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https://www.readbyqxmd.com/read/29679714/population-genetics-phylogenomics-and-hybrid-speciation-of-juglans-in-china-determined-from-whole-chloroplast-genomes-transcriptomes-and-genotyping-by-sequencing-gbs
#1
Peng Zhao, Hui-Juan Zhou, Daniel Potter, Yi-Heng Hu, Xiao-Jia Feng, Meng Dang, Li Feng, Saman Zulfiqar, Wen-Zhe Liu, Guifang Zhao, Keith Woeste
Genomic data are a powerful tool for elucidating the processes involved in the evolution and divergence of species. The speciation and phylogenetic relationships among Chinese Juglans remain unclear. Here, we used results from phylogenomic and population genetic analyses, transcriptomics, Genotyping-By-Sequencing (GBS), and whole chloroplast genomes (Cp genome) data to infer processes of lineage formation among the five native Chinese species of the walnut genus (Juglans, Juglandaceae), a widespread, economically important group...
April 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29679713/molecular-phylogenetics-of-the-genus-costularia-schoeneae-cyperaceae-reveals-multiple-distinct-evolutionary-lineages
#2
Isabel Larridon, Kenneth Bauters, Ilias Semmouri, Jan-Adriaan Viljoen, Christina J Prychid, A Muthama Muasya, Jeremy J Bruhl, Karen L Wilson, Bruno Senterre, Paul Goetghebeur
We investigated the monophyly of Costularia (25 species), a genus of tribe Schoeneae (Cyperaceae) that illustrates a remarkable distribution pattern from southeastern Africa, over Madagascar, the Mascarenes and Seychelles, to Malesia and New Caledonia. A further species, Tetraria borneensis, has been suggested to belong to Costularia. Relationships and divergence times were inferred using an existing four marker phylogeny of Cyperaceae tribe Schoeneae expanded with newly generated sequence data mainly for Costularia s...
April 18, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29679611/control-of-t-cell-effector-functions-by-mirnas
#3
Daniel P Inácio, Tiago Amado, Bruno Silva-Santos, Anita Q Gomes
The differentiation of effector T cells is a tightly regulated process that relies on the selective expression of lineage-defining master regulators that orchestrate unique transcriptional programs, including the production of distinct sets of effector cytokines. miRNAs are post-transcriptional regulators that are now viewed as critical players in these gene expression networks and help defining cell identity and function. This review summarises the role of individual miRNAs in the regulation of the differentiation of effector T cell subsets, including CD4+ T helper cells, cytotoxic CD8+ T cells and innate-like NKT cells...
April 18, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29679610/mutated-mitf-e87r-in-melanoma-enhances-tumor-progression-via-s100a4
#4
Alice Nordlinger, Shani Dror, Abdel Elkahloun, Justine Del Rio, Elisa Stubbs, Tami Golan, Hagar Malcov, Todd D Pricket, Julia C Cronin, Shivang Parikh, Sapir Labes, Laetitia Thomas, Gal Yankovitz, Yuval Tabach, Carmit Levy, Yardena Samuels, Mehdi Khaled
Melanoma, a melanocyte origin neoplasm, is the most lethal type of skin cancer and incidence is increasing. Several familial and somatic mutations have been identified in the gene encoding the melanocyte lineage master regulator, microphthalmia-associated transcription factor (MITF); however, the neoplastic mechanisms of these mutant MITF variants are mostly unknown. Here, by performing unbiased analysis of the transcriptomes in cells expressing mutant MITF, we identified calcium-binding protein S100A4, as a downstream target of MITF-E87R...
April 18, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29679048/disruption-of-hox9-10-11-function-results-in-cellular-level-lineage-infidelity-in-the-kidney
#5
Keri A Drake, Mike Adam, Robert Mahoney, S Steven Potter
Hox genes are important regulators of development. The 39 mammalian Hox genes have considerable functional overlap, greatly confounding their study. In this report, we generated mice with multiple combinations of paralogous and flanking Abd-B Hox gene mutations to investigate functional redundancies in kidney development. The resulting mice developed a number of kidney abnormalities, including hypoplasia, agenesis, and severe cysts, with distinct Hox functions observed in early metanephric kidney formation and nephron progenitor maintenance...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678979/observational-cross-sectional-study-of-nasal-staphylococcal-species-of-medical-students-of-diverse-geographical-origin-prior-to-healthcare-exposure-prevalence-of-scc-mec-fusc-fusb-and-the-arginine-catabolite-mobile-element-acme-in-the-absence-of-selective-antibiotic
#6
Paulo E Budri, Anna C Shore, David C Coleman, Peter M Kinnevey, Hilary Humpreys, Deirdre Fitzgerald-Hughes
OBJECTIVE: The aim of this study was to investigate co-located nasal Staphylococcus aureus and coagulase-negative staphylococci (CoNS) (mainly Staphylococcus epidermidis ), recovered from healthy medical students in their preclinical year, prior to exposure to the healthcare environment, for the carriage of genes and genetic elements common to both species and that may contribute to S. aureus and methicillin-resistant S. aureus (MRSA) evolution. DESIGN: Prospective observational cross-sectional study...
