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Phylogenetics software

Esther Hernández, Visitación de Castro, Ana Avellón, Itxaso González, Nerea Muniozguren, Sonia Vázquez, Milagros Muñoz-Chimeno
INTRODUCTION: The reporting of one case of hepatitis A in a food handler at a bakery and five cases in employees of a company after consuming products from the same bakery prompted an outbreak investigation. METHODS: Outbreak cases were defined as individuals with laboratory-confirmed hepatitis A (HAV) infection, with symptoms which started in June and who, during the incubation period, worked with the food handler and/or had close contact with him and/or consumed products from the bakery...
March 12, 2019: Enfermedades Infecciosas y Microbiología Clínica
Tatiana Thomas, Anne Elain, Alexis Bazire, Stéphane Bruzaud
A halophilic Gram-negative eubacterium was isolated from the Iroise Sea and identified as an efficient producer of polyhydroxyalkanoates (PHA). The strain, designated SF2003, was found to belong to the Halomonas genus on the basis of 16S rRNA gene sequence similarity. Previous biochemical tests indicated that the Halomonas sp. strain SF2003 is capable of supporting various culture conditions which sometimes can be constraining for marine strains. This versatility could be of great interest for biotechnological applications...
March 9, 2019: World Journal of Microbiology & Biotechnology
Dominik Schrempf, Bui Quang Minh, Arndt von Haeseler, Carolin Kosio
Molecular phylogenetics has neglected polymorphisms within present and ancestral populations for a long time. Recently, multispecies coalescent based methods have increased in popularity, however, their application is limited to a small number of species and individuals. We introduced a polymorphism-aware phylogenetic model (PoMo), which overcomes this limitation and scales well with the increasing amount of sequence data while accounting for present and ancestral polymorphisms. PoMo circumvents handling of gene trees and directly infers species trees from allele frequency data...
March 2, 2019: Molecular Biology and Evolution
Henrik Krehenwinkel, Aaron Pomerantz, James B Henderson, Susan R Kennedy, Jun Ying Lim, Varun Swamy, Juan Diego Shoobridge, Natalie Graham, Nipam H Patel, Rosemary G Gillespie, Stefan Prost
BACKGROUND: In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community, but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility...
March 2, 2019: GigaScience
Franck-Martin Obam Mekanda, Chavely Gwladys Monamele, Frédy Brice Simo Nemg, Francine Berlange Sado Yousseu, Dieudonné Ndjonka, Anfumbom Kitu Womeyi Kfutwah, Emily Abernathy, Maurice Demanou
Rubella is an acute, contagious viral infection whose gravidity resides in infection during pregnancy, which can result in miscarriage, foetal death, stillbirth, or infants with congenital malformations. This study aimed to describe the genome of Rubella viruses (RUBVs) circulating in Cameroon. Throat swabs were collected from health districts as part of the measles surveillance program from 2010 to 2016 and sent to the Centre Pasteur of Cameroon. Samples were amplified by genotyping RT-PCR in search of two overlapping fragments of the gene that encodes the E1 envelope glycoprotein of RUBV...
March 1, 2019: Journal of Medical Virology
Sayyedeh Rahmaneh Atyabi, Majid Bouzari, Majid Komijani
Objective: To evaluate presence of different subtypes and genetic variations of JC virus in different geographical areas is a useful tool for reconstructing of the genetic information and understanding of the evolution of the virus and also in tracing of the last and present history of human immigration. Materials and methods: This study aimed to investigate the reactivation of different genotypes of JC virus in kidney and its excretion in the urine of the 50 pregnant and 50 non-pregnant women. Phenol-chloroform method was used to extract DNA...
June 2018: Journal of Family & Reproductive Health
Anastasia A Kuzminkova, Anastasia D Sokol, Kristina E Ushakova, Konstantin Yu Popadin, Konstantin V Gunbin
BACKGROUND: Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions...
