Read by QxMD icon Read

Pan Genome

(no author information available yet)
Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed...
October 21, 2016: Briefings in Bioinformatics
Carlos Molina-Santiago, Zulema Udaondo, María Gómez-Lozano, Soren Molin, Juan Luis Ramos
Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly-tolerant DOT-T1E strain...
October 21, 2016: Environmental Microbiology
Ching-Feng Yang, Wan-Yu Tsai, Wei-An Chen, Kai-Wen Liang, Cheng-Ju Pan, Pei-Lun Lai, Pan-Chyr Yang, Hsiao-Chun Huang
During natural evolution, the spindles often scale with cell sizes to orchestrate accurate chromosome segregation. Whether in cancer evolution, when the constraints on genome integrity are relaxed, cancer cells may evolve the spindle to confer other advantages has not been investigated. Using invasion as a selective pressure in vitro, we found that a highly metastatic cancer clone displays a lengthened metaphase spindle, with faster spindle elongation that correlates with transiently elevated speed of cell migration...
October 21, 2016: Scientific Reports
Gang Li, Mengyu Shen, Shuai Le, Yinling Tan, Ming Li, Xia Zhao, Wei Shen, Yuhui Yang, Jing Wang, Hongbin Zhu, Shu Li, Xiancai Rao, Fuquan Hu, Shuguang Lu
As a third-generation sequencing method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for re-sequencing projects and de novo assembly. In this study, Pseudomonas aeruginosa PA1 was characterized and re-sequenced using SMRT technology. PA1 was also subjected to genomic, comparative, and pan-genomic analyses. The multi-drug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins, secretion system proteins, type II toxin-antitoxin pairs, and genomic islands...
October 20, 2016: Bioscience Reports
Peter R Sternes, Anthony R Borneman
No abstract text is available yet for this article.
October 20, 2016: BMC Genomics
Ying Yang, Min Chen, Zongwei Li, Abdullah M S Al-Hatmi, Sybren de Hoog, Weihua Pan, Qiang Ye, Xiaochen Bo, Zhen Li, Shengqi Wang, Junzhi Wang, Huipeng Chen, Wanqing Liao
Penicillium capsulatum is a rare Penicillium species used in paper manufacturing, but recently it has been reported to cause invasive infection. To research the pathogenicity of the clinical Penicillium strain, we sequenced the genomes and transcriptomes of the clinical and environmental strains of P. capsulatum. Comparative analyses of these two P. capsulatum strains and close related strains belonging to Eurotiales were performed. The assembled genome sizes of P. capsulatum are approximately 34.4 Mbp in length and encode 11,080 predicted genes...
2016: Frontiers in Microbiology
Ying Liu, Chaoting Zhang, Weijiao Gao, Limin Wang, Yaqi Pan, Yunong Gao, Zheming Lu, Yang Ke
HPV integration plays an important role in cervical carcinogenesis. HPV genotypes and the exact integration sites were investigated using HPV capture technology combined with next generation sequencing in 166 women. Three, one and six integration sites were verified in 7 HPV-positive 'normal cervical epithelium', 6 HPV-positive CIN2 and 15 HPV-positive CIN 3 samples, respectively. Of the 10 integrations, one and nine were involved with HPV33 and HPV16, respectively. Our study accurately evaluated HPV integration level in CINs and normal cervical tissues using high-throughput viral integration detection method providing basic evidence for HPV integration-driven cervical carcinogenesis...
October 19, 2016: Scientific Reports
Sofia A V Fortunato, Michel Vervoort, Marcin Adamski, Maja Adamska
BACKGROUND: Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons...
2016: EvoDevo
Jinpeng Wang, Jiaxiang Yu, Pengchuan Sun, Yuxian Li, Ruiyan Xia, Yinzhe Liu, Xuelian Ma, Jigao Yu, Nanshan Yang, Tianyu Lei, Zhenyi Wang, Li Wang, Weina Ge, Xiaoming Song, Xiaojian Liu, Sangrong Sun, Tao Liu, Dianchuan Jin, Yuxin Pan, Xiyin Wang
Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ∼100 million years ago. There has been a standing controversy whether there had been five or seven basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses...
2016: Frontiers in Genetics
Junting Pan, Weidong Wang, Dongqin Li, Zaifa Shu, Xiaoli Ye, Pinpin Chang, Yuhua Wang
BACKGROUND: Nitric oxide (NO) functions as a critical signaling molecule in the low-temperature stress responses in plants, including polarized pollen tube growth in Camellia sinensis. Despite this, the potential mechanisms underlying the participation of NO in pollen tube responses to low temperature remain unclear. Here, we investigate alterations to gene expression in C. sinensis pollen tubes exposed to low-temperature stress and NO using RNA-Seq technology, in order to find the potential candidate genes related to the regulation of pollen tube elongation by NO under low-temperature stress...
October 18, 2016: BMC Genomics
Chih-Ping Chen, Liang-Kai Wang, Schu-Rern Chern, Yen-Ni Chen, Shin-Wen Chen, Peih-Shan Wu, Dai-Dyi Town, Chen-Wen Pan, Chien-Wen Yang, Wayseen Wang
OBJECTIVE: We present prenatal diagnosis and molecular genetic analysis of mosaic trisomy 17 and a review of the literature of mosaic trisomy 17 at amniocentesis. MATERIALS AND METHODS: A 42-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age, which revealed a karyotype of 47,XX,+17[4]/46,XX[17]. Prenatal ultrasound findings were unremarkable. She underwent repeat amniocentesis at 20 weeks of gestation. Interphase fluorescence in situ hybridization (FISH), array comparative genomic hybridization, and quantitative fluorescent polymerase chain reaction assays were applied to uncultured amniocytes...
