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https://www.readbyqxmd.com/read/29649665/the-anti-fecundity-effect-of-5-azacytidine-5-azac-on-schistosoma-mansoni-is-linked-to-dis-regulated-transcription-translation-and-stem-cell-activities
#1
Kathrin K Geyer, Sabrina E Munshi, Martin Vickers, Michael Squance, Toby J Wilkinson, Daniel Berrar, Cristian Chaparro, Martin T Swain, Karl F Hoffmann
Uncontrolled host immunological reactions directed against tissue-trapped eggs precipitate a potentially lethal, pathological cascade responsible for schistosomiasis. Blocking schistosome egg production, therefore, presents a strategy for simultaneously reducing immunopathology as well as limiting disease transmission in endemic or emerging areas. We recently demonstrated that the ribonucleoside analogue 5-azacytidine (5-AzaC) inhibited Schistosoma mansoni oviposition, egg maturation and ovarian development...
April 1, 2018: International Journal for Parasitology, Drugs and Drug Resistance
https://www.readbyqxmd.com/read/29649143/epigenetic-and-transcriptional-modifications-in-repetitive-elements-in-petrol-station-workers-exposed-to-benzene-and-mtbe
#2
Federica Rota, Anastasia Conti, Laura Campo, Chiara Favero, Laura Cantone, Valeria Motta, Elisa Polledri, Rosa Mercadante, Giorgio Dieci, Valentina Bollati, Silvia Fustinoni
Benzene, a known human carcinogen, and methyl tert -butyl ether (MTBE), not classifiable as to its carcinogenicity, are fuel-related pollutants. This study investigated the effect of these chemicals on epigenetic and transcriptional alterations in DNA repetitive elements. In 89 petrol station workers and 90 non-occupationally exposed subjects the transcriptional activity of retrotransposons (LINE-1, Alu), the methylation on repeated-element DNA, and of H3K9 histone, were investigated in peripheral blood lymphocytes...
April 12, 2018: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29643326/identification-and-characterization-of-short-tandem-repeats-in-the-tibetan-macaque-genome-based-on-resequencing-data
#3
San-Xu Liu, Wei Hou, Xue-Yan Zhang, Chang-Jun Peng, Bi-Song Yue, Zhen-Xin Fan, Jing Li
The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples...
April 11, 2018: Zoological Research
https://www.readbyqxmd.com/read/29642859/identification-of-novel-mites-miniature-inverted-repeat-transposable-elements-in-coxiella-burnetii-implications-for-protein-and-small-rna-evolution
#4
Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F Minnick
BACKGROUND: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii's genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities...
April 11, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29618299/comparison-of-methods-of-detection-of-exceptional-sequences-in-prokaryotic-genomes
#5
I S Rusinov, A S Ershova, A S Karyagina, S A Spirin, A V Alexeevski
Many proteins need recognition of specific DNA sequences for functioning. The number of recognition sites and their distribution along the DNA might be of biological importance. For example, the number of restriction sites is often reduced in prokaryotic and phage genomes to decrease the probability of DNA cleavage by restriction endonucleases. We call a sequence an exceptional one if its frequency in a genome significantly differs from one predicted by some mathematical model. An exceptional sequence could be either under- or over-represented, depending on its frequency in comparison with the predicted one...
February 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29618053/g-anchor-a-novel-approach-for-whole-genome-comparative-mapping-utilising-evolutionary-conserved-dna-sequences
#6
Vasileios Panagiotis E Lenis, Martin Swain, Denis M Larkin
Background: Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available now from multiple projects there is an increasing demand for genome comparative analyses...
April 3, 2018: GigaScience
https://www.readbyqxmd.com/read/29615780/de-novo-draft-assembly-of-the-botrylloides-leachii-genome-provides-further-insight-into-tunicate-evolution
#7
Simon Blanchoud, Kim Rutherford, Lisa Zondag, Neil J Gemmell, Megan J Wilson
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29605134/highly-sensitive-open-cell-la-icpms-approaches-for-the-quantification-of-rare-earth-elements-in-natural-carbonates-at-parts-per-billion-levels
#8
Chung-Che Wu, Marcel Burger, Detlef Günther, Chuan-Chou Shen, Bodo Hattendorf
This work presents a high-sensitivity approach to quantify ultra-trace concentrations of rare earth elements (REEs) in speleothem carbonates using open-cell laser ablation-sector field-inductively coupled plasma mass spectrometry (open-cell LA-SF-ICPMS). Specifically, open-cell LA in combination with a gas exchange device enabled sampling of large-scale carbonate specimens in an ambient environment. The use of a "jet" vacuum interface and the addition of small amounts of N2 gas allowed for a 20-40 fold sensitivity enhancement compared to the conventional interface configuration...
