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https://www.readbyqxmd.com/read/29224154/large-scale-targeted-dna-methylation-analysis-using-bisulfite-padlock-probes
#1
Dinh Diep, Nongluk Plongthongkum, Kun Zhang
Bisulfite padlock probes (BSPP) are a method for the targeted quantification of DNA methylation in mammalian genomes. They can simultaneously characterize the level of methylcytosine modification in a large number of targeted regions at single-base resolution. A major advantage of BSPP is that it allows the flexible capture of an arbitrary subset of genomic regions (hundreds to hundreds of thousands of genomic loci) in single-tube reactions. Large number of samples can be processed efficiently and converted into multiplexed sequencing libraries with only three enzymatic steps, without the conventional library preparation procedures...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223718/complete-genome-sequence-of-the-highly-mn-ii-tolerant-staphylococcus-sp-antimn-1-isolated-from-deep-sea-sediment-in-the-clarion-clipperton-zone
#2
Xing Wang, Danqiu Lin, Xiaohuan Jing, Sidong Zhu, Jifang Yang, Jigang Chen
Staphylococcus sp. AntiMn-1 is a deep-sea bacterium inhabiting seafloor sediment in the Clarion-Clipperton Zone (CCZ) that is highly tolerant to Mn(II) and displays efficient Mn(II) oxidation. Herein, we present the assembly and annotation of its genome.
December 6, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#3
Dominique A Cowart, Katherine R Murphy, C-H Christina Cheng
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods...
December 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29221887/resistance-analysis-in-patients-with-genotype-1-6-hcv-infection-treated-with-sofosbuvir-velpatasvir-in-the-phase-3-studies
#4
Christophe Hezode, Nancy Reau, Evguenia S Svarovskaia, Brian P Doehle, Ragavi Shanmugam, Hadas Dvory-Sobol, Charlotte Hedskog, John McNally, Anu Osinusi, Diana M Brainard, Michael D Miller, Hongmei Mo, Stuart K Roberts, Jacqueline G O'Leary, Stephen D Shafran, Stefan Zeuzem
BACKGROUND & AIMS: The fixed dose combination of sofosbuvir/velpatasvir was highly efficacious in genotype (GT) 1-6 HCV infected patients in the ASTRAL studies. This analysis evaluated the impact of baseline resistance-associated substitutions (RASs) on treatment outcome and emergence of RASs in HCV GT1-6 infected patients treated with sofosbuvir/velpatasvir. METHODS: NS5A and NS5B deep sequencing was performed at baseline for all patients in the ASTRAL 1-3, ASTRAL-5 and POLARIS-2-3 studies treated with sofosbuvir/velpatasvir for 12 weeks (n=1778) and at the time of relapse...
December 5, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/29221134/a-trna-fragment-trf5-glu-regulates-bcar3-expression-and-proliferation-in-ovarian-cancer-cells
#5
Kun Zhou, Kevin W Diebel, Jon Holy, Andrew Skildum, Evan Odean, Douglas A Hicks, Brent Schotl, Juan E Abrahante, Monique A Spillman, Lynne T Bemis
Ovarian cancer is a complex disease marked by tumor heterogeneity, which contributes to difficulties in diagnosis and treatment. New molecular targets and better molecular profiles defining subsets of patients are needed. tRNA fragments (tRFs) offer a recently identified group of noncoding RNAs that are often as abundant as microRNAs in cancer cells. Initially their presence in deep sequencing data sets was attributed to the breakdown of mature tRNAs, however, it is now clear that they are actively generated and function in multiple regulatory events...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220521/trypanosomatid-mitochondrial-rna-editing-dramatically-complex-transcript-repertoires-revealed-with-a-dedicated-mapping-tool
#6
Evgeny S Gerasimov, Anna A Gasparyan, Iosif Kaurov, Boris Tichý, Maria D Logacheva, Alexander A Kolesnikov, Julius Lukeš, Vyacheslav Yurchenko, Sara L Zimmer, Pavel Flegontov
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded...
December 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29220483/prenatal-exposure-to-bisphenol-a-disrupts-naturally-occurring-bimodal-dna-methylation-at-proximal-promoter-of-fggy-an-obesity-relevant-gene-encoding-a-carbohydrate-kinase-in-gonadal-white-adipose-tissues-of-cd-1-mice
#7
Julia A Taylor, Keiko Shioda, Shino Mitsunaga, Shiomi Yawata, Brittany M Angle, Susan C Nagel, Frederick S Vom Saal, Toshi Shioda
Exposure of mammalian fetuses to endocrine disruptors can increase the risk of adult-onset diseases. For example, we previously showed that exposure of mouse fetuses to bisphenol A (BPA) caused adult-onset obesity. To obtain insights into roles of epigenetic changes in the delayed toxic effects of endocrine disruption, we determined effects of fetal mouse exposure to BPA on genome-wide DNA methylation and mRNA expression in gonadal white adipose tissues by deep sequencing (MBD-seq and RNA-seq), bisulfite pyrosequencing, and real-time qPCR...
