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https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#1
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102232/aetiology-and-management-of-hereditary-aortopathy
#2
REVIEW
Aline Verstraeten, Ilse Luyckx, Bart Loeys
Aortic aneurysms are a major health problem because they account for 1-2% of all deaths in the Western population. Although abdominal aortic aneurysms (AAAs) are more prevalent than thoracic aortic aneurysms (TAAs), TAAs have been more exhaustively studied over the past 2 decades because they have a higher heritability and affect younger individuals. Gene identification in both syndromic and nonsyndromic TAA is proceeding at a rapid pace and has already pinpointed >20 genes associated with familial TAA risk...
January 19, 2017: Nature Reviews. Cardiology
https://www.readbyqxmd.com/read/28102036/combining-one-step-sanger-sequencing-with-phasing-probe-hybridization-for-hla-class-i-typing-yields-rapid-g-group-resolution-predicting-99-of-unique-full-length-protein-sequences
#3
Bin Tu, Carly Masaberg, Lihua Hou, Daniel Behm, Peter Brescia, Nuri Cha, Kanthi Kariyawasam, Jar How Lee, Thoa Nong, John Sells, Paul Tausch, Ruyan Yang, Jennifer Ng, Carolyn Katovich Hurley
BACKGROUND: Sanger-based DNA sequencing of exons 2+3 of HLA class I alleles from a heterozygote frequently results in two or more alternative genotypes. This study was undertaken to reduce the time and effort required to produce a single high resolution HLA genotype. MATERIALS AND METHODS: Samples were typed in parallel by Sanger sequencing and oligonucleotide probe hybridization. This workflow, together with optimization of analysis software, was tested and refined during the typing of over 42,000 volunteers for an unrelated hematopoietic progenitor cell donor registry...
February 2017: HLA
https://www.readbyqxmd.com/read/28101989/diagnosis-of-peste-des-petits-ruminants-in-wild-and-domestic-animals-in-xinjiang-china-2013-2016
#4
J Li, L Li, X Wu, F Liu, Y Zou, Q Wang, C Liu, J Bao, W Wang, W Ma, H Lin, J Huang, X Zheng, Z Wang
Peste des petits ruminants viruses (PPRVs) re-emerged in China at the end of 2013 and then spread rapidly into 22 provinces through movement of live goats and sheep. In this study, 96 samples of domestic animals and 13 samples of wildlife were analysed for the presence of PPRV infection by ELISA or RT-PCR. Of 96 samples from sheep and goats, 91 were PPRV positive, whereas all of the 13 samples from three wild species, Capra ibex (Capra ibex sibirica), argali (Ovis ammon) and Goitered gazelle (Gazella subgutturosa), were found to be positive...
January 18, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28101348/evans-blue-mediated-white-light-detection-of-non-muscle-invasive-bladder-cancer-a-preclinical-feasibility-and-safety-study-using-a-rat-bladder-urothelial-cell-carcinoma-model
#5
Sanne Elsen, Evelyne Lerut, Frank Van Der Aa, Ben Van Cleynenbreugel, Hendrik Van Poppel, Peter De Witte
Photodynamic diagnosis (PDD) improves the detection of non-muscle-invasive bladder cancer (NMIBC). However, white-light (WL) cystoscopy remains the technique routinely used in urological clinics. A more cost-effective but equally performant alternative to PDD may encompass the use of an intense tumoritropic dye in combination with WL cystoscopy. Using a preclinical setting, we investigated the practical aspects of the use of Evans blue (EB) dye for the possible future detection of NMIBC using WL cystoscopy...
December 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28100819/vertically-transmitted-rhabdoviruses-are-found-across-three-insect-families-and-have-dynamic-interactions-with-their-hosts
#6
Ben Longdon, Jonathan P Day, Nora Schulz, Philip T Leftwich, Maaike A de Jong, Casper J Breuker, Melanie Gibbs, Darren J Obbard, Lena Wilfert, Sophia C L Smith, John E McGonigle, Thomas M Houslay, Lucy I Wright, Luca Livraghi, Luke C Evans, Lucy A Friend, Tracey Chapman, John Vontas, Natasa Kambouraki, Francis M Jiggins
A small number of free-living viruses have been found to be obligately vertically transmitted, but it remains uncertain how widespread vertically transmitted viruses are and how quickly they can spread through host populations. Recent metagenomic studies have found several insects to be infected with sigma viruses (Rhabdoviridae). Here, we report that sigma viruses that infect Mediterranean fruit flies (Ceratitis capitata), Drosophila immigrans, and speckled wood butterflies (Pararge aegeria) are all vertically transmitted...
