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https://www.readbyqxmd.com/read/29677560/effective-discovery-of-rare-variants-by-pooled-target-capture-sequencing-a-comparative-analysis-with-individually-indexed-target-capture-sequencing
#1
Seungjin Ryu, Jeehae Han, Trina M Norden-Krichmar, Nicholas J Schork, Yousin Suh
Identification of all genetic variants associated with complex traits is one of the most important goals in modern human genetics. Genome-wide association studies (GWAS) have been successfully applied to identify common variants, which thus far explain only small portion of heritability. Interests in rare variants have been increasingly growing as an answer for this missing heritability. While next-generation sequencing allows detection of rare variants, its cost is still prohibitively high to sequence a large number of human DNA samples required for rare variant association studies...
March 30, 2018: Mutation Research
https://www.readbyqxmd.com/read/29677511/an-integrated-genome-wide-crispra-approach-to-functionalize-lncrnas-in-drug-resistance
#2
Assaf C Bester, Jonathan D Lee, Alejandro Chavez, Yu-Ru Lee, Daphna Nachmani, Suhani Vora, Joshua Victor, Martin Sauvageau, Emanuele Monteleone, John L Rinn, Paolo Provero, George M Church, John G Clohessy, Pier Paolo Pandolfi
Resistance to chemotherapy plays a significant role in cancer mortality. To identify genetic units affecting sensitivity to cytarabine, the mainstay of treatment for acute myeloid leukemia (AML), we developed a comprehensive and integrated genome-wide platform based on a dual protein-coding and non-coding integrated CRISPRa screening (DICaS). Putative resistance genes were initially identified using pharmacogenetic data from 760 human pan-cancer cell lines. Subsequently, genome scale functional characterization of both coding and long non-coding RNA (lncRNA) genes by CRISPR activation was performed...
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29677450/complete-programmable-decoding-of-oxidized-5-methylcytosine-nucleobases-in-dna-by-chemoselective-blockage-of-universal-tale-binders
#3
Mario Giess, Anna Witte, Julia Jasper, Oliver Koch, Daniel Summerer
5-methylcytosine (5mC) and its oxidized derivatives are regulatory elements of mammalian genomes involved in development and disease. These nucleobases do not selectively modulate Watson-Crick pairing, preventing their programmable targeting and analysis by traditional hybridiza-tion probes. Transcription-activator-like effectors (TALEs) can be engineered for use as programmable probes with epi-genetic nucleobase selectivity. However, only partial selectivi-ties for oxidized 5mC have been achieved so far, preventing unambiguous target binding...
April 20, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29677397/two-ancestral-genes-shaped-the-xanthomonas-campestris-tal-effector-gene-repertoire
#4
Nicolas Denancé, Boris Szurek, Erin L Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, Ahmed Hajri, Aude Cerutti, Tristan Boureau, Stéphane Poussier, Matthieu Arlat, Adam J Bogdanove, Laurent D Noël
Xanthomonas transcription activator-like effectors (TALEs) are injected inside plant cells to promote host susceptibility by enhancing transcription of host susceptibility genes. TALE-encoding (tal) genes were thought to be absent from Brassicaceae-infecting Xanthomonas campestris (Xc) genomes based on four reference genomic sequences. We discovered tal genes in 26 of 49 Xc strains isolated worldwide and used a combination of single molecule real time (SMRT) and tal amplicon sequencing to yield a near-complete description of the TALEs found in Xc (Xc TALome)...
April 20, 2018: New Phytologist
https://www.readbyqxmd.com/read/29677183/divergent-genome-evolution-caused-by-regional-variation-in-dna-gain-and-loss-between-human-and-mouse
#5
Reuben M Buckley, R Daniel Kortschak, David L Adelson
The forces driving the accumulation and removal of non-coding DNA and ultimately the evolution of genome size in complex organisms are intimately linked to genome structure and organisation. Our analysis provides a novel method for capturing the regional variation of lineage-specific DNA gain and loss events in their respective genomic contexts. To further understand this connection we used comparative genomics to identify genome-wide individual DNA gain and loss events in the human and mouse genomes. Focusing on the distribution of DNA gains and losses, relationships to important structural features and potential impact on biological processes, we found that in autosomes, DNA gains and losses both followed separate lineage-specific accumulation patterns...
