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https://www.readbyqxmd.com/read/29332141/cultivable-fungi-present-in-antarctic-soils-taxonomy-phylogeny-diversity-and-bioprospecting-of-antiparasitic-and-herbicidal-metabolites
#1
Eldon C Q Gomes, Valéria M Godinho, Débora A S Silva, Maria T R de Paula, Gislaine A Vitoreli, Carlos L Zani, Tânia M A Alves, Policarpo A S Junior, Silvane M F Murta, Emerson C Barbosa, Jaquelline G Oliveira, Fabio S Oliveira, Camila R Carvalho, Mariana C Ferreira, Carlos A Rosa, Luiz H Rosa
Molecular biology techniques were used to identify 218 fungi from soil samples collected from four islands of Antarctica. These consisted of 22 taxa of 15 different genera belonging to the Zygomycota, Ascomycota, and Basidiomycota. Mortierella, Antarctomyces, Pseudogymnoascus, and Penicillium were the most frequently isolated genera and Penicillium tardochrysogenum, Penicillium verrucosus, Goffeauzyma gilvescens, and Mortierella sp. 2 the most abundant taxa. All fungal isolates were cultivated using solid-state fermentation to obtain their crude extracts...
January 13, 2018: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/29331867/classification-and-evolution-of-human-papillomavirus-genome-variants-alpha-5-hpv26-51-69-82-alpha-6-hpv30-53-56-66-alpha-11-hpv34-73-alpha-13-hpv54-and-alpha-3-hpv61
#2
Zigui Chen, Mark Schiffman, Rolando Herrero, Rob DeSalle, Kathryn Anastos, Michel Segondy, Vikrant V Sahasrabuddhe, Patti E Gravitt, Ann W Hsing, Paul K S Chan, Robert D Burk
HPV variants from the same type can be classified into lineages and sublineages based on the complete genome differences and the phylogenetic topologies. We examined nucleotide variations of twelve HPV types within the species Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) by analyzing 1432 partial sequences and 181 complete genomes from multiple geographic populations. The inter-lineage and inter-sublineage mean differences of HPV variants ranged between 0...
January 11, 2018: Virology
https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#3
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29330958/do-muscles-constrain-skull-shape-evolution-in-strepsirrhines
#4
Anne-Claire Fabre, Jonathan M G Perry, Adam Hartstone-Rose, AuróLien Lowie, Andy Boens, MaÏtena Dumont
Despite great interest and decades of research, the musculoskeletal relationships of the masticatory system in primates are still not fully understood. However, without a clear understanding of the interplay between muscles and bones it remains difficult to understand the functional significance of morphological traits of the skeleton. Here, we aim to study the impacts of the masticatory muscles on the shape of the cranium and the mandible as well as their co-variation in strepsirrhine primates. To do so, we use 3D geometric morphometric approaches to assess the shape of each bone of the skull of 20 species for which muscle data are available in the literature...
February 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29330949/functional-morphology-of-mimetic-musculature-in-primates-how-social-variables-and-body-size-stack-up-to-phylogeny
#5
Anne M Burrows
Mammalian skeletal muscle is influenced by the functional demands placed upon it. Functional morphology of facial expression musculature, or mimetic musculature, is largely unknown. Recently, primate mimetic musculature has been shown to respond to demands associated with social factors. Body size has also been demonstrated to affect many aspects of primate functional morphology and evolutionary morphology. The present study was designed to further examine the role of social variables and body size in influencing the morphology of primate mimetic musculature using a broad phylogenetic range of primates, primates with varying body sizes, and those that exploit differing time of day activity cycles and social group sizes...