January 25, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28100789/complex-evolutionary-history-of-the-mammalian-histone-h1-1-h1-5-gene-family
#7
Inma Ponte, Devani Romero, Daniel Yero, Pedro Suau, Alicia Roque
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions. We have examined the evolution of the H1.1 to H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100599/rapid-and-specific-detection-of-the-escherichia-coli-sequence-type-648-complex-stc648-within-phylogroup-f
#8
James R Johnson, Brian D Johnston, David M Gordon
The Escherichia coli sequence type 648 complex (STc648) is an emerging lineage within phylogroup F - formerly included within phylogroup D - that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms in icd allele 96 and gyrB allele 87, two of the multi-locus sequence typing alleles that define ST648, and (ii) the typical absence within STc648 of uidA, an E. coli-specific gene encoding β-glucuronidase...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100589/meiotic-consequences-of-genetic-divergence-across-the-murine-pseudoautosomal-region
#9
Beth L Dumont
The production of haploid gametes during meiosis is dependent on the homology-driven processes of pairing, synapsis, and recombination. On the mammalian heterogametic sex chromosomes, these key meiotic activities are confined to the pseudoautosomal region (PAR), a short region of near-perfect sequence homology between the X and Y chromosomes. Despite its established importance for meiosis, the PAR is rapidly evolving, raising the question of how proper X/Y segregation is buffered against the accumulation of homology-disrupting mutations...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28100546/accuracy-of-line-probe-assays-for-the-diagnosis-of-pulmonary-and-multidrug-resistant-tuberculosis-a-systematic-review-and-meta-analysis
#10
Ruvandhi R Nathavitharana, Patrick G T Cudahy, Samuel G Schumacher, Karen R Steingart, Madhukar Pai, Claudia M Denkinger
Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin (RIF) and isoniazid (INH) resistance and Mycobacterium tuberculosis detection. Genotype MTBDRplusV1 was WHO-endorsed in 2008 but newer LPAs have since been developed.This systematic review evaluated three LPAs: Hain Genotype MTBDRplusV1, MTBDRplusV2 and Nipro NTM+MDRTB. Study quality was assessed with QUADAS-2. Bivariate random-effects meta-analyses were performed for direct and indirect testing...
January 2017: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/28100394/replication-study-melanoma-genome-sequencing-reveals-frequent-prex2-mutations
#11
Stephen K Horrigan, Pascal Courville, Darryl Sampey, Faren Zhou, Steve Cai
In 2015, as part of the Reproducibility Project: Cancer Biology, we published a Registered Report (Chroscinski et al., 2014) that described how we intended to replicate selected experiments from the paper "Melanoma genome sequencing reveals frequent PREX2 mutations" (Berger et al., 2012). Here we report the results of those experiments. We regenerated cells stably expressing ectopic wild-type and mutant phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2 (PREX2) using the same immortalized human NRAS(G12D) melanocytes as the original study...
January 19, 2017: ELife
https://www.readbyqxmd.com/read/28100314/matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-for-rapid-identification-of-fungal-rhinosinusitis-pathogens
#12
Xinxin Lu, Yanfei Huang, Mingxin Zhang, Min Zhu, Mei Wang, Yufeng Sun, Haitong Gu, Jingjing Cao, Xue Li, Shaoya Zhang, Jinglin Wang
BACKGROUND: filamentous fungi are the most important pathogens causing fungal rhinosinusitis (FRS). Current laboratory diagnosis of FRS pathogens mainly relies on phenotypic identification by culture and microscopic examination, which is time-consuming and expertise-dependent. Although matrix -assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been employed to identify various fungi, its performance for the identification of FRS fungi is less clear...
January 17, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28100305/environment-directed-activation-the-escherichia-coli-flhdc-operon-by-transposons
#13
Zhongge Zhang, Chika Kukita, Mir Zafri Humayun, Milton H Saier
The flagellar system in E. coli K12 is expressed under the control of the flhDC-encoded master regulator, FlhDC. Transposition of insertion sequence (IS) elements to the upstream flhDC promoter region up-regulates transcription of this operon, resulting in more rapid motility. Wang and Wood (2011) provided evidence that insertion of IS5 into upstream activating sites occurs at higher rates in semisolid agar media in which swarming behavior is allowed as compared with liquid or solid media where swarming cannot occur...
