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https://www.readbyqxmd.com/read/28323858/isosel-protein-isoform-selector-for-phylogenetic-reconstructions
#1
Héloïse Philippon, Alexia Souvane, Céline Brochier-Armanet, Guy Perrière
The reliability of molecular phylogenies is strongly dependent on the quality of the assembled datasets. In the case of eukaryotes, the selection of only one protein isoform per genomic locus is mandatory to avoid biases linked to redundancy. Here, we present IsoSel, a tool devoted to the selection of alternative isoforms in the context of phylogenetic reconstruction. It provides a better alternative to the widely used approach consisting in the selection of the longest isoforms and it performs better than Guidance, its only available counterpart...
2017: PloS One
https://www.readbyqxmd.com/read/28319806/description-of-flamella-daurica-n-sp-with-notes-on-the-phylogeny-of-the-genus-flamella-and-related-taxa
#2
Anna Glotova, Alexey Smirnov
A new species of naked amoebae, Flamella daurica (Amoebozoa, Conosa, Variosea), from the Russian Far East is studied and described. In addition, we isolated a strain, identified as Flamella aegyptia from Lake Ontario in Canada. Its SSU rRNA gene sequence is almost identical with that of the type strain, except for the presence of an intron in the SSU sequence. The phylogenetic analysis of a variosean alignment after inclusion of a number of environmental sequences found in GenBank confirmed that the species Talaepolella tubasferens Lahr 2012 is closely related to the Flamella clade but probably represents an independent genus and includes no less than two different species...
March 3, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28317545/phylogeny-and-pathogenicity-of-lasiodiplodia-species-associated-with-dieback-of-mango-in-peru
#3
Edgar Rodríguez-Gálvez, Pakita Guerrero, Carla Barradas, Pedro W Crous, Artur Alves
Mango, which is an important tropical fruit crop in the region of Piura (Peru), is known to be prone to a range of diseases caused by Lasiodiplodia spp. The aim of this study was to evaluate the incidence and prevalence of mango dieback in the region of Piura, and to identify the species of Lasiodiplodia associated with the disease and evaluate their pathogenicity towards mango. Mango dieback was present in all orchards surveyed but incidence varied with location. Identification of fungal isolates was based on morphological and cultural characteristics as well as sequence data of the rDNA internal transcribed spacer region (ITS) and translation elongation factor 1-alpha gene (tef1-α)...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317544/analysis-of-phylogeny-distribution-and-pathogenicity-of-botryosphaeriaceae-species-associated-with-gummosis-of-anacardium-in-brazil-with-a-new-species-of-lasiodiplodia
#4
Mariote S B Netto, Waléria G Lima, Kamila C Correia, Christiana F B da Silva, Michael Thon, Ricardo B Martins, Robert N G Miller, Sami J Michereff, Marcos P S Câmara
Netto, M. S. B., Lima, W. G., Correia, K. C., da Silva, C. F. B., Thon, M., Martins, R. B., Miller, R. N. G., Michereff, S. J., and Câmara, M. P. S. 2016. Analysis of phylogeny, distribution, and pathogenicity of Botryosphaeriaceae species associated with gummosis of Anacardium in Brazil, with a new species of Lasiodiplodia. We identified Botryosphaeriaceae species associated with gummosis on Anacardium in Brazil. Isolates were sampled and identified on the basis morphology and phylogeny, through analysis of a partial translation elongation factor 1-α sequence, ribosomal DNA internal transcribed spacers, and β-tubulin gene sequence...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317543/phylogenetic-species-recognition-and-hybridisation-in-lasiodiplodia-a-case-study-on-species-from-baobabs
#5
Elsie M Cruywagen, Bernard Slippers, Jolanda Roux, Michael J Wingfield
Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28317541/mating-type-genes-in-the-genus-neofusicoccum-mating-strategies-and-usefulness-in-species-delimitation
#6
Anabela Lopes, Alan J L Phillips, Artur Alves
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28316883/middle-pleistocene-protein-sequences-from-the-rhinoceros-genus-stephanorhinus-and-the-phylogeny-of-extant-and-extinct-middle-late-pleistocene-rhinocerotidae
#7
Frido Welker, Geoff M Smith, Jarod M Hutson, Lutz Kindler, Alejandro Garcia-Moreno, Aritza Villaluenga, Elaine Turner, Sabine Gaudzinski-Windheuser
BACKGROUND: Ancient protein sequences are increasingly used to elucidate the phylogenetic relationships between extinct and extant mammalian taxa. Here, we apply these recent developments to Middle Pleistocene bone specimens of the rhinoceros genus Stephanorhinus. No biomolecular sequence data is currently available for this genus, leaving phylogenetic hypotheses on its evolutionary relationships to extant and extinct rhinoceroses untested. Furthermore, recent phylogenies based on Rhinocerotidae (partial or complete) mitochondrial DNA sequences differ in the placement of the Sumatran rhinoceros (Dicerorhinus sumatrensis)...