August 14, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29593912/antimicrobial-susceptibility-among-colistin-sulbactam-and-fosfomycin-and-a-synergism-study-of-colistin-in-combination-with-sulbactam-or-fosfomycin-against-clinical-isolates-of-carbapenem-resistant-acinetobacter-baumannii
#9
Sombat Leelasupasri, Wichai Santimaleeworagun, Tossawan Jitwasinkul
This in vitro study aimed to determine the activity of colistin plus sulbactam and colistin plus fosfomycin against carbapenem-resistant A. baumannii (CRAB). Fifteen clinical isolates were obtained from patients admitted to Phyathai II International Hospital, Bangkok, Thailand, from August 2014 to April 2015. The antimicrobial susceptibilities of colistin, sulbactam, and fosfomycin were evaluated using the E-test or broth microdilution and the synergistic activity of the antibacterial combinations (colistin plus sulbactam or fosfomycin) was determined using the chequerboard method...
2018: Journal of Pathogens
https://www.readbyqxmd.com/read/29593910/patients-and-health-professionals-experiences-of-using-virtual-reality-technology-for-upper-limb-training-after-stroke-a-qualitative-substudy
#10
Hanne Pallesen, Mette Brændstrup Andersen, Gunhild Mo Hansen, Camilla Biering Lundquist, Iris Brunner
Background: In recent years, virtual reality (VR) therapy systems for upper limb training after stroke have been increasingly used in clinical practice. Therapy systems employing VR technology can enhance the intensity of training and can also boost patients' motivation by adding a playful element to therapy. However, reports on user experiences are still scarce. Methods: A qualitative investigation of patients' and therapists' perspectives on VR upper limb training...
2018: Rehabilitation Research and Practice
https://www.readbyqxmd.com/read/29590185/new-insights-into-the-genome-repetitive-fraction-of-the-antarctic-bivalve-adamussium-colbecki
#11
Maria Assunta Biscotti, Marco Barucca, Adriana Canapa
Repetitive DNA represents the major component of the genome in both plant and animal species. It includes transposable elements (TEs), which are dispersed throughout the genome, and satellite DNAs (satDNAs), which are tandemly organized in long arrays. The study of the structure and organization of repetitive DNA contributes to our understanding of genome architecture and the mechanisms leading to its evolution. Molluscs represent one of the largest groups of invertebrates and include organisms with a wide variety of morphologies and lifestyles...
2018: PloS One
https://www.readbyqxmd.com/read/29588362/double-insertion-of-transposable-elements-provides-a-substrate-for-the-evolution-of-satellite-dnas
#12
Michael P McGurk, Daniel A Barbash
Eukaryotic genomes are replete with repeated sequences, in the form of transposable elements (TEs) dispersed across the genome or as satellite arrays, large stretches of tandemly repeated sequence. Many satellites clearly originated as TEs, but it is unclear how mobile genetic parasites can transform into megabase-sized tandem arrays. Comprehensive population genomic sampling is needed to determine the frequency and generative mechanisms of tandem TEs, at all stages from their initial formation to their subsequent expansion and maintenance as satellites...
March 27, 2018: Genome Research
https://www.readbyqxmd.com/read/29587867/group-consensus-peer-review-in-radiation-oncology-commitment-to-quality
#13
W Neil Duggar, Rahul Bhandari, Chunli Claus Yang, Srinivasan Vijayakumar
BACKGROUND: Peer review, especially prospective peer review, has been supported by professional organizations as an important element in optimal Radiation Oncology practice based on its demonstration of efficacy at detecting and preventing errors prior to patient treatment. Implementation of peer review is not without barriers, but solutions do exist to mitigate or eliminate some of those barriers. METHODS: Peer review practice at our institution involves three key elements: new patient conference, treatment planning conference, and chart rounds...
March 27, 2018: Radiation Oncology
https://www.readbyqxmd.com/read/29584757/transcriptome-analysis-of-genetically-matched-human-induced-pluripotent-stem-cells-disomic-or-trisomic-for-chromosome-21
#14
Patrick K Gonzales, Christine M Roberts, Virginia Fonte, Connor Jacobsen, Gretchen H Stein, Christopher D Link
Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones...