February 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/29330893/mitogenomic-differences-between-the-normal-and-tumour-cells-of-colorectal-cancer-patients
#6
Katarzyna Skonieczna, Boris Malyarchuk, Arkadiusz Jawień, Andrzej Marszałek, Zbigniew Banaszkiewicz, Paweł Jarmocik, Tomasz Grzybowski
So far, a reliable spectrum of mitochondrial DNA mutations in colorectal cancer cells is still unknown, and neither is their significance in carcinogenesis. Indeed, it remains debatable whether mtDNA mutations are "drivers" or "passengers" of colorectal carcinogenesis. Thus, we analyzed 200 mitogenomes from normal and cancer tissues of 100 colorectal cancer patients. Minority variant mutations were detected at the 1% level. We showed that somatic mutations frequently occur in colorectal cancer cells (75%) and are randomly distributed across the mitochondrial genome...
January 12, 2018: Human Mutation
https://www.readbyqxmd.com/read/29330664/an-iranian-genomic-sequence-of-beet-mosaic-virus-provides-insights-into-diversity-and-evolution-of-the-world-population
#7
Musa Mohammadi, Adrian J Gibbs, Ahmad Hosseini, Samin Hosseini
Beet mosaic virus (BtMV), the only Potyvirus known to infect sugar beet, occurs worldwide in beet crops. The full genome sequencing of a BtMV isolate from Iran (Ir-VRU), enabled us to better understand the evolutionary history of this virus. Selection analysis suggested that BtMV evolution is mainly under negative selection but its strength varies in different proteins with the multifunctional proteins under strongest selection. Recombination has played a major role in the evolution of the BtMVs; only the Ir-VRU and USA isolates show no evidence of recombination...
January 12, 2018: Virus Genes
https://www.readbyqxmd.com/read/29329347/salivary-proteomics-of-healthy-dogs-an-in-depth-catalog
#8
Sheila M F Torres, Eva Furrow, Clarissa P Souza, Jennifer L Granick, Ebbing P de Jong, Timothy J Griffin, Xiong Wang
OBJECTIVE: To provide an in-depth catalog of the salivary proteome and endogenous peptidome of healthy dogs, evaluate proteins and peptides with antimicrobial properties, and compare the most common salivary proteins and peptides between different breed phylogeny groups. METHODS: 36 healthy dogs without evidence of periodontal disease representing four breed phylogeny groups, based upon single nucleotide polymorphism haplotypes (ancient, herding/sighthound, and two miscellaneous groups)...
2018: PloS One
https://www.readbyqxmd.com/read/29327389/multivariate-analysis-of-variations-in-intrinsic-foot-musculature-among-hominoids
#9
Motoharu Oishi, Naomichi Ogihara, Daisuke Shimizu, Yasuhiro Kikuchi, Hideki Endo, Yumi Une, Satoshi Soeta, Hajime Amasaki, Nobutsune Ichihara
Comparative analysis of the foot muscle architecture among extant great apes is important for understanding the evolution of the human foot and, hence, human habitual bipedal walking. However, to our knowledge, there is no previous report of a quantitative comparison of hominoid intrinsic foot muscle dimensions. In the present study, we quantitatively compared muscle dimensions of the hominoid foot by means of multivariate analysis. The foot muscle mass and physiological cross-sectional area (PCSA) of five chimpanzees, one bonobo, two gorillas, and six orangutans were obtained by our own dissections, and those of humans were taken from published accounts...
January 12, 2018: Journal of Anatomy
https://www.readbyqxmd.com/read/29325877/dmcatd-a-cathepsin-d-like-peptidase-of-the-hematophagous-insect-dipetalogaster-maxima-hemiptera-reduviidae-purification-bioinformatic-analyses-and-the-significance-of-its-interaction-with-lipophorin-in-the-internalization-by-developing-oocytes
#10
Jimena Leyria, Leonardo L Fruttero, Rodrigo Ligabue-Braun, Marina S Defferrari, Estela L Arrese, José L Soulages, Beatriz P Settembrini, Celia R Carlini, Lilián E Canavoso
DmCatD, a cathepsin D-like peptidase of the hematophagous insect Dipetalogaster maxima, is synthesized by the fat body and the ovary and functions as yolk protein precursor. Functionally, DmCatD is involved in vitellin proteolysis. In this work, we purified and sequenced DmCatD, performed bioinformatic analyses and investigated the events involved in its targeting and storage in developing oocytes. By ion exchange and gel filtration chromatography, DmCatD was purified from egg homogenates and its identity was confirmed by mass spectrometry...
