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BMC Genomics

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https://www.readbyqxmd.com/read/27919246/adjacent-sequences-disclose-potential-for-intra-genomic-dispersal-of-satellite-dna-repeats-and-suggest-a-complex-network-with-transposable-elements
#1
Eva Satović, Tanja Vojvoda Zeljko, Andrea Luchetti, Barbara Mantovani, Miroslav Plohl
BACKGROUND: Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape...
December 6, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27919227/high-light-stress-triggers-distinct-proteomic-responses-in-the-marine-diatom-thalassiosira-pseudonana
#2
Hong-Po Dong, Yue-Lei Dong, Lei Cui, Srinivasan Balamurugan, Jian Gao, Song-Hui Lu, Tao Jiang
BACKGROUND: Diatoms are able to acclimate to frequent and large light fluctuations in the surface ocean waters. However, the molecular mechanisms underlying these acclimation responses of diaotms remain elusive. RESULTS: In this study, we investigated the mechanism of high light protection in marine diatom Thalassiosira pseudonana using comparative proteomics in combination with biochemical analyses. Cells treated under high light (800 μmol photons m(-2)s(-1)) for 10 h were subjected to proteomic analysis...
December 5, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27919223/trpm2-snp-genotype-previously-associated-with-susceptibility-to-rhodococcus-equi-pneumonia-in-quarter-horse-foals-displays-differential-gene-expression-identified-using-rna-seq
#3
Cole M McQueen, Canaan M Whitfield-Cargile, Kranti Konganti, Glenn P Blodgett, Scott V Dindot, Noah D Cohen
BACKGROUND: Rhodococcus equi (R. equi) is an intracellular bacterium that affects young foals and immuno-compromised individuals causing severe pneumonia. Currently, the genetic mechanisms that confer susceptibility and/or resistance to R. equi are not fully understood. Previously, using a SNP-based genome-wide association study, we identified a region on equine chromosome 26 associated with culture-confirmed clinical pneumonia. To better characterize this region and understand the function of the SNP located within TRPM2 that was associated with R...
December 5, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27914481/conserved-3-utr-stem-loop-structure-in-l1-and-alu-transposons-in-human-genome-possible-role-in-retrotransposition
#4
Daria Grechishnikova, Maria Poptsova
BACKGROUND: In the process of retrotransposition LINEs use their own machinery for copying and inserting themselves into new genomic locations, while SINEs are parasitic and require the machinery of LINEs. The exact mechanism of how a LINE-encoded reverse transcriptase (RT) recognizes its own and SINE RNA remains unclear. However it was shown for the stringent-type LINEs that recognition of a stem-loop at the 3'UTR by RT is essential for retrotransposition. For the relaxed-type LINEs it is believed that the poly-A tail is a common recognition element between LINE and SINE RNA...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#5
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912729/genomic-insights-from-whole-genome-sequencing-of-four-clonal-outbreak-campylobacter-jejuni-assessed-within-the-global-c-jejuni-population
#6
Clifford G Clark, Chrystal Berry, Matthew Walker, Aaron Petkau, Dillon O R Barker, Cai Guan, Aleisha Reimer, Eduardo N Taboada
BACKGROUND: Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27912746/erratum-to-non-linear-interactions-between-candidate-genes-of-myocardial-infarction-revealed-in-mrna-expression-profiles
#7
Katherine Hartmann, Michał Seweryn, Samuel K Handelman, Grzegorz A Rempała, Wolfgang Sadee
No abstract text is available yet for this article.