2017: PeerJ
https://www.readbyqxmd.com/read/28316881/occurrence-of-concurrent-infections-with-multiple-serotypes-of-dengue-viruses-during-2013-2015-in-northern-kerala-india
#8
Manchala Nageswar Reddy, Ranjeet Dungdung, Lathika Valliyott, Rajendra Pilankatta
BACKGROUND: Dengue is a global human public health threat, causing severe morbidity and mortality. The occurrence of sequential infection by more than one serotype of dengue virus (DENV) is a major contributing factor for the induction of Dengue Hemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS), two major medical conditions caused by DENV infection. However, there is no specific drug or vaccine available against dengue infection. There are reports indicating the increased incidence of concurrent infection of dengue in several tropical and subtropical regions...
2017: PeerJ
https://www.readbyqxmd.com/read/28316067/fisse-a-simple-non-parametric-test-for-the-effects-of-a-binary-character-on-lineage-diversification-rates
#9
Daniel L Rabosky, Emma E Goldberg
It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model-based tests of state-dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple non-parametric statistical test ("FiSSE") to assess the effects of a binary character on lineage diversification rates...
March 18, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28315380/primary-structures-and-partial-toxicological-characterization-of-two-phospholipases-a2-from-micrurus-mipartitus-and-micrurus-dumerilii-coral-snake-venoms
#10
Paola Rey-Suárez, Vitelbina Núñez, Mónica Saldarriaga-Córdoba, Bruno Lomonte
Snake venom phospholipases A2 (PLA2) share high sequence identities and a conserved structural scaffold, but show important functional differences. Only a few PLA2s have been purified and characterized from coral snake (Micrurus spp.) venoms, and their role in envenomation remains largely unknown. In this report, we describe the isolation, sequencing and partial functional characterization of two Micrurus PLA2s: MmipPLA2 from Micrurus mipartitus and MdumPLA2 from Micrurus dumerilii, two species of clinical importance in Colombia...
March 14, 2017: Biochimie
https://www.readbyqxmd.com/read/28315362/molecular-analyses-reveal-high-species-diversity-of-trematodes-in-a-sub-arctic-lake
#11
Miroslava Soldánová, Simona Georgieva, Jana Roháčová, Rune Knudsen, Jesper A Kuhn, Eirik H Henriksen, Anna Siwertsson, Jenny C Shaw, Armand M Kuris, Per-Arne Amundsen, Tomáš Scholz, Kevin D Lafferty, Aneta Kostadinova
To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae)...
March 14, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28314936/distribution-of-divo-in-coffea-genomes-a-poorly-described-family-of-angiosperm-ltr-retrotransposons
#12
Mathilde Dupeyron, Rogerio Fernandes de Souza, Perla Hamon, Alexandre de Kochko, Dominique Crouzillat, Emmanuel Couturon, Douglas Silva Domingues, Romain Guyot
Coffea arabica (the Arabica coffee) is an allotetraploid species originating from a recent hybridization between two diploid species: C. canephora and C. eugenioides. Transposable elements can drive structural and functional variation during the process of hybridization and allopolyploid formation in plants. To learn more about the evolution of the C. arabica genome, we characterized and studied a new Copia LTR-Retrotransposon (LTR-RT) family in diploid and allotetraploid Coffea genomes called Divo. It is a complete and relatively compact LTR-RT element (~5 kb), carrying typical Gag and Pol Copia type domains...
March 17, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28314818/allometric-analysis-detects-brain-size-independent-effects-of-sex-and-sex-chromosome-complement-on-human-cerebellar-organization
#13
Catherine Mankiw, Min Tae M Park, P K Reardon, Ari M Fish, Liv S Clasen, Deanna Greenstein, Jay N Giedd, Jonathan D Blumenthal, Jason P Lerch, M Mallar Chakravarty, Armin Raznahan
The cerebellum is a large hindbrain structure that is increasingly recognized for its contribution to diverse domains of cognitive and affective processing in human health and disease. Although several of these domains are sex-biased, our fundamental understanding of cerebellar sex differences - including their spatial distribution, potential biological determinants, and independence from brain volume variation - lags far behind that for the cerebrum. Here, we harness automated neuroimaging methods for cerebellar morphometrics in 417 individuals to (i) localize normative male-female differences in raw cerebellar volume, (ii) compare these to sex chromosome effects estimated across five rare X-/Y-chromosome aneuploidy (SCA) syndromes, and (iii) clarify brain size-independent effects of sex and SCA on cerebellar anatomy using a generalizable allometric approach which considers scaling relationships between regional cerebellar volume and brain volume in health...
March 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28306137/empirical-phylogenies-and-species-abundance-distributions-are-consistent-with-pre-equilibrium-dynamics-of-neutral-community-models-with-gene-flow
#14
Anne-Sophie Bonnet-Lebrun, Andrea Manica, Anders Eriksson, Ana S L Rodrigues
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow...