April 20, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29676997/mining-tcga-database-for-genes-of-prognostic-value-in-glioblastoma-microenvironment
#6
Di Jia, Shenglan Li, Dali Li, Haipeng Xue, Dan Yang, Ying Liu
Glioblastoma (GBM) is one of the most deadly brain tumors. The convenient access to The Cancer Genome Atlas (TCGA) database allows for large-scale global gene expression profiling and database mining for potential correlation between genes and overall survival of a variety of malignancies including GBM. Previous reports have shown that tumor microenvironment cells and the extent of infiltrating immune and stromal cells in tumors contribute significantly to prognosis. Immune scores and stromal scores calculated based on the ESTIMATE algorithm could facilitate the quantification of the immune and stromal components in a tumor...
April 16, 2018: Aging
https://www.readbyqxmd.com/read/29676996/involvement-of-spata31-copy-number-variable-genes-in-human-lifespan
#7
Cemalettin Bekpen, Chen Xie, Almut Nebel, Diethard Tautz
The SPATA31 ( alias FAM75A) gene family belongs to the core duplicon families that are thought to have contributed significantly to hominoid evolution. It is also among the gene families with the strongest signal of positive selection in hominoids. It has acquired new protein domains in the primate lineage and a previous study has suggested that the gene family has expanded its function into UV response and DNA repair. Here we show that over-expression of SPATA31A1 in fibroblast cells leads to premature senescence due to interference with aging-related transcription pathways...
April 19, 2018: Aging
https://www.readbyqxmd.com/read/29676825/histone-chaperones-play-crucial-roles-in-maintenance-of-stem-cell-niche-during-plant-root-development
#8
Jing Ma, Yuhao Liu, Wangbin Zhou, Yan Zhu, Aiwu Dong, Wen-Hui Shen
Stem cells in both plant and animal kingdoms reside in a specialized cellular context called stem-cell niche (SCN). SCN integrity is crucial for organism development. Here we show that the H3/H4 histone chaperone CHROMATIN ASSEMBLY FACTOR-1 (CAF-1) and the H2A/H2B histone chaperone NAP1-RELATED PROTEIN1/2 (NRP1/2) play synergistic roles in Arabidopsis root SCN maintenance. Compared to either the m56-1 double mutant deprived of NRP1 and NRP2 or the fas2-4 mutant deprived of CAF-1, the combined m56-1fas2-4 triple mutant displayed a much more severe short-root phenotype...
April 20, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29676730/mesorhizobium-wenxiniae-sp-nov-isolated-from-chickpea-cicer-arietinum-l-in-china
#9
Junjie Zhang, Chen Guo, Wenfeng Chen, Philippe de Lajudie, Zhiyan Zhang, Yimin Shang, En Tao Wang
Three chickpea rhizobial strains (WYCCWR 10195T =S1-3-7, WYCCWR 10198=S1-4-3 and WYCCWR 10200=S1-5-1) isolated from Northwest China formed a group affiliated to Mesorhizobium based on 16S rRNA gene sequence comparison. To clarify their species status, multilocus sequence analysis and average nucleotide identity (ANI) values of whole genome sequences between the novel group and the type strains of the related species were further performed. Similarities of 95.7-96.6 % in the concatenated sequences of atpD-recA-glnII and 91...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676726/rhodohalobacter-barkolensis-sp-nov-isolated-from-a-saline-lake-and-emended-description-of-the-genus-rhodohalobacter
#10
Shuai-Bo Han, Yang-Huan Yu, Zhao Ju, Yu Li, Ran Zhang, Xin-Jun Hou, Xin-Yuan Ma, Xiao-Yun Yu, Cong Sun, Min Wu