April 20, 2018: BMJ Open
https://www.readbyqxmd.com/read/29678948/an-rnai-screen-identifies-new-genes-required-for-normal-morphogenesis-of-larval-chordotonal-organs
#7
Abeer Hassan, Yael Timerman, Rana Hamdan, Nitzan Sela, Adel Avetisyan, Naomi Halachmi, Adi Salzberg
The proprioceptive chordotonal organs (ChO) of a fly larva respond to mechanical stimuli generated by muscle contractions and consequent deformations of the cuticle. The ability of the ChO to sense the relative displacement of its epidermal attachment sites likely depends on the correct mechanical properties of the accessory (cap and ligament) and attachment cells that connect the sensory unit (neuron and scolopale cell) to the cuticle. The genetic programs dictating the development of ChO cells with unique morphologies and mechanical properties are largely unknown...
April 20, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29678917/genomic-inference-of-recombination-mediated-evolution-in-xanthomonas-euvesicatoria-and-x-perforans
#8
Mustafa O Jibrin, Neha Potnis, Sujan Timilsina, Gerald V Minsavage, Gary E Vallad, Pamela D Roberts, Jeffrey B Jones, Erica M Goss
Recombination is a major driver of evolution in bacterial populations because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of plant bacterial pathogens are typically associated with colonization of novel hosts and emergence of new diseases. Here, we show that recombination between evolutionarily and phenotypically distinct plant pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. X. euvesicatoria ( Xe ) and X...
April 20, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29678836/tumor-suppressor-bap1-is-essential-for-thymic-development-and-proliferative-responses-of-t-lymphocytes
#9
Teresita L Arenzana, Steve Lianoglou, Akiko Seki, Celine Eidenschenk, Tommy Cheung, Dhaya Seshasayee, Thijs Hagenbeek, Arivazhagan Sambandam, Rajkumar Noubade, Ivan Peng, Justin Lesch, Jason DeVoss, Xiumin Wu, Wyne P Lee, Patrick Caplazi, Joshua Webster, Jinfeng Liu, Victoria C Pham, David Arnott, Jennie R Lill, Zora Modrusan, Anwesha Dey, Sascha Rutz
Loss of function of the nuclear deubiquitinating enzyme BRCA1-associated protein-1 (BAP1) is associated with a wide spectrum of cancers. We report that tamoxifen-induced BAP1 deletion in adult mice resulted in severe thymic atrophy. BAP1 was critical for T cell development at several stages. In the thymus, BAP1 was required for progression through the pre-T cell receptor checkpoint. Peripheral T cells lacking BAP1 demonstrated a defect in homeostatic and antigen-driven expansion. Deletion of BAP1 resulted in suppression of E2F target genes and defects in cell cycle progression, which was dependent on the catalytic activity of BAP1, but did not require its interaction with host cell factor-1 (HCF-1)...
April 20, 2018: Science Immunology
https://www.readbyqxmd.com/read/29678829/draft-genome-sequence-of-camellia-sinensis-var-sinensis-provides-insights-into-the-evolution-of-the-tea-genome-and-tea-quality
#10
Chaoling Wei, Hua Yang, Songbo Wang, Jian Zhao, Chun Liu, Liping Gao, Enhua Xia, Ying Lu, Yuling Tai, Guangbiao She, Jun Sun, Haisheng Cao, Wei Tong, Qiang Gao, Yeyun Li, Weiwei Deng, Xiaolan Jiang, Wenzhao Wang, Qi Chen, Shihua Zhang, Haijing Li, Junlan Wu, Ping Wang, Penghui Li, Chengying Shi, Fengya Zheng, Jianbo Jian, Bei Huang, Dai Shan, Mingming Shi, Congbing Fang, Yi Yue, Fangdong Li, Daxiang Li, Shu Wei, Bin Han, Changjun Jiang, Ye Yin, Tao Xia, Zhengzhu Zhang, Jeffrey L Bennetzen, Shancen Zhao, Xiaochun Wan
Tea, one of the world's most important beverage crops, provides numerous secondary metabolites that account for its rich taste and health benefits. Here we present a high-quality sequence of the genome of tea, Camellia sinensis var. sinensis (CSS), using both Illumina and PacBio sequencing technologies. At least 64% of the 3.1-Gb genome assembly consists of repetitive sequences, and the rest yields 33,932 high-confidence predictions of encoded proteins. Divergence between two major lineages, CSS and Camellia sinensis var...
