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Phylogenetics

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https://www.readbyqxmd.com/read/27922196/hiv-prevalence-and-phylogenetic-characteristics-among-entry-travelers-in-xishuangbanna-prefecture-yunnan-province-between-2003-and-2012
#1
Binghui Wang, Yaobo Liang, Yajuan Wang, Yue Feng, Yaping Li, Li Zhang, Qicai Xuan, Jing Miao, Weihong Qin, Xueshan Xia
Xishuangbanna is a popular tourist destination in southern Yunnan Province, bordering with Vietnam and Laos and Myanmar. There are more than 2 million cross-border travelers annually entering China at two land ports, Daluo and Mohan. To clarify the characteristics of HIV-1 prevalence among entry travelers, a retrospective epidemic investigation was conducted. Between 2003 and 2012, 196 among 91,432 entry travelers were detected to be HIV-1-positive, accounting for infection rate of 0.21%. Eighty-one gag-pol gene sequences were obtained for phylogenetic analyses and subsequent recombination analysis...
December 6, 2016: Journal of Medical Virology
https://www.readbyqxmd.com/read/27922191/full-length-genomic-sequence-analysis-of-new-subtype-3k-hepatitis-e-virus-isolates-with-99-97-nucleotide-identity-obtained-from-two-consecutive-acute-hepatitis-patients-in-a-city-in-northeast-japan
#2
Masahito Miura, Jun Inoue, Mio Tsuruoka, Tsutomu Nishizawa, Shigeo Nagashima, Masaharu Takahashi, Tooru Shimosegawa, Hiroaki Okamoto
Full-length genomic sequences of hepatitis E virus (HEV) obtained from two consecutive cases of acute self-limiting hepatitis E in a city in northeast Japan were determined. Interestingly, two HEV isolates from each patient shared nucleotide identity of 99.97% in 7,225 nucleotides, and a phylogenetic analysis showed that they formed a cluster of Japanese isolates that is considered as a new HEV subtype 3k. The high similarity of HEV sequences of two isolates from these patients in this study suggested that a subtype 3k HEV strain had spread via a commonly distributed food in the city, possibly pig liver...
December 6, 2016: Journal of Medical Virology
https://www.readbyqxmd.com/read/27922013/erratum-phylogenetic-and-functional-potential-links-ph-and-n2o-emissions-in-pasture-soils
#3
Md Sainur Samad, Ambarish Biswas, Lars R Bakken, Timothy J Clough, Cecile A M de Klein, Karl G Richards, Gary J Lanigan, Sergio E Morales
No abstract text is available yet for this article.
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921234/simultaneous-virus-identification-and-characterization-of-severe-unexplained-pneumonia-cases-using-a-metagenomics-sequencing-technique
#4
Xiaohui Zou, Guangpeng Tang, Xiang Zhao, Yan Huang, Tao Chen, Mingyu Lei, Wenbing Chen, Lei Yang, Wenfei Zhu, Li Zhuang, Jing Yang, Zhaomin Feng, Dayan Wang, Dingming Wang, Yuelong Shu
Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples...
December 2, 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/27921137/vertical-profiles-of-water-and-sediment-denitrifiers-in-two-plateau-freshwater-lakes
#5
Guozhu Mao, Ling Chen, Yuyin Yang, Zhen Wu, Tianli Tong, Yong Liu, Shuguang Xie
The present study investigated the abundance, richness, diversity, and community composition of denitrifiers (based on nirS and nosZ genes) in the stratified water columns and sediments in eutrophic Dianchi Lake and mesotrophic Erhai Lake using quantitative PCR assay and high-throughput sequencing analysis. Both nirS- and nosZ denitrifiers were detected in waters of these two lakes. Surface water showed higher nosZ gene density than bottom water, and Dianchi Lake waters had larger nirS gene abundance than Erhai Lake waters...
