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https://www.readbyqxmd.com/read/28545270/-correlation-between-mutation-of-p53-gene-2-4-exons-from-peripheral-blood-and-hpv16-positive-cervical-cancer-susceptibility-and-clinical-significance
#1
C M Yin, Y F Yao, Z L Yan, H Y Yang
Objective: To detect mutations of p53 gene 2-4 exons from peripheral blood and to explore their relevance in HPV16-positive cervical cancer susceptibility and clinical significance. Methods: Collected firstly cases from the Third Affiliated Hospital of Kunming Medical University from October 2012 to April 2014, included 167 cases HPV16-postive cervical cancer and 160 cases HPV-negative healthy women. Genomic DNA from the host peripheral venous blood was taken, mutations of p53 gene 2-4 exons were analyzed with software DNAstar after PCR and bidirectional sequencing...
May 25, 2017: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28545258/marker-assisted-molecular-profiling-deletion-mutant-analysis-and-rna-seq-reveal-a-disease-resistance-cluster-associated-with-uromyces-appendiculatus-infection-in-common-bean-phaseolus-vulgaris-l
#2
Antonette R Todd, Nicole Donofrio, Venkateswara R Sripathi, Phillip E McClean, Rian K Lee, Marcial Pastor-Corrales, Venu Kal Kalavacharla
Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The Ur-3 locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant "Sierra" and susceptible crg) with rust race 53 of U...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545252/cpg-and-non-cpg-methylation-in-epigenetic-gene-regulation-and-brain-function
#3
REVIEW
Hyun Sik Jang, Woo Jung Shin, Jeong Eon Lee, Jeong Tae Do
DNA methylation is a major epigenetic mark with important roles in genetic regulation. Methylated cytosines are found primarily at CpG dinucleotides, but are also found at non-CpG sites (CpA, CpT, and CpC). The general functions of CpG and non-CpG methylation include gene silencing or activation depending on the methylated regions. CpG and non-CpG methylation are found throughout the whole genome, including repetitive sequences, enhancers, promoters, and gene bodies. Interestingly, however, non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells...
May 23, 2017: Genes
https://www.readbyqxmd.com/read/28545250/endophytic-bacteria-isolated-from-panax-ginseng-improves-ginsenoside-accumulation-in-adventitious-ginseng-root-culture
#4
Xiaolin Song, Hao Wu, Zhenhao Yin, Meilan Lian, Chengri Yin
Ginsenoside is the most important secondary metabolite of ginseng. Natural sources of wild ginseng have been overexploited. Although root culture could reduce the length of the growth cycle of ginseng, the number of ginsenosides is fewer and their contents are lower in adventitious roots of ginseng than that in ginseng cultivated in the field. In this study, we investigated the effects of endophytic bacterial elicitors on biomass and ginsenoside production in adventitious roots cultures of Panax ginseng. Endophyte LB 5-3 as an elicitor could increase biomass and ginsenoside accumulation in ginseng adventitious root culture...
May 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28545236/thermal-characterization-of-dynamic-silicon-cantilever-array-sensors-by-digital-holographic-microscopy
#5
Marjan Zakerin, Antonin Novak, Masaya Toda, Yves Emery, Filipe Natalio, Hans-Jürgen Butt, Rüdiger Berger
In this paper, we apply a digital holographic microscope (DHM) in conjunction with stroboscopic acquisition synchronization. Here, the temperature-dependent decrease of the first resonance frequency (S₁(T)) and Young's elastic modulus (E₁(T)) of silicon micromechanical cantilever sensors (MCSs) are measured. To perform these measurements, the MCSs are uniformly heated from T₀ = 298 K to T = 450 K while being externally actuated with a piezo-actuator in a certain frequency range close to their first resonance frequencies...
May 23, 2017: Sensors
https://www.readbyqxmd.com/read/28545234/validation-of-splicing-events-in-transcriptome-sequencing-data
#6
Wolfgang Kaisers, Johannes Ptok, Holger Schwender, Heiner Schaal
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545165/highly-recurrent-h3f3a-mutations-with-additional-epigenetic-regulator-alterations-in-giant-cell-tumor-of-bone
#7
Koichi Ogura, Fumie Hosoda, Hiromi Nakamura, Natsuko Hama, Yasushi Totoki, Akihiko Yoshida, Shoko Ohashi, Hirofumi Rokutan, Erina Takai, Shinichi Yachida, Akira Kawai, Sakae Tanaka, Tatsuhiro Shibata
Recurrent H3F3A and IDH2 mutations have been reported in giant cell tumor of bone (GCTB). However, the reported incidences have varied, and other molecular genetic alterations have not been identified due to the small number of cases analyzed with comprehensive methods. Moreover, the relative sensitivities of Sanger sequencing and next-generation sequencing (NGS) for the detection of H3F3A mutations in DNA extracted from archival formalin-fixed paraffin-embedded (FFPE) for clinical diagnosis have not been assessed...