December 2, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27908274/a-novel-approach-to-probe-host-pathogen-interactions-of-bovine-digital-dermatitis-a-model-of-a-complex-polymicrobial-infection
#8
Paolo Marcatili, Martin W Nielsen, Thomas Sicheritz-Pontén, Tim K Jensen, Claus Schafer-Nielsen, Mette Boye, Morten Nielsen, Kirstine Klitgaard
BACKGROUND: Polymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections. RESULTS: The strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27905883/carbohydrate-metabolism-in-oenococcus-oeni-a-genomic-insight
#9
Alice Cibrario, Claire Peanne, Marine Lailheugue, Hugo Campbell-Sills, Marguerite Dols-Lafargue
BACKGROUND: Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Several studies have described a high intraspecific diversity regarding carbohydrate degradation abilities but the link between the phenotypes and the genes and metabolic pathways has been poorly described. RESULTS: A collection of 41 strains whose genomic sequences were available and representative of the species genomic diversity was analyzed for growth on 18 carbohydrates relevant in wine...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27905879/transcriptome-profiling-in-the-damselfly-ischnura-elegans-identifies-genes-with-sex-biased-expression
#10
Pallavi Chauhan, Maren Wellenreuther, Bengt Hansson
BACKGROUND: Sexual dimorphism occurs widely across the animal kingdom and has profound effects on evolutionary trajectories. Here, we investigate sex-specific gene expression in Ischnura elegans (Odonata: dragonflies and damselflies), a species with pronounced sexual differences including a female-limited colour polymorphism with two female-like gynochrome morphs and one male-mimicking, androchrome morph. Whole-organism transcriptome profiling and sex-biased gene expression analysis was conducted on adults of both sexes (pooling all females as well as separating the three morphs) to gain insights into genes and pathways potentially associated with sexual development and sexual conflict...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27905873/comparative-genomics-of-beauveria-bassiana-uncovering-signatures-of-virulence-against-mosquitoes
#11
Claudio A Valero-Jiménez, Luigi Faino, Daphne Spring In't Veld, Sandra Smit, Bas J Zwaan, Jan A L van Kan
BACKGROUND: Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27903243/analysis-of-rna-expression-of-normal-and-cancer-tissues-reveals-high-correlation-of-cop9-gene-expression-with-respiratory-chain-complex-components
#12
Christina A Wicker, Tadahide Izumi
BACKGROUND: The COP9 signalosome, composed of eight subunits, is implicated in cancer genetics with its deneddylase activity to modulate cellular concentration of oncogenic proteins such as IkB and TGFβ. However, its function in the normal cell physiology remains elusive. Primarily focusing on gene expression data of the normal tissues of the head and neck, the cancer genome atlas (TCGA) database was used to identify groups of genes that were expressed synergistically with the COP9 genes, particularly with the COPS5 (CSN5), which possesses the catalytic activity of COP9...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27894259/genomic-signatures-of-mannheimia-haemolytica-that-associate-with-the-lungs-of-cattle-with-respiratory-disease-an-integrative-conjugative-element-and-antibiotic-resistance-genes
#13
Michael L Clawson, Robert W Murray, Michael T Sweeney, Michael D Apley, Keith D DeDonder, Sarah F Capik, Robert L Larson, Brian V Lubbers, Brad J White, Theodore S Kalbfleisch, Gennie Schuller, Aaron M Dickey, Gregory P Harhay, Michael P Heaton, Carol G Chitko-McKown, Dayna M Brichta-Harhay, James L Bono, Timothy P L Smith
BACKGROUND: Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease...
November 29, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27894274/gene-cassette-knock-in-in-mammalian-cells-and-zygotes-by-enhanced-mmej
#14
Tomomi Aida, Shota Nakade, Tetsushi Sakuma, Yayoi Izu, Ayu Oishi, Keiji Mochida, Harumi Ishikubo, Takako Usami, Hidenori Aizawa, Takashi Yamamoto, Kohichi Tanaka
BACKGROUND: Although CRISPR/Cas enables one-step gene cassette knock-in, assembling targeting vectors containing long homology arms is a laborious process for high-throughput knock-in. We recently developed the CRISPR/Cas-based precise integration into the target chromosome (PITCh) system for a gene cassette knock-in without long homology arms mediated by microhomology-mediated end-joining. RESULTS: Here, we identified exonuclease 1 (Exo1) as an enhancer for PITCh in human cells...
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27894263/erratum-to-a-new-transcriptome-and-transcriptome-profiling-of-adult-and-larval-tissue-in-the-box-jellyfish-alatina-alata-an-emerging-model-for-studying-venom-vision-and-sex
#15
Cheryl Lewis Ames, Joseph F Ryan, Alexandra E Bely, Paulyn Cartwright, Allen G Collins
No abstract text is available yet for this article.