March 17, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28303622/morphology-and-phylogeny-of-the-soil-ciliate-metopus-yantaiensis-n-sp-ciliophora-metopida-with-identification-of-the-intracellular-bacteria
#15
Atef Omar, Qianqian Zhang, Songbao Zou, Jun Gong
The morphology and infraciliature of a new ciliate, Metopus yantaiensis n. sp., discovered in coastal soil of northern China, were investigated. It is distinguished from its congeners by a combination of the following features: nuclear apparatus situated in the preoral dome; 18-21 somatic ciliary rows, of which three extend onto the preoral dome (dome kineties); three to five distinctly elongated caudal cilia, and 21-29 adoral polykinetids. The 18S rRNA genes of this new species and two congeners, M. contortus and M...
March 17, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28303220/anemone-medicinal-plants-ethnopharmacology-phytochemistry-and-biology
#16
REVIEW
Da-Cheng Hao, Xiaojie Gu, Peigen Xiao
The Ranunculaceae genus Anemone (order Ranunculales), comprising more than 150 species, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine. Various medicinal compounds have been found in Anemone plants, especially triterpenoid saponins, some of which have shown anti-cancer activities. Some Anemone compounds and extracts display immunomodulatory, anti-inflammatory, antioxidant, and antimicrobial activities. More than 50 species have ethnopharmacological uses, which provide clues for modern drug discovery...
March 2017: Acta Pharmaceutica Sinica. B
https://www.readbyqxmd.com/read/28301540/tight-species-cohesion-among-sympatric-insular-wild-gingers-asarum-spp-aristolochiaceae-on-continental-islands-highly-differentiated-floral-characteristics-versus-undifferentiated-genotypes
#17
Junshi Matsuda, Yoshiyuki Maeda, Junichi Nagasawa, Hiroaki Setoguchi
The Amami Island group of the Ryukyu Archipelago, Japan, harbors extensive species diversity of Asarum in a small landmass. The fine-scale population genetic structure and diversity of nine insular endemic Asarum species were examined using nuclear DNA microsatellite loci and ITS sequences. High population genetic diversity (HS = 0.45-0.79) was estimated based on the microsatellites, implying outcrossing of Asarum species within populations accompanied by inbreeding. Bayesian clustering analyses revealed that species were divided into three robust genetic clusters and that the species within each cluster had a homogeneous genetic structure, indicating incomplete lineage sorting...
2017: PloS One
https://www.readbyqxmd.com/read/28300642/distribution-and-phylogeny-of-brachyspira-spp-in-human-intestinal-spirochetosis-revealed-by-fish-and-16s-rrna-gene-analysis
#18
Pablo Rojas, Annett Petrich, Julia Schulze, Alexandra Wiessner, Christoph Loddenkemper, Hans-Jörg Epple, William Sterlacci, Michael Vieth, Judith Kikhney, Annette Moter
During six years as National Reference Laboratory for Spirochetes we investigated 149 intestinal biopsies from 91 patients, which were histopathologically diagnosed with human intestinal spirochetosis (HIS), using fluorescence in situ hybridization (FISH) combined with 16S rRNA gene PCR and sequencing. Aim of this study was to complement histopathological findings with FISH and PCR for definite diagnosis and species identification of the causative pathogens. HIS is characterized by colonization of the colonic mucosa of the human distal intestinal tract by Brachyspira spp...
March 11, 2017: Anaerobe
https://www.readbyqxmd.com/read/28299575/phylogenetic-constrains-on-mycorrhizal-specificity-in-eight-dendrobium-orchidaceae-species
#19
Xiaoke Xing, Xueting Ma, Jinxin Men, Yanhong Chen, Shunxing Guo
Plant phylogeny constrains orchid mycorrhizal (OrM) fungal community composition in some orchids. Here, we investigated the structures of the OrM fungal communities of eight Dendrobium species in one niche to determine whether similarities in the OrM fungal communities correlated with the phylogeny of the host plants and whether the Dendrobium-OrM fungal interactions are phylogenetically conserved. A phylogeny based on DNA data was constructed for the eight coexisting Dendrobium species, and the OrM fungal communities were characterized by their roots...
March 13, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28298478/phylogeny-based-systematization-of-arabidopsis-proteins-with-histone-h1-globular-domain
#20
Maciej Kotliński, Łukasz Knizewski, Anna Muszewska, Kinga Rutowicz, Maciej Lirski, Anja Schmidt, Celia Baroux, Krzysztof Ginalski, Andrzej Jerzmanowski
H1 (or linker) histones are basic nuclear proteins that possess an evolutionarily-conserved nucleosome-binding globular domain - GH1. They perform critical functions in determining the accessibility of chromatin DNA to trans-acting factors. In most metazoan species so far studied, linker histones are highly heterogeneous, with numerous non-allelic variants co-occurring in the same cells. The phylogenetic relationships among these variants as well as their structural and functional properties have been relatively well established...
March 15, 2017: Plant Physiology
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