May 25, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28545149/persistence-of-lineage-iv-peste-des-petits-ruminants-virus-within-israel-since-1993-an-evolutionary-perspective
#8
Brian Clarke, Mana Mahapatra, Orly Friedgut, Velizar Bumbarov, Satya Parida
Peste-des-petits ruminants (PPR) is one of the most important infectious diseases of domesticated small ruminants. From the initial identification in 1942 in West Africa, PPR virus (PPRV) has spread throughout much of the developing world. PPRV is now considered endemic throughout Africa, with the notable exception of South Africa, the Middle-East and Israel, as well as South-, East-, and Central Asia. Despite this widespread dispersal, the evolution and transmission of PPRV in endemic populations is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#9
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28545147/chromosome-divergence-during-evolution-of-the-tetraploid-clawed-frogs-xenopus-mellotropicalis-and-xenopus-epitropicalis-as-revealed-by-zoo-fish
#10
Martin Knytl, Ondřej Smolík, Svatava Kubíčková, Tereza Tlapáková, Ben J Evans, Vladimír Krylov
Whole genome duplication (WGD) generates new species and genomic redundancy. In African clawed frogs of the genus Xenopus, this phenomenon has been especially important in that (i) all but one extant species are polyploid and (ii) whole genome sequences of some species provide an evidence for genomic rearrangements prior to or after WGD. Within Xenopus in the subgenus Silurana, at least one allotetraploidization event gave rise to three extant tetraploid (2n = 4x = 40) species-Xenopus mellotropicalis, X. epitropicalis, and X...
2017: PloS One
https://www.readbyqxmd.com/read/28545146/transcriptomics-technologies
#11
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28545140/the-role-of-the-zinc-finger-protein-zc3h32-in-bloodstream-form-trypanosoma-brucei
#12
Cornelia Klein, Monica Terrao, Christine Clayton
Kinetoplastids rely heavily on post-transcriptional mechanisms for control of gene expression, with regulation of mRNA processing, translation and degradation by RNA-binding proteins. ZC3H32 is a cytosolic mRNA-binding protein with three non-canonical CCCH zinc finger domains. It is much more abundant in bloodstream-form Trypanosoma brucei than in procyclic forms. Tethering of ZC3H32 to a reporter mRNA suppressed translation and resulted in mRNA degradation, and deletion analysis suggested that this activity was present in both the N- and C-terminal domains, but not the central zinc finger-containing domain...
2017: PloS One
https://www.readbyqxmd.com/read/28545139/an-example-of-host-plant-expansion-of-host-specialized-aphis-gossypii-glover-in-the-field
#13
Dao-Wu Hu, Shuai Zhang, Jun-Yu Luo, Li-Min Lü, Jin-Jie Cui, Xiao Zhang
The host plant expansion of host-specialized Aphis gossypii (Glover) has been well studied in the laboratory; however, this phenomenon is poorly understood in the field. Here, we provide a series of laboratory and field experiments to assess the role of zucchini in the host plant expansion of cotton-specialized aphids. We observed that cotton-specialized aphids possessed the ability to expand on a new host plant (cucumber), with individuals first recorded on June 12 and consequently increasing exponentially in number in a field cage...
2017: PloS One
https://www.readbyqxmd.com/read/28545131/major-changes-in-microbial-diversity-and-community-composition-across-gut-sections-of-a-juvenile-panchlora-cockroach
#14
Erin A Gontang, Frank O Aylward, Camila Carlos, Tijana Glavina Del Rio, Mansi Chovatia, Alison Fern, Chien-Chi Lo, Stephanie A Malfatti, Susannah G Tringe, Cameron R Currie, Roberto Kolter
Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica...