January 8, 2018: Journal of Insect Physiology
https://www.readbyqxmd.com/read/29325126/automated-integration-of-trees-and-traits-a-case-study-using-paired-fin-loss-across-teleost-fishes
#11
Laura M Jackson, Pasan C Fernando, Josh S Hanscom, James P Balhoff, Paula M Mabee
Data synthesis required for large-scale macroevolutionary studies is challenging with the current tools available for integration. Using a classic question regarding the frequency of paired fin loss in teleost fishes as a case study, we sought to create automated methods to facilitate the integration of broad-scale trait data with a sizable species-level phylogeny. Similar to the evolutionary pattern previously described for limbs, pelvic and pectoral fin reduction and loss are thought to have occurred independently multiple times in the evolution of fishes...
January 9, 2018: Systematic Biology
https://www.readbyqxmd.com/read/29325077/integrating-restriction-site-associated-dna-sequencing-rad-seq-with-morphological-cladistic-analysis-clarifies-evolutionary-relationships-among-major-species-groups-of-bee-orchids
#12
Richard M Bateman, Gábor Sramkó, Ovidiu Paun
Background and Aims: Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus...
January 9, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29325030/the-effect-of-rna-substitution-models-on-viroid-and-rna-virus-phylogenies
#13
Juan Ángel Patiño Galindo, Fernando González Candelas, Oliver G Pybus
Many viroids and RNA viruses have genomes that exhibit secondary structure, with paired nucleotides forming stems and loops. Such structures violate a key assumption of most methods of phylogenetic reconstruction, that sequence change is independent among sites. However, phylogenetic analyses of these transmissible agents rarely use evolutionary models that account for RNA secondary structure. Here we assess the effect of using RNA-specific nucleotide substitution models on the phylogenetic inference of viroids and RNA viruses...
January 9, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29325010/incomplete-co-cladogenesis-between-zootermopsis-termites-and-their-associated-protists
#14
Stephen J Taerum, Francesca De Martini, Jürgen Liebig, Gillian H Gile
Coevolution is a major driver of speciation in many host-associated symbionts. In the termite-protist digestive symbiosis, the protists are vertically inherited by anal feeding among nest mates. Lower termites (all termite families except Termitidae) and their symbionts have broadly co-diversified over ~170 million yr. However, this inference is based mainly on the restricted distribution of certain protist genera to certain termite families. With the exception of one study, which demonstrated congruent phylogenies for the protist Pseudotrichonympha and its Rhinotermitidae hosts, coevolution in this symbiosis has not been investigated with molecular methods...
January 6, 2018: Environmental Entomology
https://www.readbyqxmd.com/read/29325008/mineralized-trichomes-in-boraginales-complex-microscale-heterogeneity-and-simple-phylogenetic-patterns
#15
Adeel Mustafa, Hans-Jürgen Ensikat, Maximilian Weigend
Background and Aims: Boraginales are often characterized by a dense cover of stiff, mineralized trichomes, which may act as a first line of defence against herbivores. Recent studies have demonstrated that the widely reported silica and calcium carbonate in plant trichomes may be replaced by calcium phosphate. The present study investigates mineralization patterns in 42 species from nine families of the order Boraginales to investigate detailed patterns of mineralization and the possible presence of a phylogenetic signal in different mineralization patterns...
