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https://www.readbyqxmd.com/read/27748767/genome-scale-analysis-of-the-non-cultivable-treponema-pallidum-reveals-extensive-within-patient-genetic-variation
#1
Miguel Pinto, Vítor Borges, Minia Antelo, Miguel Pinheiro, Alexandra Nunes, Jacinta Azevedo, Maria José Borrego, Joana Mendonça, Dina Carpinteiro, Luís Vieira, João Paulo Gomes
Insights into the genomic adaptive traits of Treponema pallidum, the causative bacterium of syphilis, have long been hampered due to the absence of in vitro culture models and the constraints associated with its propagation in rabbits. Here, we have bypassed the culture bottleneck by means of a targeted strategy never applied to uncultivable bacterial human pathogens to directly capture whole-genome T. pallidum data in the context of human infection. This strategy has unveiled a scenario of discreet T. pallidum interstrain single-nucleotide-polymorphism-based microevolution, contrasting with a rampant within-patient genetic heterogeneity mainly targeting multiple phase-variable loci and a major antigen-coding gene (tprK)...
October 17, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27746295/turkish-and-japanese-mycobacterium-tuberculosis-sublineages-share-a-remote-common-ancestor
#2
Guislaine Refrégier, Edgar Abadia, Tomoshige Matsumoto, Hiromi Ano, Tetsuya Takashima, Izuo Tsuyuguchi, Elif Aktas, Füsun Cömert, Michel Kireopori Gomgnimbou, Stefan Panaiotov, Jody Phelan, Francesc Coll, Ruth McNerney, Arnab Pain, Taane G Clark, Christophe Sola
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity...
October 14, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27731913/effect-of-nitroglycerin-on-the-performance-of-mr-coronary-angiography
#3
Tobias Heer, Stephanie Reiter, Markus Trißler, Berthold Höfling, Florian von Knobelsdorff-Brenkenhoff, Günter Pilz
PURPOSE: To systematically investigate the effect of sublingual glyceryl trinitrate (nitroglycerin=nitro=glyceryl trinitrate=GTN=C3 H5 N3 O9 [NTG]) on the diagnostic performance of MR coronary artery imaging (MRCA) to detect relevant coronary artery disease (CAD). MATERIALS AND METHODS: Thirty-five healthy volunteers and 25 patients with suspected or proven CAD (all in sinus rhythm) underwent MRCA before and after NTG using a contrast-agent free, three-dimensional, navigator-based, steady state free precession acquisition (voxel size 1...
October 12, 2016: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/27662552/the-hepatitis-c-virus-ns3-q80k-polymorphism-is-frequently-detected-and-transmitted-among-hiv-infected-msm-in-the-netherlands
#4
Astrid M Newsum, Cynthia K Y Ho, Faydra I Lieveld, Thijs J W Van De Laar, Sylvie M Koekkoek, Sjoerd P Rebers, Jan T M Van Der Meer, Anne M J Wensing, Greet J Boland, Joop E Arends, Karel J Van Erpecum, Maria Prins, Richard Molenkamp, Janke Schinkel
OBJECTIVES: The Q80K polymorphism is a naturally occurring resistance-associated variant (RAV) in the hepatitis C virus (HCV) NS3 region and is likely transmissible between hosts. This study describes the Q80K origin and prevalence among HCV risk groups in the Netherlands and examines whether Q80K is linked to specific transmission networks. DESIGN AND METHODS: Stored blood samples from HCV genotype 1a infected patients were used for PCR and sequencing to reconstruct the NS3 maximum likelihood phylogeny...
September 20, 2016: AIDS
https://www.readbyqxmd.com/read/27388702/polymorphism-analysis-of-prion-protein-gene-in-11-pakistani-goat-breeds
#5
Mohammad Farooque Hassan, Sher Hayat Khan, Masroor Ellahi Babar, Lifeng Yang, Tariq Ali, Jamal Muhammad Khan, Syed Zahid Ali Shah, Xiangmei Zhou, Tanveer Hussain, Ting Zhu, Tariq Hussain, Deming Zhao
The association between caprine PrP gene polymorphisms and its susceptibility to scrapie has been investigated in current years. As the ORF of the PrP gene is extremely erratic in different breeds of goats, we studied the PrP gene polymorphisms in 80 goats which belong to 11 Pakistani indigenous goat breeds from all provinces of Pakistan. A total of 6 distinct polymorphic sites (one novel) with amino acid substitutions were identified in the PrP gene which includes 126 (A -> G), 304 (G -> T), 379 (A -> G), 414 (C -> T), 428 (A -> G) and 718 (C -> T)...