2018: PloS One
https://www.readbyqxmd.com/read/29565231/genomic-identity-of-fluoroquinolone-resistant-blactx-m-15-type-esbl-and-pmampc-%C3%AE-lactamase-producing-klebsiella-pneumoniae-from-buffalo-milk-india
#15
Samiran Bandyopadhyay, Jaydeep Banerjee, Debaraj Bhattacharyya, Indranil Samanta, Achintya Mahanti, Tapan K Dutta, Sarbaswarup Ghosh, Pramod K Nanda, Premanshu Dandapat, Subhasish Bandyopadhyay
We investigated the occurrence of extended-spectrum β-lactamase (ESBL) and AmpC-type β-lactamase (ACBL) producing quinolone-resistant Klebsiella pneumoniae (KP) in milk samples of apparently healthy buffaloes (n = 348) and buffaloes (n = 19) with evidence of subclinical mastitis from seven districts of West Bengal, India. In total, 12 ESBL producing KP were isolated with blaCTX-M-15 gene and 7 of them were ACBL producers, as well. The blaCTX-M-15 genes were carried by transposable element ISEcp1. The plasmid-mediated quinolone resistance genes-qnrS, qnrA, qnrB, qepA, and aac(6')-Ib-cr were detected in five, one, three, four, and one isolate (s), respectively...
March 22, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29562303/dating-the-species-network-allopolyploidy-and-repetitive-dna-evolution-in-american-daisies-melampodium-sect-melampodium-asteraceae
#16
Jamie McCann, Tae-Soo Jang, Jiri Macas, Gerald M Schneeweiss, Nicholas J Matzke, Petr Novák, Tod F Stuessy, José L Villaseñor, Hanna Weiss-Schneeweiss
Allopolyploidy has played an important role in the evolution of the flowering plants. Genome mergers are often accompanied by significant and rapid alterations of genome size and structure via chromosomal rearrangements and altered dynamics of tandem and dispersed repetitive DNA families. Recent developments in sequencing technologies and bioinformatic methods allow for a comprehensive investigation of the repetitive component of plant genomes. Interpretation of evolutionary dynamics following allopolyploidization requires both the knowledge of parentage and the age of origin of an allopolyploid...
March 19, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29556065/integrative-analysis-of-large-scale-transcriptome-data-draws-a-comprehensive-landscape-of-phaeodactylum-tricornutum-genome-and-evolutionary-origin-of-diatoms
#17
Achal Rastogi, Uma Maheswari, Richard G Dorrell, Fabio Rocha Jimenez Vieira, Florian Maumus, Adam Kustka, James McCarthy, Andy E Allen, Paul Kersey, Chris Bowler, Leila Tirichine
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes...
March 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29555392/emergence-and-characterization-of-nosocomial-multidrug-resistant-and-extensively-drug-resistant-acinetobacter-baumannii-isolates-in-tehran-iran
#18
Bahare Salehi, Hossein Goudarzi, Bahram Nikmanesh, Hamidreza Houri, Mostafa Alavi-Moghaddam, Zohreh Ghalavand
RATIONALE: Acinetobacter baumannii is one of the antibiotic-resistant superbugs that threatens hospitalized patients. Emergence and spread of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) clones cause erratic outbreaks following environmental contamination of hospital settings. OBJECTIVE: The present study intended to characterize the antimicrobial resistant profiles and the genotypes of clinical and environmental isolates of A. baumannii as a result of dissemination of resistant strains...
March 16, 2018: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/29544219/b-chromosome-diversity-and-repetitive-sequence-distribution-in-an-isolated-population-of-akodon-montensis-rodentia-sigmodontinae
#19
Amanda A Soares, Jonathan P Castro, Pedro Balieiro, Sidnei Dornelles, Tiago M Degrandi, Ives J Sbalqueiro, Roberto Ferreira Artoni, Iris Hass
B chromosomes are supernumerary chromosomes found in the karyotypes of approximately 15% of all eukaryotic species. They present parasitic behavior and do not follow the standard Mendelian pattern of inheritance, resulting in an imbalance in gametogenesis. The evolutionary dynamics of B chromosomes is still unknown for many species, but studies indicate that the accumulation of repetitive sequences plays an important role in the differentiation of these elements. We analyzed morphology, frequency, and possible homologies amongst different B chromosomes found in an isolated Akodon montensis population in southern Brazil...
March 16, 2018: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/29538441/superior-ab-initio-identification-annotation-and-characterisation-of-tes-and-segmental-duplications-from-genome-assemblies
#20
Lu Zeng, R Daniel Kortschak, Joy M Raison, Terry Bertozzi, David L Adelson
Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements...
2018: PloS One
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