December 6, 2017: Endocrinology
https://www.readbyqxmd.com/read/29220350/deep-sequencing-of-near-full-length-hiv-1-genomes-from-plasma-identifies-circulating-subtype-c-and-infrequent-occurrence-of-ac-recombinant-form-in-southern-india
#8
Shuba Varshini Alampalli, Michael M Thomson, Raghavan Sampathkumar, Karthi Sivaraman, Anto Jesuraj U K J, Chirag Dhar, George D Souza, Neil Berry, Annapurna Vyakarnam
India has the third largest number of HIV-1-infected individuals accounting for approximately 2.1 million people, with a predominance of circulating subtype C strains and a low prevalence of subtype A and A1C and BC recombinant forms, identified over the past two decades. Recovery of near full-length HIV-1 genomes from a plasma source coupled with advances in next generation sequencing (NGS) technologies and development of universal methods for amplifying whole genomes of HIV-1 circulating in a target geography or population provides the opportunity for a detailed analysis of HIV-1 strain identification, evolution and dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/29219068/predicting-enhancers-with-deep-convolutional-neural-networks
#9
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
BACKGROUND: With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of human cell lines. Nevertheless, experimental approaches are still costly and time consuming for large scale identification of enhancers across a variety of tissues under different disease status, making computational identification of enhancers indispensable. RESULTS: To facilitate the identification of enhancers, we propose a computational framework, named DeepEnhancer, to distinguish enhancers from background genomic sequences...
December 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29218875/mapping-patient-trajectories-using-longitudinal-extraction-and-deep-learning-in-the-mimic-iii-critical-care-database
#10
Brett K Beaulieu-Jones, Patryk Orzechowski, Jason H Moore
Electronic Health Records (EHRs) contain a wealth of patient data useful to biomedical researchers. At present, both the extraction of data and methods for analyses are frequently designed to work with a single snapshot of a patient's record. Health care providers often perform and record actions in small batches over time. By extracting these care events, a sequence can be formed providing a trajectory for a patient's interactions with the health care system. These care events also offer a basic heuristic for the level of attention a patient receives from health care providers...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29218722/coupling-of-microrna-directed-phased-small-interfering-rna-generation-from-long-noncoding-genes-with-alternative-splicing-and-alternative-polyadenylation-in-small-rna-mediated-gene-silencing
#11
Wuqiang Ma, Chengjie Chen, Yuanlong Liu, Ming Zeng, Blake C Meyers, Jianguo Li, Rui Xia
MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep-sequencing techniques and in-depth bioinformatic analyses. The genome-wide identification of miRNAs, their target genes, and phasiRNA-generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function...
December 8, 2017: New Phytologist
https://www.readbyqxmd.com/read/29217798/metagenome-sequence-of-a-microbial-community-from-the-gold-mine-tailings-in-the-kuzbass-area-russia
#12
Andrey V Mardanov, Alexey V Beletsky, Denis A Ivasenko, Olga V Karnachuk, Nikolai V Ravin
The metagenome of a microbial community of the sediments from a highly acidic iron-rich puddle at the tailings dump of the Komsomolskaya gold mine in the Kuzbass area, Siberia, Russia, was sequenced. Binning of contigs yielded a near-complete genome of the dominant bacterium, representing a novel deep lineage of Deltaproteobacteria.
December 7, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29217783/somatic-stat3-mutations-in-the-felty-syndrome-an-implication-for-a-common-pathogenesis-with-large-granular-lymphocyte-leukemia
#13
Paula Savola, Oscar Brück, Thomas Olson, Tiina Kelkka, Markku J Kauppi, Panu E Kovanen, Soili Kytölä, Tuulikki Sokka-Isler, Thomas P Loughran, Marjatta Leirisalo-Repo, Satu Mustjoki
Felty syndrome is a rare disease defined by neutropenia, splenomegaly, and rheumatoid arthritis. Sometimes the differential diagnosis between Felty syndrome and large granular lymphocyte leukemia is problematic. Recently, somatic STAT3 and STAT5B mutations were discovered in 30-40% of patients with large granular lymphocyte leukemia. We now aimed to study whether these mutations can also be detected in Felty syndrome, which would imply for a common pathogenic mechanism between these two disease entities. We collected samples and clinical information from 14 Felty syndrome patients who were monitored at the rheumatology outpatient clinic for Felty syndrome...
