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Evolution analysis

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https://www.readbyqxmd.com/read/29782520/polymorphic-sites-preferentially-avoid-co-evolving-residues-in-mhc-class-i-proteins
#1
Linda Dib, Nicolas Salamin, David Gfeller
Major histocompatibility complex class I (MHC-I) molecules are critical to adaptive immune defence mechanisms in vertebrate species and are encoded by highly polymorphic genes. Polymorphic sites are located close to the ligand-binding groove and entail MHC-I alleles with distinct binding specificities. Some efforts have been made to investigate the relationship between polymorphism and protein stability. However, less is known about the relationship between polymorphism and MHC-I co-evolutionary constraints...
May 21, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29781797/from-plants-to-nematodes-serratia-grimesii-bxf1-genome-reveals-an-adaptation-to-the-modulation-of-multi-species-interactions
#2
Francisco Nascimento, Cláudia Vicente, Peter Cock, Maria Tavares, Márcio Rossi, Koichi Hasegawa, Manuel Mota
Serratia grimesii BXF1 is a bacterium with the ability to modulate the development of several eukaryotic hosts. Strain BXF1 was isolated from the pinewood nematode, Bursaphelenchus xylophilus, the causative agent of pine wilt disease affecting pine forests worldwide. This bacterium potentiates Bursaphelenchus xylophilus reproduction, acts as a beneficial pine endophyte, and possesses fungal and bacterial antagonistic activities, further indicating a complex role in a wide range of trophic relationships. In this work, we describe and analyse the genome sequence of strain BXF1, and discuss several important aspects of its ecological role...
May 21, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29781541/the-two-rules-of-speciation-in-species-with-young-sex-chromosomes
#3
Dmitry A Filatov
The two "rules of speciation", Haldane's rule (HR) and the large-X effect (LXE), are thought to be caused by recessive species incompatibilities exposed in the phenotype due to the hemizygosity of X-linked genes in the heterogametic sex. Thus, the reports of HR and the LXE in species with recently evolved non- or partially-degenerate Y-chromosomes, such as Silene latifolia and its relatives, were surprising. Here I argue that rapid species-specific degeneration of Y-linked genes and associated adjustment of expression of X-linked gametologs (dosage compensation) may lead to rapid evolution of sex-linked species incompatibilities...
May 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29781443/ion-beam-induced-bending-of-semiconductor-nanowires
#4
Imran Hanif, Osmane Camara, Matheus Araújo Tunes, Robert William Harrison, Graeme Greaves, Stephen E Donnelly, Jonathan A Hinks
The miniaturization of technology increasingly requires the development of both new structures as well as novel techniques for their manufacture and modification. Semiconductor nanowires (NWs) are a prime example of this and as such have been the subject of intense scientific research for applications ranging from microelectronics to nano-electromechanical devices. Ion irradiation has long been a key processing step for semiconductors and the natural extension of this technique to the modification of semiconductor NWs has led to the discovery of ion-beam-induced deformation effects...
May 21, 2018: Nanotechnology
https://www.readbyqxmd.com/read/29781374/april-and-staci-could-be-predictors-of-severe-multiorgan-dysfunction-syndrome-in-sepsis
#5
Dajana F Lendak, Dunja M Mihajlović, Aleksandra S Novakov-Mikić, Jasmina M Boban, Milan Ubavić, Snežana V Brkić
Although the role of B cells in sepsis immunoregulation has become an interesting topic, there is lack of data on the role of B cell function regulators in prediction of multiorgan dysfunction syndrome (MODS). The aim of this study was to evaluate the prognostic value of A Proliferation Inducing Ligand (APRIL) and soluble Transmembrane Activator and CAML Interactor Protein (sTACI), the main B cell function regulators, in prediction of MODS development within the first 48h after admission to intensive care unit, among septic patients...