December 6, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27920761/diversity-and-distribution-of-phenol-oxidase-producing-fungi-from-soda-lake-and-description-of-curvularia-lonarensis-sp-nov
#6
Rahul Sharma, Om Prakash, Mahesh S Sonawane, Yogesh Nimonkar, Priyanka B Golellu, Rohit Sharma
Soda lake is hyper alkaline and saline habitat located in closed craters with high evaporation rate. In current study fungal diversity from water and sediment samples of a soda lake (Lonar lake) located in Buldhana district of Maharashtra, India was investigated using extensive culturomics approach and mimicking the natural conditions of Lonar lake in culture media. A total of 104 diverse isolates of extremophilic fungi were recovered from this study and phylogenetically characterized by internal transcribed spacer (ITS) region sequencing...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920609/two-new-liolaemus-lizards-from-the-andean-highlands-of-southern-chile-squamata-iguania-liolaemidae
#7
Jaime Troncoso-Palacios, Hugo A Diaz, German I Puas, Edvin Riveros-Riffo, Alvaro A Elorza
Liolaemus is a diverse genus of lizards, subdivided into two subgenera: Liolaemus (sensu stricto) and Eulaemus, distributed mainly in Chile and Argentina. The Liolaemus elongatus-kriegi complex is the most diverse group within Liolaemus (sensu stricto), especially the species closely related to Liolaemus elongatus, which form a clade currently comprising nine species. Several Chilean species of this group have been recently described, mainly from volcanoes and poorly explored mountains. Here molecular and morphological evidence are provided for a new species of the Liolaemus elongatus clade, which is characterized by its small size and lack of dorsal pattern, unusual features for the species of this group of lizards...
2016: ZooKeys
https://www.readbyqxmd.com/read/27920606/phylogenetic-placement-of-the-pacific-northwest-subterranean-endemic-diving-beetle-stygoporus-oregonensis-larson-labonte-dytiscidae-hydroporinae
#8
Kojun Kanda, R Antonio Gomez, Richard Van Driesche, Kelly B Miller, David R Maddison
Stygoporus oregonensis Larson & LaBonte is a little-known subterranean diving beetle, which, until recently, had not been collected since the type series was taken from a shallow well in western Oregon, USA, in 1984. Here we report the discovery of additional specimens collected from a nearby well in the Willamette Valley. Sequence data from four mitochondrial genes, wingless, and histone III place Stygoporus Larson & LaBonte in the predominantly Mediterranean subtribe Siettitiina of the Hydroporini. Morphological support for these results is discussed, and details of the collecting circumstances of the new specimens are presented...
2016: ZooKeys
https://www.readbyqxmd.com/read/27920379/domestication-impacts-on-plant-herbivore-interactions-a-meta-analysis
#9
Susan R Whitehead, Martin M Turcotte, Katja Poveda
For millennia, humans have imposed strong selection on domesticated crops, resulting in drastically altered crop phenotypes compared with wild ancestors. Crop yields have increased, but a long-held hypothesis is that domestication has also unintentionally decreased plant defences against herbivores. To test this hypothesis, we conducted a phylogenetically controlled meta-analysis comparing insect herbivore resistance and putative plant defence traits between crops and their wild relatives. Our database included 2098 comparisons made across 73 crops in 89 studies...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27920250/renal-anemia-model-mouse-established-by-transgenic-rescue-with-erythropoietin-gene-lacking-kidney-specific-regulatory-elements
#10
Ikuo Hirano, Norio Suzuki, Shun Yamazaki, Hiroki Sekine, Naoko Minegishi, Ritsuko Shimizu, Masayuki Yamamoto
The erythropoietin (Epo) gene is under tissue-specific inducible regulation. Because kidney is the primary EPO-producing tissue in adults, impaired EPO production in chronic kidney disorders results in serious renal anemia. The Epo gene contains a liver-specific enhancer in the 3' region, but the kidney-specific enhancer for gene expression in renal EPO-producing (REP) cells remains elusive. Here, we examined a Conserved-Upstream-element for Renal-Epo-regulation (CURE) region that spans 17.4 kb to 3.6 kb upstream of the Epo gene and harbors several phylogenetically conserved elements...
