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https://www.readbyqxmd.com/read/28239666/making-the-most-of-rna-seq-pre-processing-sequencing-data-with-opossum-for-reliable-snp-variant-detection
#1
Laura Oikkonen, Stefano Lise
Identifying variants from RNA-seq (transcriptome sequencing) data is a cost-effective and versatile alternative to whole-genome sequencing. However, current variant callers do not generally behave well with RNA-seq data due to reads encompassing intronic regions. We have developed a software programme called Opossum to address this problem. Opossum pre-processes RNA-seq reads prior to variant calling, and although it has been designed to work specifically with Platypus, it can be used equally well with other variant callers such as GATK HaplotypeCaller...
January 17, 2017: Wellcome Open Res
https://www.readbyqxmd.com/read/28239387/comprehensive-analysis-of-the-cdpk-snrk-superfamily-genes-in-chinese-cabbage-and-its-evolutionary-implications-in-plants
#2
Peng Wu, Wenli Wang, Weike Duan, Ying Li, Xilin Hou
The CDPK-SnRK (calcium-dependent protein kinase/Snf1-related protein kinase) gene superfamily plays important roles in signaling pathways for disease resistance and various stress responses, as indicated by emerging evidence. In this study, we constructed comparative analyses of gene structure, retention, expansion, whole-genome duplication (WGD) and expression patterns of CDPK-SnRK genes in Brassica rapa and their evolution in plants. A total of 49 BrCPKs, 14 BrCRKs, 3 BrPPCKs, 5 BrPEPRKs, and 56 BrSnRKs were identified in B...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28239231/genome-wide-discovery-of-dna-polymorphisms-in-mei-prunus-mume-sieb-et-zucc-an-ornamental-woody-plant-with-contrasting-tree-architecture-and-their-functional-relevance-for-weeping-trait
#3
Jie Zhang, Kai Zhao, Dan Hou, Junhuo Cai, Qixiang Zhang, Tangren Cheng, Huitang Pan, Weiru Yang
Next-generation sequencing technologies provide opportunities to ascertain the genetic basis of phenotypic differences, even in the closely related cultivars via detection of large amount of DNA polymorphisms. In this study, we performed whole-genome re-sequencing of two mei cultivars with contrasting tree architecture. 75.87 million 100 bp pair-end reads were generated, with 92 % coverage of the genome. Re-sequencing data of two former upright mei cultivars were applied for detecting DNA polymorphisms, since we were more interested in variations conferring weeping trait...
2017: Plant Molecular Biology Reporter
https://www.readbyqxmd.com/read/28238087/bone-regeneration-in-the-stem-cell-era-safe-play-for-the-patient
#4
Estella Musacchio, Nicola Veronese
The past decade has seen outstanding scientific progress in the field of stem cell (SC) research and clinical application. SCs are convenient both technically and biologically: they are easy to find and to culture and they can differentiate in virtually all tissues and even in whole organs. Induced pluripotent stem cells (iPSs) are a type of pluripotent SC generated in vitro directly from mature cells through the introduction of key transcription factors. The use of iPSs, however tantalizing, poses serious safety concerns because of their genomic instability...
February 25, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28237188/identification-of-acetic-acid-bacteria-through-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-and-report-of-gluconobacter-nephelii-kommanee-et-al-2011-and-gluconobacter-uchimurae-tanasupawat-et-al-2012-as-later-heterotypic-synonyms
#5
Leilei Li, Ilse Cleenwerck, Luc De Vuyst, Peter Vandamme
The classification and identification of acetic acid bacteria (AAB) underwent much change during the last two decades. However, several closely related AAB species are difficult to differentiate and rapid and correct species level identification remains challenging. In the present study, 281 well-characterized AAB strains representing AAB species of the family Acetobacteraceae were used to construct a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification database...
