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https://www.readbyqxmd.com/read/27914115/molecular-phylogeny-and-taxonomy-of-a-new-freshwater-hymenostomatid-from-northeastern-china-with-the-establishment-of-a-new-genus-anteglaucoma-gen-n-protista-ciliophora-oligohymenophorea
#1
Xuming Pan, Zihan Shi, Chundi Wang, William A Bourland, Ying Chen, Weibo Song
The morphology, infraciliature and SSU rDNA sequence of a new freshwater hymenostomatid ciliate, Anteglaucoma harbinensis gen. nov., spec. nov., collected from a farmland pond in Harbin, China, were investigated. The new genus Anteglaucoma is characterized as follows: small to medium-sized Glaucomidae with oral apparatus in anterior one-third of cell; paroral membrane composed of almost longitudinally arranged dikinetids; three adoral membranelles nearly equal in length and arranged almost longitudinally in parallel; silverline pattern tetrahymenid...
November 7, 2016: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/27914076/reconstructing-the-ancestral-relationships-between-bacterial-pathogen-genomes
#2
Caitlin Collins, Xavier Didelot
Following recent developments in DNA sequencing technology, it is now possible to sequence hundreds of whole genomes from bacterial isolates at relatively low cost. Analyzing this growing wealth of genomic data in terms of ancestral relationships can reveal many interesting aspects of the evolution, ecology, and epidemiology of bacterial pathogens. However, reconstructing the ancestry of a sample of bacteria remains challenging, especially for the majority of species where recombination is frequent. Here, we review and describe the computational techniques currently available to infer ancestral relationships, including phylogenetic methods that either ignore or account for the effect of recombination, as well as model-based and model-free phylogeny-independent approaches...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913309/sequence-determinants-of-the-caenhorhabditis-elegansdopamine-transporter-dictating-in-vivoaxonal-export-and-synaptic-localization
#3
Sarah B Robinson, J Andrew Hardaway, Shannon L Hardie, Jane Wright, Ryan M Glynn, Daniel P Bermingham, Qiao Han, Sarah M Sturgeon, Phyllis Freeman, Randy D Blakely
The monoamine neurotransmitter dopamine (DA) acts across phylogeny to modulate both simple and complex behaviors. The presynaptic DA transporter (DAT) is a major determinant of DA signaling capacity in ensuring efficient extracellular DA clearance. In humans, DAT is also a major target for prescribed and abused psychostimulants. Multiple structural determinants of DAT function and regulation have been defined, though largely these findings have arisen from heterologous expression or ex vivo cell culture studies...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27909932/complete-nucleotide-sequences-of-seven-soybean-mosaic-viruses-smv-isolated-from-wild-soybeans-glycine-soja-in-china
#4
Yun-Xia Chen, Mian Wu, Fang-Fang Ma, Jian-Qun Chen, Bin Wang
Soybean mosaic virus (SMV) is a devastating plant virus classified in the family Potyviridae, and known to infect cultivated soybeans (Glycine max). In this study, seven new SMVs were isolated from wild soybean samples and analyzed by whole-genome sequencing. An updated SMV phylogeny was built with the seven new and 83 known SMV genomic sequences. Results showed that three northeastern SMV isolates were distributed in clade III and IV, while four southern SMVs were grouped together in clade II and all contained a recombinant BCMV fragment (~900 bp) in the upstream part of the genome...
December 1, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27908771/molecular-detection-and-genetic-characterization-of-babesia-theileria-and-anaplasma-amongst-apparently-healthy-sheep-and-goats-in-the-central-region-of-turkey
#5
Mo Zhou, Shinuo Cao, Ferda Sevinc, Mutlu Sevinc, Onur Ceylan, Sepil Ekici, Charoonluk Jirapattharasate, Paul Franck Adjou Moumouni, Mingming Liu, Guanbo Wang, Aiko Iguchi, Patrick Vudriko, Hiroshi Suzuki, Xuenan Xuan
Babesia spp., Theileria spp. and Anaplasma spp. are significant tick-borne pathogens of livestock globally. In this study, we investigated the presence and distribution of Babesia ovis, Theileria ovis and Anaplasma ovis in 343 small ruminants (249 sheep and 94 goats) from 13 towns in the Central Anatolia region of Turkey using species-specific PCR assays. The PCR were conducted using the primers based on the B. ovis ssu rRNA (BoSSUrRNA), T. ovis ssu rRNA (ToSSUrRNA) and A. ovis major surface protein 4 (AoMSP4) genes, respectively...
November 16, 2016: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/27908741/resolving-interspecific-relationships-within-evolutionarily-young-lineages-using-rna-seq-data-an-example-from-pedicularis-section-cyathophora-orobanchaceae
#6
Hong-Juan Wang, Wei-Tao Li, Ya-Nan Liu, Fu-Sheng Yang, Xiao-Quan Wang
Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species...
