatogonial stem cells. Long Evans rat spermatogonial lines were derived from freshly isolated laminin-binding spermatogonia. Laminin-binding spermatogonia were cultured over multiple passages on fibroblast feeder layers in serum-free culture medium containing GDNF and FGF2. Long Evans rat spermatogonial lines were genetically modified by transposon transduction to express a germline, tdTomato reporter gene...
June 12, 2017: Transgenic Research
https://www.readbyqxmd.com/read/28606843/the-effect-of-diosmin-on-the-blood-proteome-in-a-rat-model-of-venous-thrombosis
#20
Cuilin Cheng, Hong Zhang, Yongzhi Li, Yingyu Zhou, Weihong Lu, Lei Yao
This study was designed to find the protein changes of venous thrombosis in Wistar rats with and without diosmin treatment by two-dimensional gel electrophoresis (2-DE) and investigate the effect of a crucial protein known as CEP350 on human vascular endothelial cell growth. Diosmin was prepared from G.verum L. by solvent extraction and identified 98% purification by HPLC after chromatographic purification using macroporous absorption resin (AB-8) and polyamide. Wistar rats were divided into three groups respectively control group, model group and prevention group...
June 9, 2017: International Journal of Biological Macromolecules
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