July 3, 2016: Prion
https://www.readbyqxmd.com/read/27267372/equine-rhinitis-b-viruses-in-horse-fecal-samples-from-the-middle-east
#6
Patrick C Y Woo, Susanna K P Lau, Garnet K Y Choi, Yi Huang, Renate Wernery, Sunitha Joseph, Emily Y M Wong, Shyna K Elizabeth, Nissy Annie Georgy Patteril, Tong Li, Ulrich Wernery, Kwok-Yung Yuen
BACKGROUND: Among all known picornaviruses, only two species, equine rhinitis A virus and equine rhinitis B virus (ERBV) are known to infect horses, causing respiratory infections. No reports have described the detection of ERBV in fecal samples of horses and no complete genome sequences of ERBV3 are available. METHODS: We performed a molecular epidemiology study to detect ERBVs in horses from Dubai and Hong Kong. Complete genome sequencing of the ERBVs as well as viral loads and genome, phylogenetic and evolutionary analysis were performed on the positive samples...
2016: Virology Journal
https://www.readbyqxmd.com/read/27264728/new-insights-into-the-hepatitis-e-virus-genotype-3-phylodynamics-and-evolutionary-history
#7
Santiago Mirazo, Daiana Mir, Gonzalo Bello, Natalia Ramos, Héctor Musto, Juan Arbiza
Hepatitis E virus (HEV) is an emergent hepatotropic virus endemic mainly in Asia and other developing areas. However, in the last decade it has been increasingly reported in high-income countries. Human infecting HEV strains are currently classified into four genotypes (1-4). Genotype 3 (HEV-3) is the prevalent virus genotype and the mostly associated with autochthonous and sporadic cases of HEV in developed areas. The evolutionary history of HEV worldwide remains largely unknown. In this study we reconstructed the spatiotemporal and population dynamics of HEV-3 at global scale, but with particular emphasis in South America, where case reports have increased dramatically in the last years...
September 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27154330/sixteen-years-of-evolution-of-human-respiratory-syncytial-virus-subgroup-a-in-buenos-aires-argentina-ga2-the-prevalent-genotype-through-the-years
#8
M Viegas, S Goya, A S Mistchenko
Human respiratory syncytial virus (HRSV) is the main viral cause of acute lower respiratory tract infections (LRTI) in children worldwide. In recent years, several preclinical trials with vaccine candidates have been reported. It is in this sense that molecular epidemiological studies become important. Understanding viral dispersion patterns before and after the implementation of a vaccine can provide insight into the effectiveness of the control strategies. In this work we analyzed the molecular epidemiology of HRSV-A over a period of sixteen years (1999-2014) in Buenos Aires...
September 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/26924208/highly-divergent-dengue-virus-type-1-genotype-sets-a-new-distance-record
#9
Alyssa T Pyke, Peter R Moore, Carmel T Taylor, Sonja Hall-Mendelin, Jane N Cameron, Glen R Hewitson, Dennis S Pukallus, Bixing Huang, David Warrilow, Andrew F van den Hurk
Dengue viruses (DENVs) are the leading cause of mosquito-borne viral disease of humans. They exist in both endemic and sylvatic ecotypes. In 2014, a viremic patient who had recently visited the rainforests of Brunei returned to Australia displaying symptoms consistent with DENV infection. A unique DENV strain was subsequently isolated from the patient, which we propose belongs to a new genotype within DENV serotype 1 (DENV-1). Bayesian evolutionary phylogenetic analysis suggests that the putative sylvatic DENV-1 Brunei 2014 (Brun2014) is the most divergent DENV-1 yet recorded and increases the time to the most recent common ancestor (MRCA) for DENV-1 from ≈120 years to ≈315 years...
2016: Scientific Reports
https://www.readbyqxmd.com/read/26901621/comparison-of-french-and-worldwide-bacillus-anthracis-strains-favors-a-recent-post-columbian-origin-of-the-predominant-north-american-clade
#10
Gilles Vergnaud, Guillaume Girault, Simon Thierry, Christine Pourcel, Nora Madani, Yann Blouin
BACKGROUND: Bacillus anthracis, the highly dangerous zoonotic bacterial pathogen species is currently composed of three genetic groups, called A, B and C. Group A is represented worldwide whereas group B is present essentially in Western Europe and Southern Africa. Only three strains from group C have been reported. This knowledge is derived from the genotyping of more than 2000 strains collected worldwide. Strains from both group A and group B are present in France. Previous investigations showed that the majority of sporadic French strains belong to the so-called A...