December 7, 2017: Haematologica
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#14
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29216758/iron-age-italic-population-genetics-the-piceni-from-novilara-8th-7th-century-bc
#15
P Serventi, C Panicucci, R Bodega, S De Fanti, S Sarno, M Fondevila Alvarez, F Brisighelli, B Trombetta, P Anagnostou, G Ferri, A Vazzana, C Delpino, G Gruppioni, D Luiselli, E Cilli
BACKGROUND: Archaeological data provide evidence that Italy, during the Iron Age, witnessed the appearance of the first communities with well defined cultural identities. To date, only a few studies report genetic data about these populations and, in particular, the Piceni have never been analysed. AIMS: To provide new data about mitochondrial DNA (mtDNA) variability of an Iron Age Italic population, to understand the contribution of the Piceni in shaping the modern Italian gene pool and to ascertain the kinship between some individuals buried in the same grave within the Novilara necropolis...
December 7, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/29216634/lysine-restriction-affects-feed-intake-and-amino-acid-metabolism-via-gut-microbiome-in-piglets
#16
Jie Yin, Hui Han, Yuying Li, Zhaojin Liu, Yurong Zhao, Rejun Fang, Xingguo Huang, Jie Zheng, Wenkai Ren, Fei Wu, Gang Liu, Xin Wu, Kai Wang, Liping Sun, Chunyong Li, Tiejun Li, Yulong Yin
BACKGROUND/AIMS: Our previous reports suggested that dietary supplementation with lysine influenced intestinal absorption and metabolism of amino acids. In this study, we further investigated the effect of lysine restriction (30%) on feed intake and we also tested the hypothesis that gut microbiome contributed to the potential mechanism of lysine restriction-mediated feeding behavior. Here, we profiled gut microbial communities by sequencing 16S ribosomal ribonucleic acid (rRNA) genes from gut samples as well as growth performance, serum hormones, and intestinal lysine transport in a piglet model...
December 6, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#17
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29215744/identification-of-virus-derived-sirnas-and-their-targets-in-rbsdv-infected-rice-by-deep-sequencing
#18
Ying Lan, Yanwu Li, Zhiguo E, Feng Sun, Linlin Du, Qiufang Xu, Tong Zhou, Yijun Zhou, Yongjian Fan
RNA interference (RNAi) is a conserved mechanism against viruses in plants and animals. It is thought to inactivate the viral genome by producing virus-derived small interfering RNAs (vsiRNAs). Rice black-streaked dwarf virus (RBSDV) is transmitted to plants by the small brown planthopper (Laodelphax striatellus), and seriously threatens production of rice in East Asia, particularly Oryza sativa japonica subspecies. Through deep sequencing, genome-wide comparisons of RBSDV-derived vsiRNAs were made between the japonica variety Nipponbare, and the indica variety 9311...
December 7, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/29214993/microrna-like-rnas-from-the-same-mirna-precursors-play-a-role-in-cassava-chilling-responses
#19
Changying Zeng, Jing Xia, Xin Chen, Yufei Zhou, Ming Peng, Weixiong Zhang
MicroRNAs (miRNAs) are known to play important roles in various cellular processes and stress responses. MiRNAs can be identified by analyzing reads from high-throughput deep sequencing. The reads realigned to miRNA precursors besides canonical miRNAs were initially considered as sequencing noise and ignored from further analysis. Here we reported a small-RNA species of phased and half-phased miRNA-like RNAs different from canonical miRNAs from cassava miRNA precursors detected under four distinct chilling conditions...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213115/modulation-of-immune-signaling-and-metabolism-highlights-host-and-fungal-transcriptional-responses-in-mouse-models-of-invasive-pulmonary-aspergillosis
#20
Shiv D Kale, Tariq Ayubi, Dawoon Chung, Nuria Tubau-Juni, Andrew Leber, Ha X Dang, Saikumar Karyala, Raquel Hontecillas, Christopher B Lawrence, Robert A Cramer, Josep Bassaganya-Riera
Incidences of invasive pulmonary aspergillosis, an infection caused predominantly by Aspergillus fumigatus, have increased due to the growing number of immunocompromised individuals. While A. fumigatus is reliant upon deficiencies in the host to facilitate invasive disease, the distinct mechanisms that govern the host-pathogen interaction remain enigmatic, particularly in the context of distinct immune modulating therapies. To gain insights into these mechanisms, RNA-Seq technology was utilized to sequence RNA derived from lungs of 2 clinically relevant, but immunologically distinct murine models of IPA on days 2 and 3 post inoculation when infection is established and active disease present...
December 6, 2017: Scientific Reports
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