2017: PloS One
https://www.readbyqxmd.com/read/28545124/cornet-assigning-function-to-networks-of-co-evolving-residues-by-automated-literature-mining
#15
Tom van den Bergh, Giorgio Tamo, Alberto Nobili, Yifeng Tao, Tianwei Tan, Uwe T Bornscheuer, Remko K P Kuipers, Bas Vroling, René M de Jong, Kalyanasundaram Subramanian, Peter J Schaap, Tom Desmet, Bernd Nidetzky, Gert Vriend, Henk-Jan Joosten
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity...
2017: PloS One
https://www.readbyqxmd.com/read/28545106/serum-microrna-signatures-as-liquid-biopsies-for-interrogating-hepatotoxic-mechanisms-and-liver-pathogenesis-in-human
#16
Julian Krauskopf, Theo M de Kok, Shelli J Schomaker, Mark Gosink, Deborah A Burt, Patricia Chandler, Roscoe L Warner, Kent J Johnson, Florian Caiment, Jos C Kleinjans, Jiri Aubrecht
MicroRNAs (miRNAs) released into the peripheral circulation upon cellular injury have shown a promise as a new class of tissue-specific biomarkers. We were first to demonstrate that next-generation sequencing analysis of serum from human subjects with acetaminophen-induced liver injury revealed a specific signature of circulating miRNAs. We consequently hypothesized that different types of hepatic liver impairments might feature distinct signatures of circulating miRNAs and that this approach might be useful as minimally invasive diagnostic "liquid biopsies" enabling the interrogation of underlying molecular mechanisms of injury in distant tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28545102/effect-of-dietary-restriction-and-subsequent-re-alimentation-on-the-transcriptional-profile-of-bovine-ruminal-epithelium
#17
Kate Keogh, Sinead M Waters, Paul Cormican, Alan K Kelly, Emma O'Shea, David A Kenny
Compensatory growth (CG) is utilised worldwide in beef production systems as a management approach to reduce feed costs. However the underlying biology regulating the expression of CG remains to be fully elucidated. The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced CG on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n = 60) were assigned to one of two groups: restricted feed allowance (RES; n = 30) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n = 30)...
2017: PloS One
https://www.readbyqxmd.com/read/28545083/simultaneous-inference-of-phylogenetic-and-transmission-trees-in-infectious-disease-outbreaks
#18
Don Klinkenberg, Jantien A Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga
Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28545070/pou4f3-mutation-screening-in-japanese-hearing-loss-patients-massively-parallel-dna-sequencing-based-analysis-identified-novel-variants-associated-with-autosomal-dominant-hearing-loss
#19
Tomohiro Kitano, Maiko Miyagawa, Shin-Ya Nishio, Hideaki Moteki, Kiyoshi Oda, Kenji Ohyama, Hiromitsu Miyazaki, Hiroshi Hidaka, Ken-Ichi Nakamura, Takaaki Murata, Rina Matsuoka, Yoko Ohta, Nobuhiro Nishiyama, Kozo Kumakawa, Sakiko Furutate, Satoshi Iwasaki, Takechiyo Yamada, Yumi Ohta, Natsumi Uehara, Yoshihiro Noguchi, Shin-Ichi Usami
A variant in a transcription factor gene, POU4F3, is responsible for autosomal dominant nonsyndromic hereditary hearing loss, DFNA15. To date, 14 variants, including a whole deletion of POU4F3, have been reported to cause HL in various ethnic groups. In the present study, genetic screening for POU4F3 variants was carried out for a large series of Japanese hearing loss (HL) patients to clarify the prevalence and clinical characteristics of DFNA15 in the Japanese population. Massively parallel DNA sequencing of 68 target candidate genes was utilized in 2,549 unrelated Japanese HL patients (probands) to identify genomic variations responsible for HL...
2017: PloS One
https://www.readbyqxmd.com/read/28545050/prevalence-and-extent-of-heteroresistance-by-next-generation-sequencing-of-multidrug-resistant-tuberculosis
#20
Darwin J Operario, Alexander F Koeppel, Stephen D Turner, Yongde Bao, Suporn Pholwat, Sayera Banu, Suporn Foongladda, Stellah Mpagama, Jean Gratz, Oleg Ogarkov, Svetlana Zhadova, Scott K Heysell, Eric R Houpt
Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides. Across these gene regions, complete resistance or heteroresistance (defined as 1%-99% mutation) was present in at least one isolate in 6.3% of loci. The number of isolates with heteroresistance was highest for gyrA codon 94, rpoB codons 526 and 531, and embB codons 306, 372 and 406 (range 11-26% of isolates exhibited heteroresistance)...
2017: PloS One
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