January 6, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29324799/comprehensive-untargeted-metabolomics-of-lychnnophorinae-subtribe-asteraceae-vernonieae-in-a-phylogenetic-context
#16
Maria Elvira Poleti Martucci, Benoit Loeuille, José Rubens Pirani, Leonardo Gobbo-Neto
Members of the subtribe Lychnophorinae occur mostly within the Cerrado domain of the Brazilian Central Plateau. The relationships between its 11 genera, as well as between Lychnophorinae and other subtribes belonging to the tribe Vernonieae, have recently been investigated upon a phylogeny based on molecular and morphological data. We report the use of a comprehensive untargeted metabolomics approach, combining HPLC-MS and GC-MS data, followed by multivariate analyses aiming to assess the congruence between metabolomics data and the phylogenetic hypothesis, as well as its potential as a chemotaxonomic tool...
2018: PloS One
https://www.readbyqxmd.com/read/29324289/phylogenetic-analysis-reveals-three-distinct-epidemiological-profiles-in-dutch-and-flemish-blood-donors-with-hepatitis-b-virus-infection
#17
Thijs J van de Laar, Véronique A Van Gaever, Peter van Swieten, An Muylaert, Veerle Compernolle, Hans L Zaaijer
During 2006-2016, hepatitis B virus (HBV) was detected in nearly 400 blood donors in the Netherlands and Flanders. Donor demographics and self-reported risk factors as disclosed during the donor exit interview were compared to HBV phylogenies of donor and reference sequences. First-time donors with chronic HBV-infection were often immigrants (67%) infected with genetically highly diverse strains of genotypes A (32%), B (8%), C (6%), D (53%) and E to H (1%). Each subtype was strongly associated with donor ethnicity...
January 8, 2018: Virology
https://www.readbyqxmd.com/read/29324039/phylogeny-and-evolution-of-neuropterida-where-have-wings-of-lace-taken-us
#18
Michael S Engel, Shaun L Winterton, Laura C V Breitkreuz
The last 25 years of phylogenetic investigation into the three orders constituting the superorder Neuropterida-Raphidioptera, Megaloptera, and Neuroptera-have brought about a dramatic revision in our understanding of the evolution of lacewings, snakeflies, dobsonflies, and their diverse relatives. Phylogenetic estimations based on combined analyses of diverse data sources, ranging from adult and larval morphology to full mitochondrial genomic DNA, have begun to converge on similar patterns, many times in accordance with hypotheses put forth by Cyril Withycombe nearly a century ago...
January 7, 2018: Annual Review of Entomology
https://www.readbyqxmd.com/read/29322322/functional-traits-can-improve-our-understanding-of-niche-and-dispersal-based-processes
#19
Feng Jiang, Yanhan Xun, Huiying Cai, Guangze Jin
Ecologists often determine the relative importance of niche- and dispersal-based processes via variation partitioning based on species composition. Functional traits and their proxies of phylogeny are expected to increase the detection of niche-based processes and reduce the unexplained variation relative to species identity. We collected eight adult tree traits and phylogenetic data of 41 species and employed a phylogenetic fuzzy weighting method to address this issue in a 9-ha temperate forest dynamics plot...
January 10, 2018: Oecologia
https://www.readbyqxmd.com/read/29321872/relative-contribution-of-neutral-and-deterministic-processes-in-shaping-fruit-feeding-butterfly-assemblages-in-afrotropical-forests
#20
Kwaku Aduse-Poku, Freerk Molleman, William Oduro, Samuel K Oppong, David J Lohman, Rampal S Etienne
The unified neutral theory of biodiversity and biogeography has gained the status of a quantitative null model for explaining patterns in ecological (meta)communities. The theory assumes that individuals of trophically similar species are functionally equivalent. We empirically evaluate the relative contribution of neutral and deterministic processes in shaping fruit-feeding butterfly assemblages in three tropical forests in Africa, using both direct (confronting the neutral model with species abundance data) and indirect approaches (testing the predictions of neutral theory using data other than species abundance distributions)...
January 2018: Ecology and Evolution
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