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https://www.readbyqxmd.com/read/28943727/a-genomic-signature-for-genotyping-mycobacterium-tuberculosis
#1
David Tarazona, Luis Jaramillo, Victor Borda, Kelly Levano, Marco Galarza, Heinner Guio
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB...
2017: Bioinformation
https://www.readbyqxmd.com/read/28943405/detection-and-characterization-of-a-novel-rhabdovirus-in-aedes-cantans-mosquitoes-and-evidence-for-a-mosquito-associated-new-genus-in-the-family-rhabdoviridae
#2
Nariman Shahhosseini, Renke Lühken, Hanna Jöst, Stephanie Jansen, Jessica Börstler, Toni Rieger, Andreas Krüger, Anges Yadouleton, Renata de Mendonça Campos, Claudio Cesar Cirne-Santos, Davis Fernandes Ferreira, Rolf Garms, Norbert Becker, Egbert Tannich, Daniel Cadar, Jonas Schmidt-Chanasit
Thanks to recent advances in random amplification technologies, metagenomic surveillance expanded the number of novel, often unclassified viruses within the family Rhabdoviridae. Using a vector-enabled metagenomic (VEM) tool, we identified a novel rhabdovirus in Aedes cantans mosquitoes collected from Germany provisionally named Ohlsdorf virus (OHSDV). The OHSDV genome encodes the canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORF in the P gene. Sequence analysis indicated that OHSDV exhibits a similar genome organization and characteristics compared to other mosquito-associated rhabdoviruses (Riverside virus, Tongilchon virus and North Creek virus)...
September 21, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28942768/advances-in-spermatological-characters-in-the-digenea-review-and-proposal-of-spermatozoa-models-and-their-phylogenetic-importance
#3
Abdoulaye J S Bakhoum, Jordi Miquel, Papa I Ndiaye, Jean-Lou Justine, Alessandra Falchi, Cheikh T Bâ, Bernard Marchand, Yann Quilichini
The wide biodiversity and economic importance of digeneans have motivated a great deal of research in the last decade, focussing on their phylogenetic positions. Molecular research was instrumental for our understanding of phylogeny in the Digenea, but spermatological studies have also provided many results, which are potentially useful for phylogeny; however, the complete spermatological data set has never been reviewed in a whole phylogenetic perspective. Spermatological data are now available for more than 100 species, belonging to 15 superfamilies and 46 families...
2017: Advances in Parasitology
https://www.readbyqxmd.com/read/28942502/insights-into-hydrocarbon-assimilation-by-eurotialean-and-hypocrealean-fungi-roles-for-cyp52-and-cyp53-clans-of-cytochrome-p450-genes
#4
Carla Huarte-Bonnet, Suresh Kumar, Mario C N Saparrat, Juan R Girotti, Marianela Santana, John E Hallsworth, Nicolás Pedrini
Several filamentous fungi are able to concomitantly assimilate both aliphatic and polycyclic aromatic hydrocarbons that are the biogenic by-products of some industrial processes. Cytochrome P450 monooxygenases catalyze the first oxidation reaction for both types of substrate. Among the cytochrome P450 (CYP) genes, the family CYP52 is implicated in the first hydroxylation step in alkane-assimilation processes, while genes belonging to the family CYP53 have been linked with oxidation of aromatic hydrocarbons...
September 23, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28939989/the-cotesia-sesamiae-story-insight-into-host-range-evolution-in-a-hymenoptera-parasitoid-and-implication-for-its-use-in-biological-control-programs
#5
REVIEW
L Kaiser, S Dupas, A Branca, E A Herniou, C W Clarke, C Capdevielle Dulac, J Obonyo, R Benoist, J Gauthier, P A Calatayud, J F Silvain, B P Le Ru
This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding...
September 22, 2017: Genetica
https://www.readbyqxmd.com/read/28939913/a-novel-fast-vector-method-for-genetic-sequence-comparison
#6
Yongkun Li, Lily He, Rong Lucy He, Stephen S-T Yau
With sharp increasing in biological sequences, the traditional sequence alignment methods become unsuitable and infeasible. It motivates a surge of fast alignment-free techniques for sequence analysis. Among these methods, many sorts of feature vector methods are established and applied to reconstruction of species phylogeny. The vectors basically consist of some typical numerical features for certain biological problems. The features may come from the primary sequences, secondary or three dimensional structures of macromolecules...