October 2016: Taiwanese Journal of Obstetrics & Gynecology
Zhaojun Cao, Yue Yin, Xuan Sun, Jun Han, Qing Peng Sun, Min Lu, Jinbao Pan, Weixiang Wang
Ash1 is a known H3K36-specific histone demethylase that is required for normal Hox gene expression and fertility in Drosophila and mammals. However, little is known about the expression and function of the fungal ortholog of Ash1 in phytopathogenic fungus Magnaporthe oryzae. Here we report that MoKMT2H, an Ash1-like protein, is required for conidium germination and virulence in rice. We obtained MoKMT2H null mutant (ΔMoKMT2H) using a target gene replacement strategy. In the ΔMoKMT2H null mutants, global histone methyltransferase modifications (H3K4me3, H3K9me3, H3K27me3, and H3K36me2/3) of the genome were unaffected...
2016: BioMed Research International
Julian Lange, Shintaro Yamada, Sam E Tischfield, Jing Pan, Seoyoung Kim, Xuan Zhu, Nicholas D Socci, Maria Jasin, Scott Keeney
Heritability and genome stability are shaped by meiotic recombination, which is initiated via hundreds of DNA double-strand breaks (DSBs). The distribution of DSBs throughout the genome is not random, but mechanisms molding this landscape remain poorly understood. Here, we exploit genome-wide maps of mouse DSBs at unprecedented nucleotide resolution to uncover previously invisible spatial features of recombination. At fine scale, we reveal a stereotyped hotspot structure-DSBs occur within narrow zones between methylated nucleosomes-and identify relationships between SPO11, chromatin, and the histone methyltransferase PRDM9...
October 20, 2016: Cell
Tsai-Wen Wan, Olga E Khokhlova, Yasuhisa Iwao, Wataru Higuchi, Wei-Chun Hung, Ivan V Reva, Olga A Singur, Vladimir V Gostev, Sergey V Sidorenko, Olga V Peryanova, Alla B Salmina, Galina V Reva, Lee-Jene Teng, Tatsuo Yamamoto
ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split...
2016: PloS One
J C Cohen
Genetic variation arises through multiple different alleles that vary in frequency and severity of effect. Mutations that give rise to Mendelian disorders, such as the LDL receptor (LDLR) mutations that result in familial hypercholesterolaemia, are efficiently winnowed from the population by purifying selection and are almost inevitably rare. Conversely, alleles that are common in the population (such that homozygotes for the minor allele are present even in modest sample sizes) typically have very modest phenotypic effects...
October 14, 2016: Journal of Internal Medicine
Wanjun Zhu, Xiao-Yan Zhang, Sadie L Marjani, Jialing Zhang, Wengeng Zhang, Shixiu Wu, Xinghua Pan
Single-cell sequencing (SCS) is a fast-growing, exciting field in genomic medicine. It enables the high-resolution study of cellular heterogeneity, and reveals the molecular basis of complicated systems, which facilitates the identification of new biomarkers for diagnosis and for targeting therapies. It also directly promotes the next generation of genomic medicine because of its ultra-high resolution and sensitivity that allows for the non-invasive and early detection of abnormalities, such as aneuploidy, chromosomal translocation, and single-gene disorders...
October 13, 2016: Cellular and Molecular Life Sciences: CMLS
Nicole Ben Salem, Fabian H Leendertz, Bernhard Ehlers
We identified with PCR and sequencing the full genomes of the recently discovered Pan troglodytes verus polyomavirus 8 and Piliocolobus badius polyomavirus 2 in a western chimpanzee and a western red colobus free-ranging in Taï National Park of Côte d'Ivoire.
October 13, 2016: Genome Announcements
Jongoh Shin, Yoseb Song, Yujin Jeong, Byung-Kwan Cho
Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (H2) or carbon monoxide (CO), via the Wood-Ljungdahl pathway. Owing to the metabolic capability of CO2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of CO2 fixation to energy conservation. Most known acetogens are phylogenetically and metabolically diverse bacteria present in 23 different bacterial genera...
2016: Frontiers in Microbiology
Zhikai Guo, Guohui Pan, Zhengren Xu, Dong Yang, Hindra, Xiangcheng Zhu, Yong Huang, Li-Xing Zhao, Yi Jiang, Yanwen Duan, Ben Shen
Isofuranonaphthoquinones (IFQs) and Isoindolequinones (IIQs) comprise a small family of natural products, with the latter ones are especially uncommon in nature. Here we report the discovery of seven new IFQs, IFQ A-G (1-7), and three new IIQs, IIQ A-C (8-10), along with the known anthraquinone desoxyerythrolaccin (11), from Streptomyces sp. CB01883, expanding the chemical diversity of this family of natural products. The structures of these natural products were established on the basis of their HR-ESI-MS and nuclear magnetic resonance (NMR) spectroscopic data...
October 12, 2016: Journal of Antibiotics
Wu Ren, Jian Zhang, Wei Li, Zongcheng Li, Shuofeng Hu, Jian Suo, Xiaomin Ying
BACKGROUND Aberrant expression of long non-coding RNAs (lncRNAs) is associated with prognosis of gastric cancer, some of which could be further evaluated as potential biomarkers. In this study, we attempted to identify a specific lncRNA signature to predict the prognosis of gastric cancer. MATERIAL AND METHODS The genome-wide lncRNA expression in the high-throughput RNA-sequencing data was retrieved from the Cancer Genome Atlas (TCGA). Differential expression of lncRNAs was identified using the Limma package...
October 11, 2016: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"