December 5, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27920231/bayesian-morphological-clock-methods-resurrect-placoderm-monophyly-and-reveal-rapid-early-evolution-in-jawed-vertebrates
#11
Benedict King, Tuo Qiao, Michael S Y Lee, Min Zhu, John A Long
The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches...
December 5, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27920138/culprit-or-bystander-the-role-of-the-fallopian-tube-in-ovarian-high-grade-serous-carcinoma
#12
Elizabeth M Swisher, Rochelle L Garcia, Mark R Kilgore, Barbara M Norquist
The concurrence of intraepithelial high-grade neoplasia in the fallopian tube with metastatic implants has been taken as evidence of a tubal origin for high-grade serous pelvic carcinomas. In the current issue, Eckert and colleagues perform detailed genomic phylogenetic analyses and demonstrate that some cases of high-grade serous intraepithelial tubal neoplasia are metastatic implants and not precursor lesions. Cancer Discov; 6(12); 1309-11. ©2016 AACR.See related article by Eckert and colleagues, p. 1342...
December 2016: Cancer Discovery
https://www.readbyqxmd.com/read/27920057/acropora-digitifera-encodes-the-largest-known-family-of-fluorescent-proteins-that-has-persisted-during-the-evolution-of-acropora-species
#13
Shiho Takahashi-Kariyazono, Jun Gojobori, Yoko Satta, Kazuhiko Sakai, Yohey Terai
Fluorescent proteins (FPs) are well known and broadly used as bio-imaging markers in molecular biology research. Many FP genes were cloned from anthozoan species and it was suggested that multi-copies of these genes are present in their genomes. However, the full complement of FP genes in any single coral species remained unidentified. In this study, we analyzed the FP genes in two stony coral species. FP cDNA sequences from Acropora digitifera and Acropora tenuis revealed the presence of a multi-gene family with an unexpectedly large number of genes, separated into short-/middle-wavelength emission (S/MWE), middle-/long-wavelength emission (M/LWE), and chromoprotein (CP) clades...
December 5, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27919924/gradual-vs-abrupt-reduction-of-carpels-in-syncarpous-gynoecia-a-case-study-from-polyscias-subg-arthrophyllum-araliaceae-apiales
#14
Polina V Karpunina, Alexei A Oskolski, Maxim S Nuraliev, Porter P Lowry, Galina V Degtjareva, Tahir H Samigullin, Carmen M Valiejo-Roman, Dmitry D Sokoloff
PREMISE OF THE STUDY: Revealing the relative roles of gradual and abrupt transformations of morphological characters is an important topic of evolutionary biology. Gynoecia apparently consisting of one carpel have evolved from pluricarpellate syncarpous gynoecia in several angiosperm clades. The process of reduction can involve intermediate stages, with one fertile and one or more sterile carpels (pseudomonomery). The possible origin of monomery directly via an abrupt change of gynoecium merism has been a matter of dispute...
December 5, 2016: American Journal of Botany
https://www.readbyqxmd.com/read/27919807/a-cryptic-species-produced-by-autopolyploidy-and-subsequent-introgression-involving-medicago-prostrata-fabaceae
#15
J S Eriksson, J L Blanco-Pastor, F D Sousa, Y J K Bertrand, B E Pfeil
Although hybridisation through genome duplication is well known, hybridisation without genome duplication (homoploid hybrid speciation, HHS) is not. Few well-documented cases have been reported. A possible instance of HHS in Medicago prostrata Jacq. was suggested previously, based on only two genes and one individual. We tested whether this species was formed through HHS by sampling eight nuclear loci and 22 individuals, with additional individuals from related species, using gene capture and Illumina sequencing...