September 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28939497/molecular-typing-and-phylogeny-of-wolbachia-a-study-from-assam-north-eastern-part-of-india
#7
Monika Soni, Chandrakanta Bhattacharya, Jitendra Sharma, Siraj Ahmed Khan, Prafulla Dutta
BACKGROUND: Wolbachia are maternally inherited endosymbiotic alphaproteobacteria, infecting 40-75% of arthropod species. Knowledge on distribution of native strains infecting mosquito vectors from endemic regions is essential for successful implementation of vector control interventions utilizing potential strains of Wolbachia. Study identified various native strains of Wolbachia inhabiting different mosquito species from field and colonised conditions of Assam. The fly Drosophila melanogaster was also included in our study...
September 19, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28935583/role-of-elasmobranchs-and-holocephalans-in-understanding-peptide-evolution-in-the-vertebrates-lessons-learned-from-gonadotropin-releasing-hormone-gnrh-and-corticotropin-releasing-factor-crf-phylogenies
#8
REVIEW
David A Lovejoy, Ola M Michalec, David W Hogg, David I Wosnick
The cartilaginous fishes (Class Chondrichthyes) comprise two morphologically distinct subclasses; Elasmobranchii and Holocephali. Evidence indicates early divergence of these subclasses, suggesting monophyly of their lineage. However, such a phylogenetic understanding is not yet developed within two highly conserved peptide lineages, GnRH and CRF. Various GnRH forms exist across the Chondrichthyes. Although 4-7 immunoreactive forms have been described in Elasmobranchii, only one has been elucidated in Holocephali...
September 18, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28934957/phylogenetic-analyses-of-bat-associated-bugs-hemiptera-cimicidae-cimicinae-and-cacodminae-indicate-two-new-species-close-to-cimex-lectularius
#9
Sándor Hornok, Krisztina Szőke, Sándor A Boldogh, Attila D Sándor, Jenő Kontschán, Vuong Tan Tu, Ali Halajian, Nóra Takács, Tamás Görföl, Péter Estók
BACKGROUND: Bats are regarded as the primary (ancestral) hosts of bugs of the family Cimicidae. The historically and economically most important species in the family is the common bedbug (Cimex lectularius), because of its worldwide occurrence and association with humans. This molecular-phylogenetic study was initiated in order to expand the knowledge on the phylogeny of cimicid bugs of bats, by investigating samples from Hungary, Romania (representing central-eastern Europe) and two further countries (South Africa and Vietnam)...
September 21, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28934931/mitochondrial-genomes-of-african-pangolins-and-insights-into-evolutionary-patterns-and-phylogeny-of-the-family-manidae
#10
Zelda du Toit, Morné du Plessis, Desiré L Dalton, Raymond Jansen, J Paul Grobler, Antoinette Kotzé
BACKGROUND: This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla). RESULTS: The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934927/evolution-and-expression-analysis-reveal-the-potential-role-of-the-hd-zip-gene-family-in-regulation-of-embryo-abortion-in-grapes-vitis-vinifera-l
#11
Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
BACKGROUND: The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS: A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934400/genomic-characterisation-of-environmental-pseudomonas-aeruginosa-isolated-from-dental-unit-waterlines-revealed-the-insertion-sequence-ispa11-as-a-chaotropic-element
#12
Antony T Vincent, Luca Freschi, Julie Jeukens, Irena Kukavica-Ibrulj, Jean-Guillaume Emond-Rheault, Annie Leduc, Brian Boyle, Fabrice Jean-Pierre, Marie-Christine Groleau, Eric Déziel, Jean Barbeau, Steve J Charette, Roger C Levesque
The bacterium Pseudomonas aeruginosa is well known to have a remarkable adaptive capacity allowing it to colonise many environments. A recent study on environmental isolates from dental unit waterlines (DUWLs) hinted at a genetic clustering into two groups. Isolates from one of these groups, named cluster III, were shown to have unusual phenotypes for environmental isolates, such as an increased biofilm production. To have a better ecological view, more specifically on isolates from cluster III, the complete genomes of 39 isolates including 16 from DUWLs were sequenced...