February 15, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28237031/single-nucleotide-polymorphisms-may-explain-the-contrasting-phenotypes-of-two-variants-of-a-multidrug-resistant-mycobacterium-tuberculosis-strain
#6
María Mercedes Bigi, Beatriz Lopez, Federico Carlos Blanco, María Del Carmen Sasiain, Silvia De la Barrera, Marcelo A Marti, Ezequiel Jorge Sosa, Darío Augusto Fernández Do Porto, Viviana Ritacco, Fabiana Bigi, Marcelo Abel Soria
Globally, about 4.5% of new tuberculosis (TB) cases are multi-drug-resistant (MDR), i.e. resistant to the two most powerful first-line anti-TB drugs. Indeed, 480,000 people developed MDR-TB in 2015 and 190,000 people died because of MDR-TB. The MDR Mycobacterium tuberculosis M family, which belongs to the Haarlem lineage, is highly prosperous in Argentina and capable of building up further drug resistance without impairing its ability to spread. In this study, we sequenced the whole genomes of a highly prosperous M-family strain (Mp) and its contemporary variant, strain 410, which produced only one recorded tuberculosis case in the last two decades...
March 2017: Tuberculosis
https://www.readbyqxmd.com/read/28236343/tarseqqc-quality-control-on-targeted-sequencing-experiments-in-r
#7
Gabriela A Merino, Yanina A Murua, Cristóbal Fresno, Juan M Sendoya, Mariano Golubicki, Soledad Iseas, Mariana Coraglio, Osvaldo L Podhajcer, Andrea S Llera, Elmer A Fernández
Targeted sequencing is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, under-covered relevant clinical variants may not be reported, impacting on pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions...
February 24, 2017: Human Mutation
https://www.readbyqxmd.com/read/28236292/the-role-of-genomics-in-common-variable-immunodeficiency-disorders
#8
REVIEW
Anne-Kathrin Kienzler, Chantal E Hargreaves, Smita Y Patel
The advent of next generation sequencing (NGS) and 'omic' technologies has revolutionised the field of genetics and its implementation in healthcare has the potential to realise precision medicine. Primary immunodeficiencies (PID) are a group of rare diseases which have benefitted from NGS, with a massive increase in causative genes identified in the past few years. Common Variable Immunodeficiency Disorders (CVID) are a heterogeneous form of PID and the most common form of antibody failure in children and adults...
February 25, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28236054/gene-expression-signature-for-early-prediction-of-late-occurring-pancytopenia-in-irradiated-baboons
#9
Matthias Port, Francis Hérodin, Marco Valente, Michel Drouet, Andreas Lamkowski, Matthäus Majewski, Michael Abend
Based on gene expression changes measured in the peripheral blood within the first 2 days after irradiation, we predicted a pancytopenia in a baboon model. Eighteen baboons were irradiated with 2.5 or 5 Gy. According to changes in blood cell counts, the surviving baboons (n = 17) exhibited a hematological acute radiation syndrome (HARS) either with or without a pancytopenia. We used a two stage study design where stage I was a whole genome screen (microarrays) for mRNA combined with a qRT-PCR platform for simultaneous detection of 667 miRNAs using a part of the samples...
February 24, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28235989/bacillus-thuringiensis-a-successful-insecticide-with-new-environmental-features-and-tidings
#10
REVIEW
Gholamreza Salehi Jouzani, Elena Valijanian, Reza Sharafi
Bacillus thuringiensis (Bt) is known as the most successful microbial insecticide against different orders of insect pests in agriculture and medicine. Moreover, Bt toxin genes also have been efficiently used to enhance resistance to insect pests in genetically modified crops. In light of the scientific advantages of new molecular biology technologies, recently, some other new potentials of Bt have been explored. These new environmental features include the toxicity against nematodes, mites, and ticks, antagonistic effects against plant and animal pathogenic bacteria and fungi, plant growth-promoting activities (PGPR), bioremediation of different heavy metals and other pollutants, biosynthesis of metal nanoparticles, production of polyhydroxyalkanoate biopolymer, and anticancer activities (due to parasporins)...