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27894253/latitudinal-clines-in-gene-expression-and-cis-regulatory-element-variation-in-drosophila-melanogaster
#16
Punita Juneja, Andrew Quinn, Francis M Jiggins
BACKGROUND: Organisms can rapidly adapt to their environment when colonizing a new habitat, and this could occur by changing protein sequences or by altering patterns of gene expression. The importance of gene expression in driving local adaptation is increasingly being appreciated, and cis-regulatory elements (CREs), which control and modify the expression of the nearby genes, are predicted to play an important role. Here we investigate genetic variation in gene expression in immune-challenged Drosophila melanogaster from temperate and tropical or sub-tropical populations in Australia and United States...
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27894252/transcriptome-analysis-reveals-the-genetic-basis-underlying-the-seasonal-development-of-keratinized-nuptial-spines-in-leptobrachium-boringii
#17
Wei Zhang, Yue Guo, Jun Li, Li Huang, Eric Gilbert Kazitsa, Hua Wu
BACKGROUND: The expression of sexually selected traits often varies with populations' breeding cycles in many animals. The elucidation of mechanisms underlying the expression of such traits is a research topic in evolutionary biology; however, the genetic basis of the seasonal development of their expression remains unknown. Male Leptobrachium boringii develop keratinized nuptial spines on their upper jaw during the breeding season that fall off when the breeding season ends. To illuminate the genetic basis for the expression of this trait and its seasonal development, we assessed the de novo transcriptome for L...
November 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27887573/in-vitro-function-of-upstream-visfatin-polymorphisms-that-are-associated-with-adverse-cardiometabolic-parameters-in-obese-children
#18
Delicia Shu Qin Ooi, Siong Gim Ong, Chew Kiat Heng, Kah Yin Loke, Yung Seng Lee
BACKGROUND: Visfatin is an adipokine associated with glucose and lipid metabolism. We previously reported two visfatin upstream single nucleotide polymorphisms (SNPs), c.-3187G > A (rs11977021) and c.-1537C > T (rs61330082), which were in perfect linkage disequilibrium, in a Singaporean cohort of severely obese children and are associated with visfatin level and adverse cardiometabolic parameters. We aim to functionally characterize the effect of c.-3187G > A and c...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27887572/maternal-smoking-impacts-key-biological-pathways-in-newborns-through-epigenetic-modification-in-utero
#19
Daniel M Rotroff, Bonnie R Joubert, Skylar W Marvel, Siri E Håberg, Michael C Wu, Roy M Nilsen, Per M Ueland, Wenche Nystad, Stephanie J London, Alison Motsinger-Reif
BACKGROUND: Children exposed to maternal smoking during pregnancy exhibit increased risk for many adverse health effects. Maternal smoking influences methylation in newborns at specific CpG sites (CpGs). Here, we extend evaluation of individual CpGs to gene-level and pathway-level analyses among 1062 participants in the Norwegian Mother and Child Cohort Study (MoBa) using the Illumina 450 K platform to measure methylation in newborn DNA and maternal smoking in pregnancy, assessed using the biomarker, plasma cotinine...
November 25, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27887567/fluorescence-chromosome-banding-and-fish-mapping-in-perennial-ryegrass-lolium-perenne-l
#20
Helal A Ansari, Nicholas W Ellison, Shalome A Bassett, Syed W Hussain, Gregory T Bryan, Warren M Williams
BACKGROUND: The unambiguous identification of individual chromosomes is a key part of the genomic characterization of any species. In this respect, the development and application of chromosome banding techniques has revolutionised mammalian and especially, human genomics. However, partly because of the traditional use of chromosome squash preparations, consistent fluorescence banding has rarely been achieved in plants. Here, successful fluorescence chromosome banding has been achieved for the first time in perennial ryegrass (Lolium perenne), a forage and turf grass with a large genome and a symmetrical karyotype with chromosomes that are difficult to distinguish...
November 25, 2016: BMC Genomics
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