November 28, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27907126/variability-in-the-sxt-gene-clusters-of-psp-toxin-producing-aphanizomenon-gracile-strains-from-norway-spain-germany-and-north-america
#7
Andreas Ballot, Leonardo Cerasino, Vladyslava Hostyeva, Samuel Cirés
Paralytic shellfish poisoning (PSP) toxin production has been detected worldwide in the cyanobacterial genera Anabaena, Lyngbya, Scytonema, Cuspidothrix and Aphanizomenon. In Europe Aphanizomenon gracile and Cuspidothrix issatschenkoi are the only known producers of PSP toxins and are found in Southwest and Central European freshwater bodies. In this study the PSP toxin producing Aphanizomenon sp. strain NIVA-CYA 851 was isolated from the Norwegian Lake Hillestadvannet. In a polyphasic approach NIVA-CYA 851 was morphologically and phylogenetically classified, and investigated for toxin production...
2016: PloS One
https://www.readbyqxmd.com/read/27907107/a-time-calibrated-mitogenome-phylogeny-of-catfish-teleostei-siluriformes
#8
Ilias Kappas, Spiros Vittas, Chrysoula N Pantzartzi, Elena Drosopoulou, Zacharias G Scouras
A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data...
2016: PloS One
https://www.readbyqxmd.com/read/27906993/ancient-mitochondrial-capture-as-factor-promoting-mitonuclear-discordance-in-freshwater-fishes-a-case-study-in-the-genus-squalius-actinopterygii-cyprinidae-in-greece
#9
Silvia Perea, Jasna Vukić, Radek Šanda, Ignacio Doadrio
Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data...
2016: PloS One
https://www.readbyqxmd.com/read/27905886/multi-locus-phylogeny-using-topotype-specimens-sheds-light-on-the-systematics-of-niviventer-rodentia-muridae-in-china
#10
Bin Zhang, Kai He, Tao Wan, Peng Chen, Guozheng Sun, Shaoying Liu, Truong Son Nguyen, Liangkong Lin, Xuelong Jiang
BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4)...
December 1, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27905820/evidence-based-validation-of-quorum-quenching-from-lysinibacillus-sphaericus-and-geobacillus-sp-in-bioremediation-of-oil-sludge
#11
Camilo Gómez-Garzón, Jenny Dussán
Many studies on quorum quenching focus on the discovery and characterization of novel acyl-homoserine lactonases (AHL-lactonases) because these enzymes could be used in the control of diseases caused by Gram-negative bacteria. The effects of quorum quenching are also remarkable in the performance of bacterial consortia in applications such as bioremediation. In the current work, we demonstrated the presence of a potential novel AHL-lactonase-encoding locus (Bsph_3377) from Lysinibacillus sphaericus and Geobacillus sp...
September 1, 2016: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/27905437/phylogeny-tree-of-life-took-root-150-years-ago
#12
Uwe Hossfeld, Georgy S Levit
No abstract text is available yet for this article.
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27904879/the-establishment-and-diversification-of-epidemic-associated-serogroup-w-meningococcus-in-the-african-meningitis-belt-1994-to-2012
#13
Adam C Retchless, Fang Hu, Abdoul-Salam Ouédraogo, Seydou Diarra, Kristen Knipe, Mili Sheth, Lori A Rowe, Lassana Sangaré, Absetou Ky Ba, Soumeya Ouangraoua, Dhwani Batra, Ryan T Novak, Rasmata Ouédraogo Traoré, Xin Wang
Epidemics of invasive meningococcal disease (IMD) caused by meningococcal serogroup A have been eliminated from the sub-Saharan African so-called "meningitis belt" by the meningococcal A conjugate vaccine (MACV), and yet, other serogroups continue to cause epidemics. Neisseria meningitidis serogroup W remains a major cause of disease in the region, with most isolates belonging to clonal complex 11 (CC11). Here, the genetic variation within and between epidemic-associated strains was assessed by sequencing the genomes of 92 N...
November 2016: MSphere
https://www.readbyqxmd.com/read/27902408/sequencing-rare-marine-actinomycete-genomes-reveals-high-density-of-unique-natural-product-biosynthetic-gene-clusters
#14
Michelle Antoinette Schorn, Mohammad M Alanjary, Kristen Aguinaldo, Anton Korobeynikov, Sheila Podell, Nastassia V Patin, Tommie Lincecum, Paul R Jensen, Nadine Ziemert, Bradley S Moore
Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study we sequenced twenty-one marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and underrepresented in current genomic databases...
October 27, 2016: Microbiology
https://www.readbyqxmd.com/read/27902382/the-genetic-diversity-and-phenotypic-associations-of-feline-caliciviruses-from-cats-in-switzerland
#15
Andrea M Spiri, Julien Thézé, Marina L Meli, Valentino Cattori, Alice Berger, Adolf Steinrigl, Oliver G Pybus, Regina Hofmann-Lehmann, Barbara Willi
Feline calicivirus (FCV) is a common viral pathogen in domestic cats worldwide. The variable regions of the capsid (VP1) gene of FCV have one of the highest recorded rates of molecular evolution. Understanding the genetic diversity and phylogeny of FCV is a prerequisite to exploring the epidemiology and pathogenesis of this virus and to the development of efficacious vaccine strategies. In this study, we undertook a nationwide molecular characterization of FCV using for the first time nearly complete capsid (VP1) gene sequences...