February 26, 2019: BMC Evolutionary Biology
Sevan N Alwan, Haidar A Shamran, Avan H Ghaib, Qasim S Al-Mayah, Atheer J Al-Saffar, Ali H Bayati, Hala S Arif, Jianmin Fu, Brian L Wickes
Among all other viruses, human cytomegalovirus (HCMV) is the most frequent cause of congenital infection worldwide. Strain variation in HCMV may predict severity or outcome of congenital HCMV disease. Previous studies have associated a particular genotype with specific sequelae or more severe illness, but the results were contradictory. There are no previous studies addressing the genotype of HCMV in Iraq. Therefore, the present study is aimed at molecular detection and genotyping of HCMV isolated from symptomatic congenitally/perinatally infected neonates...
February 25, 2019: American Journal of Tropical Medicine and Hygiene
Xavier Meyer, Linda Dib, Daniele Silvestro, Nicolas Salamin
Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy...
March 12, 2019: Proceedings of the National Academy of Sciences of the United States of America
Wei Liang, Yu Tang, Gang Li, Pinghua Shen, Yueru Tian, Haoqin Jiang, Xiaofei Jiang, Yuan Lu
Carbapenemase-producing Klebsiella pneumoniae has emerged and spread widely throughout the world. The mechanisms involved remain unclear. To provide insight, five plasmids were obtained from carbapenemase-producing K. pneumoniae clinical isolates. The five sequences were acquired, aligned and analyzed. In addition to the blaKPC-2 gene, which encodes beta lactamase, essentially all the plasmids contained a putative anti-restriction protein-encoding gene, KlcAHS . The KlcAHS gene was found in 98.2% of the blaKPC-2 -positive, imipenem-resistant K...
February 23, 2019: Infection, Genetics and Evolution
Jin Feng, Mi Wu, Wulan, Tianpeng Huang, Jinbao Zhang, Na Renbatu, Ge Riletu
Ticks are important vectors and reservoirs of several zoonotic pathogens. Recently, both known and unknown tick-borne pathogens have emerged and re-emerged, causing unpredictable epidemics. In this study, 211 soft tick samples were collected from Tongliao and Alxa in Inner Mongolia, China. Tick species were identified by morphological and molecular biological analyses. Morphological analysis showed that there was no significant difference in surface features between ticks from the 2 areas. Cloning by polymerase chain reaction (PCR) and sequencing of the 16S rRNA gene showed that all ticks belonged to the species Argas persicus...
February 2019: Journal of Parasitology
Caroline Rouard, Nadège Bourgeois-Nicolaos, Lalaina Rahajamanana, Olivier Romain, Lydia Pouga, Véronique Derouin, Daniele De Luca, Florence Doucet-Populaire
BACKGROUND: Meticillin-susceptible and resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are less often studied. Whole genome sequencing (WGS) is increasingly used for outbreak monitoring but still requires specific installation and trained personnel to obtain and analyse the data. AIM: To evaluate the workflow and the benefits of the bioMerieux Episeq® (bioMerieux, France) solution in exploring an increased incidence of S...
February 13, 2019: Journal of Hospital Infection
Seyed Mahmoud Sadjjadi, Mohammad Ebrahimipour, Fatemeh Sadat Sadjjadi
BACKGROUND: Cystic echinococcosis (CE) as a zoonotic parasitic disease, remains a health challenge in many parts of the world. There are different species of Echinococcus granulosus sensu lato with different pathogenicity and host preferences.Different procedures have been applied for characterization of Echinococcus taxa in which two mitochondrial genes, cox1 and nad1 have been used more common. They have been able to differentiate E. granulosus sensu stricto and E. canadensis species in different hosts...
February 5, 2019: Computational Biology and Chemistry
A Ahsana, Ganesh Jeevanandan, E M G Subramanian
Background: The study of morphology of dentition can provide information on the phylogenetic relationship between species and diversities among population. There is a difference in opinions regarding influence of ethnicity on dental morphology. Using quantitative methods, few studies have shown the associations between these dental features and crown traits in humans. The present study is to find the correlation between the occlusal morphology and forensic anthropological research. Aim and Objective: The aim of this study is to determine the prevalence of different types of primary mandibular second molars in South Indian which can be used in forensic anthropological research...
