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https://www.readbyqxmd.com/read/28537229/-genomics-and-transcriptomics-of-the-chinese-liver-fluke-clonorchis-sinensis-opisthorchiidae-trematoda
#1
G N Chelomina
The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships...
March 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28527335/dissection-of-cis-regulatory-element-architecture-of-the-rice-oleosin-gene-promoters-to-assess-abscisic-acid-responsiveness-in-suspension-cultured-rice-cells
#2
Sol Kim, Soo-Bin Lee, Chae-Seong Han, Mi-Na Lim, Sung-Eun Lee, In Sun Yoon, Yong-Sic Hwang
Oleosins are the most abundant proteins in the monolipid layer surrounding neutral storage lipids that form oil bodies in plants. Several lines of evidence indicate that they are physiologically important for the maintenance of oil body structure and for mobilization of the lipids stored inside. Rice has six oleosin genes in its genome, the expression of all of which was found to be responsive to abscisic acid (ABA) in our examination of mature embryo and aleurone tissues. The 5'-flanking region of OsOle5 was initially characterized for its responsiveness to ABA through a transient expression assay system using the protoplasts from suspension-cultured rice cells...
May 1, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28525572/crosstalk-between-vertical-and-horizontal-gene-transfer-plasmid-replication-control-by-a-conjugative-relaxase
#3
Fabián Lorenzo-Díaz, Cris Fernández-López, Rudi Lurz, Alicia Bravo, Manuel Espinosa
Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28523221/reading-lines-within-the-cocaine-addicted-brain
#4
Glenn A Doyle, Tara T Doucet-O'Hare, Matthew J Hammond, Richard C Crist, Adam D Ewing, Thomas N Ferraro, Deborah C Mash, Haig H Kazazian, Wade H Berrettini
INTRODUCTION: Long interspersed element (LINE)-1 (L1) is a type of retrotransposon capable of mobilizing into new genomic locations. Often studied in Mendelian diseases or cancer, L1s may also cause somatic mutation in the developing central nervous system. Recent reports showed L1 transcription was activated in brains of cocaine-treated mice, and L1 retrotransposition was increased in cocaine-treated neuronal cell cultures. We hypothesized that the predisposition to cocaine addiction may result from inherited L1s or somatic L1 mobilization in the brain...
May 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28510215/species-specific-supercoil-dynamics-of-the-bacterial-nucleoid
#5
N Patrick Higgins
Bacteria organize DNA into self-adherent conglomerates called nucleoids that are replicated, transcribed, and partitioned within the cytoplasm during growth and cell division. Three classes of proteins help condense nucleoids: (1) DNA gyrase generates diffusible negative supercoils that help compact DNA into a dynamic interwound and multiply branched structure; (2) RNA polymerase and abundant small basic nucleoid-associated proteins (NAPs) create constrained supercoils by binding, bending, and forming cooperative protein-DNA complexes; (3) a multi-protein DNA condensin organizes chromosome structure to assist sister chromosome segregation after replication...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28503377/analysis-of-reca-independent-recombination-events-between-short-direct-repeats-related-to-a-genomic-island-and-to-a-plasmid-in-escherichia-coli-k12
#6
María F Azpiroz, Magela Laviña
RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, also in the E. coli K12 context. However, it did not encode a site-specific recombinase as mobile genomic islands usually do. It was then deduced that the host cells should provide the recombination function...
2017: PeerJ
https://www.readbyqxmd.com/read/28499400/epiteome-simultaneous-detection-of-transposable-element-insertion-sites-and-their-dna-methylation-levels
#7
Josquin Daron, R Keith Slotkin
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a program that detects both new transposable element insertion sites and their methylation states from a single MethylC-seq dataset. EpiTEome outperforms other split-read insertion site detection programs, even while functioning on bisulfite-converted reads...
May 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28491150/dynamic-silencing-of-somatic-l1-retrotransposon-insertions-reflects-the-developmental-and-cellular-contexts-of-their-genomic-integration
#8
Manoj Kannan, Jingfeng Li, Sarah E Fritz, Kathryn E Husarek, Jonathan C Sanford, Teresa L Sullivan, Pawan Kumar Tiwary, Wenfeng An, Jef D Boeke, David E Symer
BACKGROUND: The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. RESULTS: Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28486636/natural-variation-in-the-distribution-and-abundance-of-transposable-elements-across-the-caenorhabditis-elegans-species
#9
K M Laricchia, S Zdraljevic, D E Cook, E C Andersen
Transposons are mobile DNA elements that generate both adaptive and deleterious phenotypic variation thereby driving genome evolution. For these reasons, genomes have mechanisms to regulate transposable element (TE) activity. Approximately 12-16% of the Caenorhabditis elegans genome is composed of TEs, of which the majority are likely inactive. However, most studies of TE activity have been conducted in the laboratory strain N2, which limits our knowledge of the effects of these mobile elements across natural populations...
May 9, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28482231/mobile-self-splicing-introns-and-inteins-as-environmental-sensors
#10
REVIEW
Marlene Belfort
Self-splicing introns and inteins are often mobile at the level of the genome. Although these RNA and protein elements, respectively, are generally considered to be selfish parasites, group I and group II introns and inteins can be triggered by environmental cues to splice and/or to mobilize. These cues include stressors such as oxidizing agents, reactive oxygen and nitrogen species, starvation, temperature, osmolarity and DNA damage. Their sensitivity to these stimuli leads to a carefully choreographed dance between the mobile element and its host that is in tune with the cellular environment...