2016: PloS One
https://www.readbyqxmd.com/read/26778258/pliocene-pleistocene-lineage-diversifications-in-the-eastern-indigo-snake-drymarchon-couperi-in-the-southeastern-united-states
#11
Kenneth L Krysko, Leroy P Nuñez, Catherine A Lippi, Daniel J Smith, Michael C Granatosky
Indigo Snakes (Drymarchon; with five currently recognized species) occur from northern Argentina, northward to the United States in southern Texas and eastward in disjunct populations in Florida and Georgia. Based on this known allopatry and a difference in supralabial morphology the two United States taxa previously considered as subspecies within D. corais (Boie 1827), the Western Indigo Snake, D. melanurus erebennus (Cope 1860), and Eastern Indigo Snake, D. couperi (Holbrook 1842), are currently recognized as separate species...
May 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/26662033/diagnostic-accuracy-of-magnetic-resonance-angiography-for-detection-of-coronary-artery-disease-a-systematic-review-and-meta-analysis
#12
Giovanni Di Leo, Erica Fisci, Francesco Secchi, Marco Alì, Federico Ambrogi, Luca Maria Sconfienza, Francesco Sardanelli
OBJECTIVES: To review the diagnostic performance of MR coronary angiography (MRCA) for coronary artery disease (CAD). METHODS: Two independent reviewers searched on MEDLINE/EMBASE with the following inclusion criteria: 01/01/2000-03/23/2015 publication date; per-patient sensitivity/specificity for >50 % stenosis confirmed by conventional coronary angiography with raw data provided or retrievable; sample size >10. Quality was appraised using QUADAS2. RESULTS: Nine hundred eighteen studies were retrieved, 24 of them, including 1,638 patients, were selected...
October 2016: European Radiology
https://www.readbyqxmd.com/read/26659921/timing-and-scope-of-genomic-expansion-within-annelida-evidence-from-homeoboxes-in-the-genome-of-the-earthworm-eisenia-fetida
#13
Allison S Zwarycz, Carlos W Nossa, Nicholas H Putnam, Joseph F Ryan
Annelida represents a large and morphologically diverse group of bilaterian organisms. The recently published polychaete and leech genome sequences revealed an equally dynamic range of diversity at the genomic level. The availability of more annelid genomes will allow for the identification of evolutionary genomic events that helped shape the annelid lineage and better understand the diversity within the group. We sequenced and assembled the genome of the common earthworm, Eisenia fetida. As a first pass at understanding the diversity within the group, we classified 363 earthworm homeoboxes and compared them with those of the leech Helobdella robusta and the polychaete Capitella teleta...
December 10, 2015: Genome Biology and Evolution
https://www.readbyqxmd.com/read/26558341/rapid-whole-genome-sequencing-of-miyazaki-bali-2007-pteropine-orthoreovirus-by-modified-rolling-circular-amplification-with-adaptor-ligation-next-generation-sequencing
#14
Harpal Singh, Tomoki Yoshikawa, Takeshi Kobayashi, Shuetsu Fukushi, Hideki Tani, Satoshi Taniguchi, Aiko Fukuma, Ming Yang, Masami Sugamata, Masayuki Shimojima, Masayuki Saijo
The emergence of orthoreoviruses as the causative agent of human respiratory illness over the past few years has led to a demand to determine their viral genome sequences. The whole genome sequencing of such RNA viruses using traditional methods, such as Sanger dideoxy sequencing following rapid amplification of cDNA ends presents a laborious challenge due to the numerous preparatory steps required before sequencing can commence. We developed a practical, time-efficient novel combination method capable of reducing the total time required from months to less than a week in the determination of whole genome sequence of Pteropine orthoreoviruses (PRV); through a combination of viral RNA purification and enrichment, adaptor ligation, reverse transcription, cDNA circularization and amplification, and next generation sequencing...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26254485/found-and-lost-the-fates-of-horizontally-acquired-genes-in-arthropod-symbiotic-spiroplasma
#15
Wen-Sui Lo, Gail E Gasparich, Chih-Horng Kuo
Horizontal gene transfer (HGT) is an important mechanism that contributed to biological diversity, particularly in bacteria. Through acquisition of novel genes, the recipient cell may change its ecological preference and the process could promote speciation. In this study, we determined the complete genome sequence of two Spiroplasma species for comparative analyses and inferred the putative gene gains and losses. Although most Spiroplasma species are symbionts of terrestrial insects, Spiroplasma eriocheiris has evolved to be a lethal pathogen of freshwater crustaceans...