May 21, 2018: Virulence
https://www.readbyqxmd.com/read/29781362/the-era-of-the-large-databases-outcomes-after-gastroesophageal-surgery-according-to-nsqip-nis-and-ncdb-databases-systematic-literature-review
#6
Gabriela Batista Rodríguez, Andrea Balla, Sonia Fernández-Ananín, Carmen Balagué, Eduard M Targarona
BACKGROUND: The term big data refers to databases that include large amounts of information used in various areas of knowledge. Currently, there are large databases that allow the evaluation of postoperative evolution, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP), the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample (NIS), and the National Cancer Database (NCDB). The aim of this review was to evaluate the clinical impact of information obtained from these registries regarding gastroesophageal surgery...
May 1, 2018: Surgical Innovation
https://www.readbyqxmd.com/read/29781136/physcomitrella-patens-max2-characterization-suggests-an-ancient-role-for-this-f-box-protein-in-photomorphogenesis-rather-than-strigolactone-signalling
#7
Mauricio Lopez-Obando, Ruan de Villiers, Beate Hoffmann, Linnan Ma, Alexandre de Saint Germain, Jens Kossmann, Yoan Coudert, C Jill Harrison, Catherine Rameau, Paul Hills, Sandrine Bonhomme
Strigolactones (SLs) are key hormonal regulators of flowering plant development and are widely distributed amongst streptophytes. In Arabidopsis, SLs signal via the F-box protein MORE AXILLARY GROWTH2 (MAX2), affecting multiple aspects of development including shoot branching, root architecture and drought tolerance. Previous characterization of a Physcomitrella patens moss mutant with defective SL synthesis supports an ancient role for SLs in land plants, but the origin and evolution of signalling pathway components are unknown...
May 21, 2018: New Phytologist
https://www.readbyqxmd.com/read/29780476/trends-in-activity-for-the-oxygen-evolution-reaction-on-transition-metal-m-fe-co-ni-phosphide-pre-catalysts
#8
Junyuan Xu, Junjie Li, Dehua Xiong, Bingsen Zhang, Yuefeng Liu, Kuang-Hsu Wu, Isilda Amorim, Wei Li, Lifeng Liu
Transition metal phosphides (TMPs) have recently emerged as a new class of pre-catalysts that can efficiently catalyze the oxygen evolution reaction (OER). However, how the OER activity of TMPs varies with the catalyst composition has not been systematically explored. Here, we report the alkaline OER electrolysis of a series of nanoparticulate phosphides containing different equimolar metal (M = Fe, Co, Ni) components. Notable trends in OER activity are observed, following the order of FeP < NiP < CoP < FeNiP < FeCoP < CoNiP < FeCoNiP, which indicate that the introduction of a secondary metal(s) to a mono-metallic TMP substantially boosts the OER performance...
April 14, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780362/characterization-and-genomic-study-of-phage-vb_ecos-b2-infecting-multidrug-resistant-escherichia-coli
#9
Yue Xu, Xinyan Yu, Yu Gu, Xu Huang, Genyan Liu, Xiaoqiu Liu
The potential of bacteriophage as an alternative antibacterial agent has been reconsidered for control of pathogenic bacteria due to the widespread occurrence of multi-drug resistance bacteria. More and more lytic phages have been isolated recently. In the present study, we isolated a lytic phage named vB_EcoS-B2 from waste water. VB_EcoS-B2 has an icosahedral symmetry head and a long tail without a contractile sheath, indicating that it belongs to the family Siphoviridae . The complete genome of vB_EcoS-B2 is composed of a circular double stranded DNA of 44,283 bp in length, with 54...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780157/targeting-acquired-hemophilia-a-with-rheumatoid-arthritis-by-a-rituximab-shot-a-case-report-and-review-of-the-literature
#10
Imad Ghozlani, Aziza Mounach, Mirieme Ghazi, Anass Kherrab, Radouane Niamane
BACKGROUND Acquired hemophilia A (AH) is a rare hemorrhagic diathesis, characterized by the presence of autoantibodies directed against the pro-coagulant activity of factor VIII. It is associated with rheumatoid arthritis (RA) in 4% to 8% of cases and its prognosis remains severe. CASE REPORT A 66-year-old patient has been followed up for 20 years for deforming and severe RA, which was in low-disease activity. However, the patient presented a polyarticular flare involving the metacarpophalangeal and the proximal interphalangeal joints, the left elbow, and the right knee, which was warm and swollen...