January 17, 2017: Microbiology
https://www.readbyqxmd.com/read/28100271/evaluation-of-three-sample-preparation-methods-for-the-direct-identification-of-bacteria-in-positive-blood-cultures-by-maldi-tof
#14
Hannah Tanner, Jason T Evans, Savita Gossain, Abid Hussain
BACKGROUND: Patient mortality is significantly reduced by rapid identification of bacteria from sterile sites. MALDI-TOF can identify bacteria directly from positive blood cultures and multiple sample preparation methods are available. We evaluated three sample preparation methods and two MALDI-TOF score cut-off values. Positive blood culture bottles with organisms present in Gram stains were prospectively analysed by MALDI-TOF. Three lysis reagents (Saponin, SDS, and SepsiTyper lysis bufer) were applied to each positive culture followed by centrifugation, washing and protein extraction steps...
January 18, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28100185/an-improved-genome-assembly-uncovers-prolific-tandem-repeats-in-atlantic-cod
#15
Ole K Tørresen, Bastiaan Star, Sissel Jentoft, William B Reinar, Harald Grove, Jason R Miller, Brian P Walenz, James Knight, Jenny M Ekholm, Paul Peluso, Rolf B Edvardsen, Ave Tooming-Klunderud, Morten Skage, Sigbjørn Lien, Kjetill S Jakobsen, Alexander J Nederbragt
BACKGROUND: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28099864/satb1-expression-governs-epigenetic-repression-of-pd-1-in-tumor-reactive-t-cells
#16
Tom L Stephen, Kyle K Payne, Ricardo A Chaurio, Michael J Allegrezza, Hengrui Zhu, Jairo Perez-Sanz, Alfredo Perales-Puchalt, Jenny M Nguyen, Ana E Vara-Ailor, Evgeniy B Eruslanov, Mark E Borowsky, Rugang Zhang, Terri M Laufer, Jose R Conejo-Garcia
Despite the importance of programmed cell death-1 (PD-1) in inhibiting T cell effector activity, the mechanisms regulating its expression remain poorly defined. We found that the chromatin organizer special AT-rich sequence-binding protein-1 (Satb1) restrains PD-1 expression induced upon T cell activation by recruiting a nucleosome remodeling deacetylase (NuRD) complex to Pdcd1 regulatory regions. Satb1 deficienct T cells exhibited a 40-fold increase in PD-1 expression. Tumor-derived transforming growth factor β (Tgf-β) decreased Satb1 expression through binding of Smad proteins to the Satb1 promoter...
January 17, 2017: Immunity
https://www.readbyqxmd.com/read/28099825/transmission-of-extensively-drug-resistant-tuberculosis-in-south-africa
#17
N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, Neel R Gandhi
Background Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions. Methods We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014...
19, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28099181/adverse-events-and-risk-factors-during-emergency-intubation-in-a-tertiary-paediatric-emergency-department
#18
Ruth M C Löllgen, Jennifer Pontin, Matthew Gow, Mary E McCaskill
BACKGROUND: Rapid sequence intubation and emergency intubation in the emergency department (ED) can be life-saving procedures, but require the appropriate skills, experience and preparation to avoid complications ranging from simple trauma to life-threatening desaturation. Only scarce data exist in the published literature on complications following emergency intubation in children and most guidelines are extrapolated from the adult population. PATIENTS AND METHODS: We reviewed all emergency intubations of patients in our tertiary paediatric ED within a 2-year period to estimate the incidence of complications and to analyse the risk factors associated with this procedure...
January 17, 2017: European Journal of Emergency Medicine: Official Journal of the European Society for Emergency Medicine
https://www.readbyqxmd.com/read/28098301/optical-dna-mapping-in-nanofluidic-devices-principles-and-applications
#19
Vilhelm Müller, Fredrik Westerlund
Optical DNA mapping has over the last decade emerged as a very powerful tool for obtaining long range sequence information from single DNA molecules. In optical DNA mapping, intact large single DNA molecules are labeled, stretched out, and imaged using a fluorescence microscope. This means that sequence information ranging over hundreds of kilobasepairs (kbp) can be obtained in one single image. Nanochannels offer homogeneous and efficient stretching of DNA that is crucial to maximize the information that can be obtained from optical DNA maps...
January 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28097865/molecular-requirements-of-high-fidelity-replication-competent-dna-backbones-for-orthogonal-chemical-ligation
#20
Arun Shivalingam, Agnes E S Tyburn, Afaf H El-Sagheer, Tom Brown
The molecular properties of the phosphodiester backbone that made it the evolutionary choice for the enzymatic replication of genetic information are not well understood. To address this, and to develop new chemical ligation strategies for assembly of biocompatible modified DNA, we have synthesized oligonucleotides containing several structurally and electronically varied artificial linkages. This has yielded a new highly promising ligation method based on amide backbone formation that is chemically orthogonal to CuAAC "click" ligation...
January 18, 2017: Journal of the American Chemical Society
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