May 5, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28469420/in-silico-approach-for-characterization-and-comparison-of-repeats-in-the-genomes-of-oil-and-date-palms
#11
Jaire Alves Ferreira Filho, Lucas Soares de Brito, André Pereira Leão, Alexandre Alonso Alves, Eduardo Fernandes Formighieri, Manoel Teixeira Souza Júnior
Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/28466841/arabidopsis-proteins-with-a-transposon-related-domain-act-in-gene-silencing
#12
Yoko Ikeda, Thierry Pélissier, Pierre Bourguet, Claude Becker, Marie-Noëlle Pouch-Pélissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon, Olivier Mathieu
Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin...
May 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28458094/in-and-out-contribution-of-natural-transformation-to-the-shuffling-of-large-genomic-regions
#13
REVIEW
Melanie Blokesch
Naturally competent bacteria can pull free DNA from their surroundings. This incoming DNA can serve various purposes, ranging from acting as a source of nutrients or DNA stretches for repair to the acquisition of novel genetic information. The latter process defines the natural competence for transformation as a mode of horizontal gene transfer (HGT) and led to its discovery almost a century ago. However, although it is widely accepted that natural competence can contribute to the spread of genetic material among prokaryotes, the question remains whether this mode of HGT can foster the transfer of larger DNA regions or only transfers shorter fragments, given that extracellular DNA is often heavily fragmented...
April 27, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28452176/microbial-acceleration-of-aerobic-pyrite-oxidation-at-circumneutral-ph
#14
E Percak-Dennett, S He, B Converse, H Konishi, H Xu, A Corcoran, D Noguera, C Chan, A Bhayyacharyya, T Borch, E Boyd, E E Roden
Pyrite (FeS2 ) is the most abundant sulfide mineral on Earth and represents a significant reservoir of reduced iron and sulfur both today and in the geologic past. In modern environments, oxidative transformations of pyrite and other metal sulfides play a key role in terrestrial element partitioning with broad impacts to contaminant mobility and the formation of acid mine drainage systems. Although the role of aerobic micro-organisms in pyrite oxidation under acidic-pH conditions is well known, to date there is very little known about the capacity for aerobic micro-organisms to oxidize pyrite at circumneutral pH...
April 27, 2017: Geobiology
https://www.readbyqxmd.com/read/28450881/line-insertion-polymorphisms-are-abundant-but-at-low-frequencies-across-populations-of-anolis-carolinensis
#15
Robert P Ruggiero, Yann Bourgeois, Stéphane Boissinot
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28448614/obtaining-retrotransposon-sequences-analysis-of-their-genomic-distribution-and-use-of-retrotransposon-derived-genetic-markers-in-lentil-lens-culinaris-medik
#16
Rita Rey-Baños, Luis E Sáenz de Miera, Pedro García, Marcelino Pérez de la Vega
Retrotransposons with long terminal repeats (LTR-RTs) are widespread mobile elements in eukaryotic genomes. We obtained a total of 81 partial LTR-RT sequences from lentil corresponding to internal retrotransposon components and LTRs. Sequences were obtained by PCR from genomic DNA. Approximately 37% of the LTR-RT internal sequences presented premature stop codons, pointing out that these elements must be non-autonomous. LTR sequences were obtained using the iPBS technique which amplifies sequences between LTR-RTs...
2017: PloS One
https://www.readbyqxmd.com/read/28447635/a-chromosome-conformation-capture-ordered-sequence-of-the-barley-genome
#17
Martin Mascher, Heidrun Gundlach, Axel Himmelbach, Sebastian Beier, Sven O Twardziok, Thomas Wicker, Volodymyr Radchuk, Christoph Dockter, Pete E Hedley, Joanne Russell, Micha Bayer, Luke Ramsay, Hui Liu, Georg Haberer, Xiao-Qi Zhang, Qisen Zhang, Roberto A Barrero, Lin Li, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz-Amatriaín, Rachid Ounit, Steve Wanamaker, Daniel Bolser, Christian Colmsee, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Anna Chailyan, Dharanya Sampath, Darren Heavens, Leah Clissold, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K McCooke, Cong Tan, Penghao Wang, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse A Poland, Matthew I Bellgard, Ljudmilla Borisjuk, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Paul Kersey, Peter Langridge, Gary J Muehlbauer, Matthew D Clark, Mario Caccamo, Alan H Schulman, Klaus F X Mayer, Matthias Platzer, Timothy J Close, Uwe Scholz, Mats Hansson, Guoping Zhang, Ilka Braumann, Manuel Spannagl, Chengdao Li, Robbie Waugh, Nils Stein
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28444372/quantifying-the-number-of-independent-organelle-dna-insertions-in-genome-evolution-and-human-health
#18
Einat Hazkani-Covo, William F Martin
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28444231/whole-genome-sequencing-of-seven-strains-of-staphylococcus-lugdunensis-allows-identification-of-mobile-genetic-elements
#19
Xavier Argemi, Véronique Martin, Valentin Loux, Sandrine Dahyot, Jérémie Lebeurre, Aurélien Guffroy, Mickael Martin, Aurélie Velay, Daniel Keller, Philippe Riegel, Yves Hansmann, Nicodème Paul, Gilles Prévost
Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28442219/virulence-potential-of-staphylococcus-aureus-isolates-from-buruli-ulcer-patients
#20
Nana Ama Amissah, Monika A Chlebowicz, Anthony Ablordey, Caitlin S Tetteh, Isaac Prah, Tjip S van der Werf, Alex W Friedrich, Jan Maarten van Dijl, Ymkje Stienstra, John W Rossen
Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins...
April 19, 2017: International Journal of Medical Microbiology: IJMM
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