A Gram-stain-negative, non-motile, aerobic, rod-shaped bacterium, designated 15182T , was isolated from a saline lake in China. The novel strain 15182T was able to grow at 10-40 °C (optimum, 37 °C), pH 7.0-8.0 (optimum, 7.5) and with 0.5-4 % NaCl (optimum, 2-3 %, w/v). The phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 15182T was most closely related to the genus Rhodohalobacter by sharing the highest sequence similarity of 97.0 % with Rhodohalobacter halophilus JZ3C29T ...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676719/vibrio-gangliei-sp-nov-a-novel-member-of-vibrionaceae-isolated-from-sawdust-in-a-pigpen
#11
Yu-Chen Meng, Hong-Can Liu, Yu-Guang Zhou, Man Cai, Yingqian Kang
A Gram-stain-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic, and motile bacterium, designated strain SZDIS-1T , was isolated from pigpen sawdust bedding in Xiamen, Fujian Province, China. Cells grew at 10-50 °C, pH 6.0-9.0, up to 12 % (w/v) NaCl, resisted vibriostatic agent O/129 and were negative for gelatin and alginate hydrolysis. No growth on thiosulfate citrate bile salts sucrose agar medium. Based on 16S rRNA gene sequences and multilocus sequence analysis, this strain should be assigned to the genus Vibrio, with the closest relatives being Vibrio aphrogenes CA-1004T (97...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676718/propionicimonas-ferrireducens-sp-nov-isolated-from-dissimilatory-iron-iii-reducing-microbial-enrichment-obtained-from-paddy-soil
#12
Guo-Wei Zhou, Xiao-Ru Yang, Mohammed A M Wadaan, Wael N Hozzein, Bang-Xiao Zheng, Jian-Qiang Su, Yong-Guan Zhu
A novel strain, designated Y1A-10 4-9-1T , with Gram-stain-positive and rod-shaped cells, was isolated from paddy soil in Yingtan, Jiangxi, China. Cells were 0.15-0.2 µm wide and 1.5-3.3 µm long. The optimal growth temperature was 30 °C and the optimal pH was 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel strain is closely related to Propionicimonas paludicola JCM 11933T (98.57 %). The genomic DNA G+C content was 63.9 mol%. The predominant menaquinone was MK-9(H4) and meso-diaminopimelic acid was present in the cell-wall peptidoglycan layer...
April 20, 2018: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29676638/identification-of-novel-targets-for-lung-cancer-therapy-using-an-induced-pluripotent-stem-cell-model
#13
Vivek Shukla, Mahadev Rao, Hongen Zhang, Jeanette Beers, Darawalee Wangsa, Danny Wangsa, Floryne O Buishand, Yonghong Wang, Zhiya Yu, Holly Stevenson, Emily Reardon, Kaitlin C McLoughlin, Andrew Kaufman, Eden Payabyab, Julie A Hong, Mary Zhang, Sean R Davis, Daniel C Edelman, Guokai Chen, Markku Miettinen, Nicholas Restifo, Thomas Ried, Paul S Meltzer, David S Schrump
RATIONALE: Despite extensive studies, the genetic and epigenetic mechanisms that mediate initiation and progression of lung cancers have not been fully elucidated. Previously, we have demonstrated that via complementary mechanisms, including DNA methylation, polycomb repressive complexes, and noncoding RNAs, cigarette smoke induces stem-like phenotypes that coincide with progression to malignancy in normal respiratory epithelia as well as enhanced growth and metastatic potential of lung cancer cells...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676290/increased-expression-of-pelp1-in-human-sperm-is-correlated-with-decreased-semen-quality
#14
Izabela Skibinska, Miroslaw Andrusiewicz, Michal Soin, Magdalena Jendraszak, Paulina Urbaniak, Piotr Jedrzejczak, Malgorzata Kotwicka
Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1) is a scaffolding protein involved in both genomic and nongenomic estrogen signal transduction pathways. To date, the role of PELP1 protein has yet to be characterized in human sperm and has not been associated with sperm parameters. To confirm the presence of PELP1 in human sperm, fresh semen samples were obtained from 178 donors. The study was designed to establish both mRNA and protein presence, and protein cellular localization. Additionally, the number of PELP1-positive spermatozoa was analyzed in men with normal and abnormal semen parameters...