May 21, 2018: American Journal of Case Reports
https://www.readbyqxmd.com/read/29779790/a-hyperthermophilic-phage-decoration-protein-suggests-common-evolutionary-origin-with-herpesvirus-triplex-proteins-and-an-anti-crispr-protein
#11
Nicholas P Stone, Brendan J Hilbert, Daniel Hidalgo, Kevin T Halloran, Jooyoung Lee, Erik J Sontheimer, Brian A Kelch
Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs...
April 26, 2018: Structure
https://www.readbyqxmd.com/read/29779780/on-sunspots-click-science-and-molecular-iconography
#12
Igor Mokrousov
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29778766/first-genetic-characterization-of-usutu-virus-from-culex-pipiens-mosquitoes-serbia-2014
#13
Gábor Kemenesi, Dóra Buzás, Brigitta Zana, Kornélia Kurucz, Bosiljka Krtinic, Anett Kepner, Fanni Földes, Ferenc Jakab
Since its first appearance in Europe, Usutu virus (USUV) diverged to several different genetic lineages. The virus was reported to date from multiple countries across Europe (Hungary, Italy, Switzerland, Spain, Germany, Czech Republic and Belgium). Considering the more frequently published impact of the virus on humans it is crucial to investigate locally circulating genetic variants and trace its evolution. We retrospectively analyzed mosquito samples from Serbia Vojvodina region, collected during 2014. In this study we report the results of the screening of 23,753 female mosquitoes (753 pools) for USUV-specific nucleic-acid...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778724/a-tangle-of-forms-and-phylogeny-extensive-morphological-homoplasy-and-molecular-clock-heterogeneity-in-bonnetina-and-related-tarantulas
#14
David Ortiz, Oscar F Francke, Jason E Bond
Tarantula spider systematics has long been considered problematic. Species diagnosis and phylogenetic hypotheses have historically relied on morphological features, which are known to be relatively conserved and/or highly homoplastic across the family. Morphology-based attempts to clarify the phylogeny of the highly diverse New World Theraphosinae, have only been moderately successful, and the time-frame of tarantulas' evolution is nearly terra incognita. Here we present a molecular phylogenetic analysis of the Theraphosinae genus Bonnetina and related lineages, employing one mitochondrial (COI) and five nuclear (ITS1, EF1G, MID1IP1, MRPL44, and I3568) loci...
May 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29778640/work-factors-associated-with-return-to-work-in-out-of-hospital-cardiac-arrest-survivors
#15
Alexis Descatha, Florence Dumas, Wulfran Bougouin, Alain Cariou, Guillaume Geri
INTRODUCTION: Although the survival rate after out-of-hospital cardiac arrest (OHCA) has increased over time, little is known about the return to work of OHCA survivors. We aim to evaluate prevalence and factors associated with return to work (RTW) in OHCA survivors. PATIENTS AND METHODS: All consecutive OHCA survivors aged 18-65 years and discharged alive from a Paris tertiary intensive care unit between 2000 and 2013 were included. Pre-hospital care, in-hospital care, and after-hospital discharge data, such as work description (work location, job classification, nature of the job) were compared relative to work status and RTW...
May 17, 2018: Resuscitation
https://www.readbyqxmd.com/read/29778634/genetic-characterization-of-anaplasma-marginale-strains-from-tunisia-using-single-and-multiple-gene-typing-reveals-novel-variants-with-an-extensive-genetic-diversity
#16
Mourad Ben Said, Alaa Ben Asker, Hanène Belkahia, Raoua Ghribi, Rachid Selmi, Lilia Messadi
Anaplasma marginale, which is responsible for bovine anaplasmosis in tropical and subtropical regions, is a tick-borne obligatory intraerythrocytic bacterium of cattle and wild ruminants. In Tunisia, information about the genetic diversity and the phylogeny of A. marginale strains are limited to the msp4 gene analysis. The purpose of this study is to investigate A. marginale isolates infecting 16 cattle located in different bioclimatic areas of northern Tunisia with single gene analysis and multilocus sequence typing methods on the basis of seven partial genes (dnaA, ftsZ, groEL, lipA, secY, recA and sucB)...