May 2018: Journal of Forensic Dental Sciences
Y H Wan, L Zhuang, L J Ren, Q N Zheng, L Fu, Z Z Shan, F F Pei, W J Jiang, G P Tang, S J Li
The number of H7N9 bird flu cases was high and the situation was grim in guizhou province in 2017. To understand the molecular characteristics of the hemagglutinin gene (HA) and the risk of human infection with avian influenza virus A(H7N9) in Guizhou Province, 2017. Homology, genetic evolution and pivotal sites related to receptor binding regions, pathogenicity and potential glycosylation of 14 avian influenza viruses A(H7N9) were analyzed by a series of bioinformation softwares. It was cleared that there was 95...
February 6, 2019: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
M Y Luo, X H Pan, Q Fan, J F Zhang, R Ge, J Jiang, W J Chen
Objective: To understand the epidemiological characteristics of one large HIV molecular transmission cluster in Jiaxing city, Zhejiang province, 2017 in order to select those people under high-risk and providing basis for programs on prevention. Methods: During 2017, newly diagnosed HIV/AIDS cases in this city were recruited. Plasma samples were collected from subjects, followed by RNA extraction, RT-PCR and nest-PCR for pol gene amplification, before being sequenced and aligned. Mega 6.0 software was used to construct phylogenetic tree, and Cytoscape 3...
February 10, 2019: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Manojit Bhattacharya, Arpita Hota, Avijit Kar, Deep Sankar Chini, Ramesh Chandra Malick, Bidhan Chandra Patra, Basanta Kumar Das
Antifreeze proteins (AFPs) are known to polypeptide components formed by certain plants, animals, fungi and bacteria which support to survive in sub-zero temperature. Current study highlighted the seven different antifreeze proteins of fish Ocean pout ( Zoarces americanus ), in which protein (amino acids sequence) were collected from National Centre for Biotechnology Information and finely characterized using several in silico tools. Such biocomputational techniques applied to figure out the physicochemical, functional and conformational characteristics of targeted AFPs...
December 2018: Journal, Genetic Engineering & Biotechnology
Samo Jeverica, József Sóki, Manica Mueller Premru, Elizabeth Nagy, Lea Papst
Bacteroides fragilis can be classified into division I (cfiA negative) and division II (cfiA positive) isolates. Division II isolates have a silent chromosomal carbapenemase gene (cfiA) that can become overexpressed by an insertion of a mobile genetic element and thus develop a phenotypic resistance to carbapenems. Aims of our study were (i) to determine the prevalence of B. fragilis division II (cfiA positive) isolates among blood stream and non-blood stream isolates from two major Slovenian tertiary-care hospitals and (ii) to assess its influence on phenotypic resistance to imipenem...
February 1, 2019: Anaerobe
Soumya Kundu, Mukul S Bansal
Summary: SaGePhy is a software package for improved phylogenetic simulation of gene and subgene evolution. SaGePhy can be used to generate species trees, gene trees, and subgene or (protein) domain trees using a probabilistic birth-death process that allows for gene and subgene duplication, horizontal gene and subgene transfer, and gene and subgene loss. SaGePhy implements a range of important features not found in other phylogenetic simulation frameworks/software. These include (i) simulation of subgene or domain level evolution inside one or more gene trees, (ii) simultaneous simulation of both additive and replacing horizontal gene/subgene transfers, and (iii) probabilistic sampling of species tree and gene tree nodes, respectively, for gene-family and domain-family birth...
February 1, 2019: Bioinformatics
Nicole K Reynolds, Gerald L Benny, Hsiao-Man Ho, Yu-Han Hou, Pedro W Crous, Matthew E Smith
The Piptocephalidaceae (Zoopagales, Zoopagomycota) contains three genera of mycoparasitic, haustoria-forming fungi: Kuzuhaea, Piptocephalis, and Syncephalis. Although the species in this family are diverse and ubiquitous in soil and dung, they are among the least studied fungi. Co-cultures of Piptocephalis and their hosts are relatively easy to isolate from soil and dung samples across the globe, making them a good model taxon for the order Zoopagales. This study focuses on the systematics of the genus Piptocephalis...
February 4, 2019: Mycologia
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