December 2, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27919803/germ-cell-proliferation-and-cluster-behavior-in-ovarioles-of-sialis-flavilatera-megaloptera-sialidae-during-larval-growth
#16
Ralph Rübsam, Jürgen Büning
Telotrophic meroistic insect ovaries are assigned to four different types. The Sialis type is found in Sialidae (Megaloptera), Raphidioptera and a coleopteran subgroup (Myxophaga: Hydroscaphidae). King and Büning (1985) proposed a hypothetical model for the development of this ovariole type, a detailed description of ovarian development in Sialis was missing so far. Using light and electron microscopy, we investigated developing ovaries of Sialis flavilatera starting in the 10(th) month of the biennial larval phase until adulthood...
December 2, 2016: Arthropod Structure & Development
https://www.readbyqxmd.com/read/27919758/the-chemokinome-superfamily-in-channel-catfish-i-cxc-subfamily-and-their-involvement-in-disease-defense-and-hypoxia-responses
#17
Qiang Fu, Qifan Zeng, Yun Li, Yujia Yang, Chao Li, Shikai Liu, Tao Zhou, Ning Li, Jun Yao, Chen Jiang, Daoji Li, Zhanjiang Liu
Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. They are defined by the presence of four conserved cysteine residues and are divided into four subfamilies depending on the arrangement of the first two conserved cysteines residues: CXC, CC, C and CX3C. In this study, a complete set of 17 CXC chemokine ligand (CXCL) genes was systematically identified and characterized from channel catfish genome through data mining of existing genomic resources...
December 2, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27919705/the-complete-mitochondrial-genome-of-thitarodes-sejilaensis-lepidoptera-hepialidae-a-host-insect-of-ophiocordyceps-sinensis-and-its-implication-in-taxonomic-revision-of-hepialusadopted-in-china
#18
Zhiwen Zou, Qiang Min, Shiyu Cheng, Tianrong Xin, Bin Xia
The mitochondrial genome is widely used for phylogenetic analyses and evolutionary biology. The complete mitochondrial genome of Thitarodes sejilaensis (Lepidoptera: Hepialidae) was sequenced and analyzed in this study. This mitogenome is a typical circular molecule of 15,290bp, with the gene content, orientation and order identical to other insects in the family Hepialidae. The genome nucleotide composition is heavily biased towards As and Ts, accounting for 80.87% of total nucleotide content. The major strand shows a positive AT-skew and negative GC-skew...
December 2, 2016: Gene
https://www.readbyqxmd.com/read/27919272/enhanced-lipid-and-biomass-production-by-a-newly-isolated-and-identified-marine-microalga
#19
Mouna Dammak, Sandra Mareike Haase, Ramzi Miladi, Faten Ben Amor, Mohamed Barkallah, David Gosset, Chantal Pichon, Bernhard Huchzermeyer, Imen Fendri, Michel Denis, Slim Abdelkafi
BACKGROUND: The increasing demand for microalgae lipids as an alternative to fish has encouraged researchers to explore oleaginous microalgae for food uses. In this context, optimization of growth and lipid production by the marine oleaginous V2-strain-microalgae is of great interest as it contains large amounts of mono-unsaturated (MUFAs) and poly-unsaturated fatty acids (PUFAs). METHODS: In this study, the isolated V2 strain was identified based on 23S rRNA gene...
December 5, 2016: Lipids in Health and Disease
https://www.readbyqxmd.com/read/27918626/evolutionary-origins-of-abnormally-large-shoot-sodium-accumulation-in-nonsaline-environments-within-the-caryophyllales
#20
Philip J White, Helen C Bowen, Martin R Broadley, Hamed A El-Serehy, Konrad Neugebauer, Anna Taylor, Jacqueline A Thompson, Gladys Wright
The prevalence of sodium (Na)-'hyperaccumulator' species, which exhibit abnormally large shoot sodium concentrations ([Na]shoot ) when grown in nonsaline environments, was investigated among angiosperms in general and within the Caryophyllales order in particular. Shoot Na concentrations were determined in 334 angiosperm species, representing 35 orders, grown hydroponically in a nonsaline solution. Many Caryophyllales species exhibited abnormally large [Na]shoot when grown hydroponically in a nonsaline solution...
December 5, 2016: New Phytologist
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