September 2015: Genome Biology and Evolution
https://www.readbyqxmd.com/read/26190450/phylogenetics-of-hiv-1-subtype-g-env-greater-complexity-and-older-origins-than-previously-reported
#16
Marcel Tongo, René G Essomba, Frederick Nindo, Fatima Abrahams, Aubin Joseph Nanfack, Joseph Fokam, Desire Takou, Judith N Torimiro, Eitel Mpoudi-Ngole, Wendy A Burgers, Darren P Martin, Jeffrey R Dorfman
HIV-1 subtype G has played an early and central role in the emergent complexity of the HIV-1 group M (HIV-1M) epidemic in central/west Africa. Here, we analysed new subtype G env sequences sampled from 8 individuals in Yaoundé, Cameroon during 2007-2010, together with all publically available subtype G-attributed full-length env sequences with known sampling dates and locations. We inferred that the most recent common ancestor (MRCA) of the analysed subtype G env sequences most likely occurred in ∼1953 (95% Highest Posterior Density interval [HPD] 1939-1963): about 15 years earlier than previous estimates...
October 2015: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/26160365/myocardial-perfusion-is-impaired-in-asymptomatic-renal-and-liver-transplant-recipients-a-cardiovascular-magnetic-resonance-study
#17
Susie Parnham, Jonathan M Gleadle, Darryl Leong, Suchi Grover, Craig Bradbrook, Richard J Woodman, Carmine G De Pasquale, Joseph B Selvanayagam
BACKGROUND: Myocardial ischemia is a major cause of death in chronic kidney disease (CKD) patients, which can be caused by either epicardial or microvascular coronary artery disease (CAD). Although renal transplantation improves survival, cardiovascular disease remains a major cause of mortality in post renal transplant recipients, including those with no significant epicardial CAD pre-transplant. We aim to utilize stress cardiovascular magnetic resonance (CMR) and MR coronary angiography (MRCA) to assess silent myocardial ischemia and epicardial CAD in renal transplant recipients...
July 10, 2015: Journal of Cardiovascular Magnetic Resonance
https://www.readbyqxmd.com/read/26144024/the-effect-of-inbreeding-constraints-and-offspring-distribution-on-time-to-the-most-recent-common-ancestor
#18
R B Campbell
The expected time to the most recent common ancestor (MRCA) of two alleles in a diploid individual is 4N+2 under random mating with a Poisson progeny distribution, but 8N-2 under maximum avoidance of inbreeding, which entails two progeny per mating pair. (N is the number of mating pairs, hence 2N is the number of individuals, hence 4N is the number of alleles.) The interrelationship of inbreeding constraints and offspring distribution is investigated by varying the level of sib mating: prohibiting sib mating increases the time to MRCA by four generations and decreases the variance of the offspring distribution by 2/N...
October 7, 2015: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/26014920/an-evolutionary-insight-into-newcastle-disease-viruses-isolated-in-antarctica
#19
Martin Soñora, Pilar Moreno, Natalia Echeverría, Sabrina Fischer, Victoria Comas, Alvaro Fajardo, Juan Cristina
The disease caused by Newcastle disease virus (NDV) is a severe threat to the poultry industry worldwide. Recently, NDV has been isolated in the Antarctic region. Detailed studies on the mode of evolution of NDV strains isolated worldwide are relevant for our understanding of the evolutionary history of NDV. For this reason, we have performed Bayesian coalescent analysis of NDV strains isolated in Antarctica to study evolutionary rates, population dynamics, and patterns of evolution. Analysis of F protein cleavage-site sequences of NDV isolates from Antarctica suggested that these strains are lentogenic...
August 2015: Archives of Virology
https://www.readbyqxmd.com/read/25925241/ancestries-of-a-recombining-diploid-population
#20
R Sainudiin, B Thatte, A Véber
We derive the exact one-step transition probabilities of the number of lineages that are ancestral to a random sample from the current generation of a bi-parental population that is evolving under the discrete Wright-Fisher model with n diploid individuals. Our model allows for a per-generation recombination probability of r . When r = 1, our model is equivalent to Chang's (Adv Appl Probab 31:1002-1038, 1999) model for the karyotic pedigree. When r = 0, our model is equivalent to Kingman's (Stoch Process Appl 13:235-248, 1982) discrete coalescent model for the cytoplasmic tree or sub-karyotic tree containing a DNA locus that is free of intra-locus recombination...
January 2016: Journal of Mathematical Biology
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