October 7, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27902306/description-of-gloeomargarita-lithophora-gen-nov-sp-nov-a-thylakoid-bearing-basal-branching-cyanobacterium-with-intracellular-carbonates-and-proposal-for-gloeomargaritales-ord-nov
#16
David Moreira, Rosaluz Tavera, Karim Benzerara, Fériel Skouri-Panet, Estelle Couradeau, Emmanuelle Gérard, Céline Loussert Fonta, Eberto Novelo, Yvan Zivanovic, Purificación López-García
A unicellular cyanobacterium, strain Alchichica-D10, was isolated from microbialites of the alkaline Lake Alchichica, Mexico. The cells were short rods (3.9 ± 0.6 μm in length and 1.1 ± 0.1 μm in width) forming biofilms of intense emerald green color. They exhibited red autofluorescence under UV light excitation. UV-visible absorption spectra revealed that they contain chlorophyll a and phycocyanin, and electron microscopy showed the presence of thylakoids. The strain grew within a temperature range of 15-30 °C...
November 21, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902204/flavobacterium-inkyongense-sp-nov-isolated-from-an-artificial-freshwater-pond
#17
Miri Park, Yochan Joung, Gi Gyun Nam, Suhyun Kim, Jang-Cheon Cho
A Gram-staining-negative, non-motile, yellow-pigmented bacterium, designated strain IMCC27201T, was isolated from an artificial freshwater pond (Inkyong). Growth of strain IMCC27201T occurred at 10-37 °C (optimum, 30 °C), at pH 7.0-8.0 (optimum, pH 7.0) and with 0-0.25 % NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC27201T belonged to the genus Flavobacterium and is most closely related to Flavobacterium columnare IFO 15943T (97.8  % sequence similarity), Flavobacterium terrae R2A1-13T (97...
October 16, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902186/multigenetic-characterization-of-candidatus-xenohaliotis-californiensis
#18
Francesco Cicala, James D Moore, Jorge Cáceres-Martínez, Miguel A Del Río-Portilla, Mónica Hernández-Rodríguez, Rebeca Vásquez-Yeomans, Axayácatl Rocha-Olivares
"Candidatus Xenohaliotis californiensis" (or Ca. Xc) is the etiological agent of the withering syndrome (WS), a chronic wasting disease affecting most if not all North American species of abalone, and has been described as a Rickettsiales-like prokaryote. Genetic data about this species is limited to the 16S rRNA gene. The inability to grow it axenically has hindered its genetic and genomic characterization and, in consequence, a thorough analysis of its systematics. Here, we amplified and sequenced five genes (16S rRNA, 23S rRNA, ftsZ, virD4, and virB11) of Ca...
October 11, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902180/phylogenomic-analysis-of-the-family-peptostreptococcaceae-clostridium-cluster-xi-and-proposal-for-reclassification-of-clostridium-litorale-fendrich-et-al-1991-and-eubacterium-acidaminophilum-zindel-et-al-1989-as-peptoclostridium-litorale-gen-nov-comb-nov-and
#19
Michael Y Galperin, Vyacheslav Brover, Igor Tolstoy, Natalya Yutin
In 1994, analyses of clostridial 16S rRNA gene sequences led to the assignment of 18 species to Clostridium cluster XI, separating them from Clostridium sensu stricto (Clostridium cluster I). Subsequently, most cluster XI species have been assigned to the family Peptostreptococcaceae; some of them have been reassigned to new genera. However, several Clostridium species were left with their old names, creating a taxonomic conundrum and confusion regarding their status. Here, we have re-examined the phylogeny of cluster XI species by comparing the 16S rRNA gene-based trees with protein- and genome-based trees, where available...
October 7, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27901448/phylogeny-and-haplotype-analysis-of-fungi-within-the-fusarium-incarnatum-equiseti-species-complex
#20
H Ramdial, R K Latchoo, F N Hosein, S N Rampersad
Fusarium spp. are ranked among the top 10 most economically and scientifically important plant-pathogenic fungi in the world and are associated with plant diseases that include fruit decay of a number of crops. Fusarium isolates infecting bell pepper in Trinidad were identified based on sequence comparisons of the translation elongation factor gene (EF-1a) with sequences of Fusarium incarnatum-equiseti species complex (FIESC) verified in the FUSARIUM-ID database. Eighty-two isolates were identified as belonging to one of four phylogenetic species within the subclades FIESC-1, FIESC-15, FIESC-16, and FIESC-26, with the majority of isolates belonging to FIESC-15...
November 30, 2016: Phytopathology
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