February 24, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28235956/genomic-complexity-and-targeted-genes-in-anaplastic-thyroid-cancer-cell-lines
#11
Eleanor Louise Woodward, Andrea Biloglav, Naveen Ravi, Minjun Yang, Lars Ekblad, Johan Wennerberg, Kajsa Paulsson
Anaplastic thyroid cancer (ATC) is a highly malignant disease with very short median survival times. Few studies have addressed the underlying somatic mutations, and the genomic landscape of ATC thus remains largely unknown. In the present study, we have ascertained copy number aberrations, gene fusions, gene expression patterns, and mutations in early-passage cells from ten newly established ATC cell lines using single nucleotide polymorphism (SNP) array analysis, RNA-sequencing and whole exome sequencing...
February 24, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28235832/one-thousand-somatic-snvs-per-skin-fibroblast-cell-set-baseline-of-mosaic-mutational-load-with-patterns-that-suggest-proliferative-origin
#12
Alexej Abyzov, Livia Tomasini, Bo Zhou, Nikolaos Vasmatzis, Gianfilippo Coppola, Mariangela Amenduni, Reenal Pattni, Michael Wilson, Mark Gerstein, Sherman Weissman, Alexander E Urban, Flora M Vaccarino
Few studies have been conducted to understand post-zygotic accumulation of mutations in cells of the healthy human body. We reprogrammed 32 skin fibroblast cells from families of donors into human induced pluripotent stem cell (hiPSC) lines. The clonal nature of hiPSC lines allows a high-resolution analysis of the genomes of the founder fibroblast cells without being confounded by the artifacts of single cell whole genome amplification. We estimate that on average a fibroblast cell in children has 1,035 mostly benign mosaic SNVs...
February 24, 2017: Genome Research
https://www.readbyqxmd.com/read/28235829/a-dense-brown-trout-salmo-trutta-linkage-map-reveals-recent-chromosomal-rearrangements-in-the-salmo-genus-and-the-impact-of-selection-on-linked-neutral-diversity
#13
Maeva Leitwein, Bruno Guinand, Juliette Pouzadoux, Erick Desmarais, Patrick Berrebi, Pierre-Alexandre Gagnaire
High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socio-economically important species heavily impacted by human activities. A total of 3,977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235825/genome-wide-screen-reveals-sec21-mutants-of-saccharomyces-cerevisiae-are-methotrexate-resistant
#14
Lai H Wong, Stephane Flibotte, Sunita Sinha, Jennifer Chiang, Guri Giaever, Corey Nislow
Exposure of cells to small molecules and drug therapies imposes a strong selective pressure. As a result, cells rapidly acquire mutations in order to survive. These include resistant variants of the drug target as well as those that modulate drug transport and detoxification. To systematically explore how cells acquire drug resistance in an unbiased manner, rapid cost-effective approaches are required. Methotrexate, as one of the first rationally designed anticancer drug, has served as a prototypic example of such acquired resistance...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28235824/a-nonsense-variant-in-the-st14-gene-in-akhal-teke-horses-with-naked-foal-syndrome
#15
Anina Bauer, Theresa Hiemesch, Vidhya Jagannathan, Markus Neuditschko, Iris Bachmann, Stefan Rieder, Sofia Mikko, M Cecilia Penedo, Nadja Tarasova, Martina Vitková, Nicolò Sirtori, Paola Roccabianca, Tosso Leeb, Monika M Welle
Naked foal syndrome (NFS) is a genodermatosis in the Akhal-Teke horse breed. We provide the first scientific description of this phenotype. Affected horses had almost no hair and showed a mild ichthyosis. So far, all known NFS affected horses died between a few weeks and 3 years of age. It is not clear whether a specific pathology caused the premature deaths. NFS is inherited as a monogenic autosomal recessive trait. We mapped the disease causing genetic variant to two segments on chromosomes 7 and 27 in the equine genome...