April 20, 2018: Asian Journal of Andrology
https://www.readbyqxmd.com/read/29676245/structure-and-interaction-prediction-in-prokaryotic-rna-biology
#15
Patrick R Wright, Martin Mann, Rolf Backofen
Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in "wet" laboratory techniques have produced unprecedented amounts of data that require efficient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classification of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29676044/hla-dq%C3%AE-1-amino-acid-position-87-and-dqb1-0301-are-associated-with-chinese-han-sle
#16
Jingying Sun, Chao Yang, Wenmin Fei, Xuelei Zhang, Yujun Sheng, Xiaodong Zheng, Huayang Tang, Wanling Yang, Sen Yang, Xing Fan, Xuejun Zhang
BACKGROUND: Several susceptibility loci have been identified associated with Chinese Han systemic lupus erythematosus (SLE). METHODS: We carried out imputation of classical HLA alleles, amino acids and Single Nucleotide Polymorphisms (SNPs) across the MHC region in Chinese Han SLE genome-wide association study (GWAS) of mainland and Hong Kong populations for the first time using newly constructed Han-MHC reference panel followed by stepwise conditional analysis...
April 19, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29676042/meta-analysis-of-chromosome-scale-crossover-rate-variation-in-eukaryotes-and-its-significance-to-evolutionary-genomics
#17
Quiterie Haenel, Telma G Laurentino, Marius Roesti, Daniel Berner
Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because the crossover rate determines how strongly a genome region is influenced by natural selection on linked sites. Nevertheless, generalities in the chromosome-scale distribution of crossovers have not been investigated formally. We fill this gap by synthesizing joint information on genetic and physical maps across 62 animal, plant, and fungal species. Our quantitative analysis reveals a strong and taxonomically wide-spread reduction of the crossover rate in the center of chromosomes relative to their peripheries...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29676027/phylogenetic-analyses-of-the-genus-aeromonas-based-on-housekeeping-gene-sequencing-and-its-influence-on-systematics
#18
Aaron Navarro, Antonio Martínez-Murcia
The phylogenies derived from housekeeping gene sequence alignments, although mere evolutionary hypotheses, have increased our knowledge about the Aeromonas genetic diversity, providing a robust species delineation framework invaluable for reliable, easy and fast species identification. Previous classifications of Aeromonas, have been fully surpassed by recently developed phylogenetic (natural) classification obtained from the analysis of so-called "molecular chronometers". Despite ribosomal RNAs cannot split all known Aeromonas species, the conserved nature of 16S rRNA offers reliable alignments containing mosaics of sequence signatures which may serve as targets of genus-specific oligonucleotides for subsequent identification/detection tests in samples without culturing...
April 19, 2018: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29675902/demography-or-selection-on-linked-cultural-traits-or-genes-investigating-the-driver-of-low-mtdna-diversity-in-the-sperm-whale-using-complementary-mitochondrial-and-nuclear-genome-analyses
#19
Phillip A Morin, Andrew D Foote, C Scott Baker, Brittany L Hancock-Hanser, Kristin Kaschner, Bruce R Mate, Sarah L Mesnick, Victoria L Pease, Patricia E Rosel, Alana Alexander
Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates, and cultural hitchhiking (linkage of genetic variation to culturally transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29675811/systematic-analysis-and-comparison-of-the-phd-finger-gene-family-in-chinese-pear-pyrus-bretschneideri-and-its-role-in-fruit-development
#20
Yunpeng Cao, Yahui Han, Dandan Meng, Muhammad Abdullah, Dahui Li, Qing Jin, Yi Lin, Yongping Cai
PHD-finger proteins, which belongs to the type of zinc finger family, and that play an important role in the regulation of both transcription and the chromatin state in eukaryotes. Currently, PHD-finger proteins have been well studied in animals, while few studies have been carried out on their function in plants. In the present study, 129 non-redundant PHD-finger genes were identified from 5 Rosaceae species (pear, apple, strawberry, mei, and peach); among them, 31 genes were identified in pear. Subsequently, we carried out a bioinformatics analysis of the PHD-finger genes...
April 20, 2018: Functional & Integrative Genomics
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