September 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28934378/investigating-difficult-nodes-in-the-placental-mammal-tree-with-expanded-taxon-sampling-and-thousands-of-ultraconserved-elements
#13
Jacob A Esselstyn, Carl H Oliveros, Mark T Swanson, Brant C Faircloth
The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28932209/the-mobilome-a-major-contributor-to-escherichia-coli-stx2-positive-o26-h11-strains-intra-serotype-diversity
#14
Sabine Delannoy, Patricia Mariani-Kurkdjian, Hattie E Webb, Stephane Bonacorsi, Patrick Fach
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28931649/sequencing-of-the-variable-region-of-rpsb-to-discriminate-between-streptococcus-pneumoniae-and-other-streptococcal-species
#15
Anne L Wyllie, Yvonne Pannekoek, Sandra Bovenkerk, Jody van Engelsdorp Gastelaars, Bart Ferwerda, Diederik van de Beek, Elisabeth A M Sanders, Krzysztof Trzciński, Arie van der Ende
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28931453/molecular-characterization-and-distribution-of-plasmodium-matutinum-a-common-avian-malaria-parasite
#16
Gediminas Valkiūnas, Mikas Ilgūnas, Dovilė Bukauskaitė, Vaidas Palinauskas, Rasa Bernotienė, Tatjana A Iezhova
Species of Plasmodium (Plasmodiidae, Haemosporida) are widespread and cause malaria, which can be severe in avian hosts. Molecular markers are essential to detect and identify parasites, but still absent for many avian malaria and related haemosporidian species. Here, we provide first molecular characterization of Plasmodium matutinum, a common agent of avian malaria. This parasite was isolated from a naturally infected thrush nightingale Luscinia luscinia (Muscicapidae). Fragments of mitochondrial, apicoplast and nuclear genomes were obtained...
September 21, 2017: Parasitology
https://www.readbyqxmd.com/read/28929018/inferring-weak-spots-in-phylogenetic-trees-application-to-mosasauroid-nomenclature
#17
Daniel Madzia, Andrea Cau
Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades...
2017: PeerJ
https://www.readbyqxmd.com/read/28929008/early-branching-euteleost-relationships-areas-of-congruence-between-concatenation-and-coalescent-model-inferences
#18
Matthew A Campbell, Michael E Alfaro, Max Belasco, J Andrés López
Phylogenetic inference based on evidence from DNA sequences has led to significant strides in the development of a stable and robustly supported framework for the vertebrate tree of life. To date, the bulk of those advances have relied on sequence data from a small number of genome regions that have proven unable to produce satisfactory answers to consistently recalcitrant phylogenetic questions. Here, we re-examine phylogenetic relationships among early-branching euteleostean fish lineages classically grouped in the Protacanthopterygii using DNA sequence data surrounding ultraconserved elements...
2017: PeerJ
https://www.readbyqxmd.com/read/28928723/analysis-of-the-sequences-structures-and-functions-of-product-releasing-enzyme-domains-in-fungal-polyketide-synthases
#19
Lu Liu, Zheng Zhang, Chang-Lun Shao, Chang-Yun Wang
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I-VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28927877/gonadotropin-releasing-hormone-by-any-other-name-would-smell-as-sweet
#20
Pei-San Tsai
The goal of this article is to discuss the nomenclature of members of the gonadotropin-releasing hormone (GnRH) superfamily. This superfamily currently consists of 5 families: (1) vertebrate GnRH, (2) adipokinetic hormone, (3) corazonin, (4) adipokinetic hormone/corazonin-related peptide and (5) invertebrate GnRH (or GnRH/corazonin). The naming of some of these peptides, especially members of the invertebrate GnRH family, may not have reflected their true evolutionary origin, leading to some confusion and controversy...
September 18, 2017: General and Comparative Endocrinology
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