February 24, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28230817/common%C3%A2-chemical%C3%A2-inductors%C3%A2-of%C3%A2-replication%C3%A2-stress-%C3%A2-focus%C3%A2-on%C3%A2-cell-based%C3%A2-studies
#16
REVIEW
Eva Vesela, Katarina Chroma, Zsofia Turi, Martin Mistrik
DNA replication is a highly demanding process regarding the energy and material supply and must be precisely regulated, involving multiple cellular feedbacks. The slowing down or stalling of DNA synthesis and/or replication forks is referred to as replication stress (RS). Owing to the complexity and requirements of replication, a plethora of factors may interfere and challenge the genome stability, cell survival or affect the whole organism. This review outlines chemical compounds that are known inducers of RS and commonly used in laboratory research...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230522/multinational-outbreak-of-travel-related-salmonella-chester-infections-in-europe-summers-2014-and-2015
#17
Laure Fonteneau, Nathalie Jourdan Da Silva, Laetitia Fabre, Philip Ashton, Mia Torpdahl, Luise Müller, Brahim Bouchrif, Abdellah El Boulani, Eleni Valkanou, Wesley Mattheus, Ingrid Friesema, Silvia Herrera Leon, Carmen Varela Martínez, Joël Mossong, Ettore Severi, Kathie Grant, François-Xavier Weill, Céline M Gossner, Sophie Bertrand, Tim Dallman, Simon Le Hello
Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year...
February 16, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28230192/an-endoparasitoid-wasp-influences-host-dna-methylation
#18
Sunil Kumar, Yonggyun Kim
Parasitism by endoparasitoid wasps changes the expression of various host genes, and alters host immune and developmental processes. However, it is not clearly understood how parasitism changes host gene expression in a whole genome scale. This study focused on an epigenetic control of Cotesia plutellae, an endoparasitoid wasp, against its host, Plutella xylostella. Two DNA methyltransferases (DNMT-1 and DNMT-2) are encoded in the genome of P. xylostella. In addition, methyl-binding domain proteins (MBDs) and DNA demethylation factor, ten-eleven translation protein (TET) are encoded...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230168/phylogenetic-characterizations-of-highly-mutated-ev-b106-recombinants-showing-extensive-genetic-exchanges-with-other-ev-b-in-xinjiang-china
#19
Yang Song, Yong Zhang, Qin Fan, Hui Cui, Dongmei Yan, Shuangli Zhu, Haishu Tang, Qiang Sun, Dongyan Wang, Wenbo Xu
Human enterovirus B106 (EV-B106) is a new member of the enterovirus B species. To date, only three nucleotide sequences of EV-B106 have been published, and only one full-length genome sequence (the Yunnan strain 148/YN/CHN/12) is available in the GenBank database. In this study, we conducted phylogenetic characterisation of four EV-B106 strains isolated in Xinjiang, China. Pairwise comparisons of the nucleotide sequences and the deduced amino acid sequences revealed that the four Xinjiang EV-B106 strains had only 80...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230102/identification-of-a-new-virulent-clade-in-enterohemorrhagic-escherichia-coli-o26-h11-h-sequence-type-29
#20
Nozomi Ishijima, Ken-Ichi Lee, Tomomi Kuwahara, Haruyuki Nakayama-Imaohji, Saori Yoneda, Atsushi Iguchi, Yoshitoshi Ogura, Tetsuya Hayashi, Makoto Ohnishi, Sunao Iyoda
Enterohemorrhagic Escherichia coli (EHEC) O26 infections cause severe human diseases such as hemolytic uremic syndrome and encephalopathy, and is the predominant serogroup among non-O157 EHEC in many countries. Shiga toxin (Stx), which consists of two distinct types (Stx1 and Stx2), plays a central role in EHEC pathogenesis. The major stx gene type in EHEC O26 strains is stx1, although isolates with only stx2 have emerged in Japan since 2012 and have been reported in Europe. In this study, we selected 27 EHEC O26 strains isolated in Japan and identified a distinct genetic clade within sequence type (ST) 29, designated ST29C1, that carried only stx2 and had the plasmid gene profile ehxA+/katP-/espP+/etpD-...
February 23, 2017: Scientific Reports
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