May 12, 2018: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29778329/the-kinetoplast-dna-of-the-australian-trypanosome-trypanosoma-copemani-shares-features-with-trypanosoma-cruzi-and-trypanosoma-lewisi
#17
Adriana Botero, Irit Kapeller, Crystal Cooper, Peta L Clode, Joseph Shlomai, R C Andrew Thompson
Kinetoplast DNA (kDNA) is the mitochondrial genome of trypanosomatids. It consists of a few dozen maxicircles and several thousand minicircles, all catenated topologically to form a two-dimensional DNA network. Minicircles are heterogeneous in size and sequence among species. They present one or several conserved regions that contain three highly conserved sequence blocks (CSBs). CSB-1 (10 bp sequence) and CSB-2 (8 bp sequence) present lower interspecies homology, while CSB-3 (12 bp sequence) or the Universal Minicircle Sequence (UMS) is conserved within most trypanosomatids...
May 17, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29778197/genetic-analysis-and-biological-characteristics-of-different-internal-gene-origin-h5n6-reassortment-avian-influenza-virus-in-china-in-2016
#18
Wenqiang Sun, Jiaxin Li, Jiao Hu, Daxiu Jiang, Chaonan Xing, Tiansong Zhan, Xiufan Liu
Clade 2.3.4.4 of H5N6 subtype Avian Influenza Viruses (AIVs) has become dominant clade in South-East Asia. So far, a total of 16 cases of human infection, including 6 deaths, have been confirmed since 2014. In this study, we systematically investigated the genetic evolution and biological characteristics of these viruses. We first carried out phylogenetic and statistical analysis of all H5N6 viruses that were downloaded from Influenza Research Database, GISAID and isolates from our lab. We found that H5N6 AIVs continued to reassort with other AIVs subtypes since 2014...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29778163/impacts-of-sodium-hydroxide-and-sodium-hypochlorite-aging-on-polyvinylidene-fluoride-membranes-fabricated-with-different-methods
#19
Qilong Wu, Xihui Zhang, Guodong Cao
This study compared the effects of chemical aging on the polyvinylidene fluoride (PVDF) membranes fabricated with the methods of non-solvent induced phase separation (NIPS) (named NIPS-PVDF) and thermally induced phase separation (TIPS) (named TIPS-PVDF). The chemical solutions of sodium hypochlorite (NaClO) and sodium hydroxide (NaOH) were chosen at the concentration of 5000mg/L. The equivalence of 5 and 10years was respectively selected as the time of aging. The physicochemical evolutions of membrane aging are characterized on the base of morphology analysis, chemical components, permeation ability and mechanical properties...
May 2018: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29777994/analysis-of-incidence-mortality-and-survival-for-pancreatic-and-biliary-tract-cancers-across-europe-with-assessment-of-influence-of-revised-european-age-standardisation-on-estimates
#20
Pamela Minicozzi, Tiziana Cassetti, Claudia Vener, Milena Sant
BACKGROUND: Pancreatic (PC) and biliary tract (BTC) cancers have higher incidence and mortality in Europe than elsewhere. We analysed time-trends in PC/BTC incidence, mortality, and survival across Europe. Since the European standard population (ESP) was recently revised to better represent European age structure, we also assessed the effect of adopting the revised ESP to age-standardise incidence and mortality data. METHODS: We analysed PCs/BTCs (≥15 years) diagnosed in 2000-2007 and followed-up to end of 2008, in 29 European countries across five regions: UK/Ireland, and northern, central, southern, and eastern Europe...
May 16, 2018: Cancer Epidemiology
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