April 20, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29678646/inferring-spatial-patterns-and-drivers-of-population-divergence-of-neolitsea-sericea-lauraceae-based-on-molecular-phylogeography-and-landscape-genomics
#11
Ya-Nan Cao, Ian J Wang, Lu-Yao Chen, Yan-Qian Ding, Lu-Xian Liu, Ying-Xiong Qiu
The relative roles of geography, climate and ecology in driving population divergence and (incipient) speciation has so far been largely neglected in studies addressing the evolution of East Asia's island flora. Here, we employed chloroplast and ribosomal DNA sequences and restriction site-associated DNA sequencing (RADseq) loci to investigate the phylogeography and drivers of population divergence of Neolitsea sericea. These data sets support the subdivision of N. sericea populations into the Southern and Northern lineages across the 'Tokara gap'...
April 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29678645/gene-tree-discordance-and-coalescent-methods-support-ancient-intergeneric-hybridisation-between-dasymaschalon-and-friesodielsia-annonaceae
#12
Xing Guo, Daniel C Thomas, Richard M K Saunders
Although hybridisation between closely related species is common and known to be important in plant evolution, hybridisation at the generic level or above is comparatively rare. We address ancient intergeneric hybridisation in the early-divergent angiosperm family Annonaceae by phylogenetic reconstruction, divergence time estimation and coalescent simulation of the genus Dasymaschalon using a multi-locus approach based on molecular data from five chloroplast (matK, psbA-trnH, ndhF, rbcL, and trnL-F) and five nuclear (ITS, ETS, AP3, PhyA, and PhyC) DNA markers...
April 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29678644/a-revised-phylogeny-of-macropathine-cave-crickets-orthoptera-rhaphidophoridae-uncovers-a-paraphyletic-australian-fauna
#13
Perry G Beasley-Hall, Simon M Tierney, Phillip Weinstein, Andrew D Austin
Australian cave crickets are members of the subfamily Macropathinae (Orthoptera: Rhaphidophoridae). The subfamily is thought to have originated prior to the tectonic separation of the supercontinent Gondwana based on distributions of extant lineages and molecular phylogenetic evidence, although the Australian fauna have been underrepresented in previous studies. The current study augments existing multigene data (using 12S, 16S, and 28S rRNA genes) to investigate the placement of the Australian representatives within the Macropathinae and to assess divergence dates of select clades...
April 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29678571/the-transcription-factor-mef2a-plays-a-key-role-in-the-differentiation-maturation-of-rat-neural-stem-cells-into-neurons
#14
Bangfu Zhu, Ruth E Carmichael, Luis Solabre Valois, Kevin A Wilkinson, Jeremy M Henley
Neural stem cells (NSCs) are self-renewing multipotent stem cells that can be proliferated in vitro and differentiated into neuronal and/or glial lineages, making them an ideal model to study the processes involved in neuronal differentiation. Here we have used NSCs to investigate the role of the transcription factor MEF2A in neuronal differentiation and development in vitro. We show that although MEF2A is present in undifferentiated NSCs, following differentiation it is expressed at significantly higher levels in a subset of neuronal compared to non-neuronal cells...
April 17, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29678445/spatial-patterns-of-gene-expression-are-unveiled-in-the-chick-primitive-streak-by-ordering-single-cell-transcriptomes
#15
Katie L Vermillion, Rhonda Bacher, Alex P Tannenbaum, Scott Swanson, Peng Jiang, Li-Fang Chu, Ron Stewart, James A Thomson, David T Vereide
During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos...
April 17, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29678226/multispectral-fluorescence-activated-cell-sorting-of-b-and-t-cell-subpopulations-from-equine-peripheral-blood
#16
Joy E Tomlinson, Bettina Wagner, M Julia B Felippe, Gerlinde R Van de Walle
Immune phenotyping of equine peripheral blood mononuclear cells (PBMC) is commonly described by single or double marker labeling, which limits complex phenotypic descriptions and subpopulation identification. Our objective was to develop a new multispectral flow cytometry protocol to identify and sort equine lymphocyte subpopulations using commercially available, pre-conjugated monoclonal antibodies to cell surface markers. Two clones of anti-equine CD8 (CVS8 and CVS21) were compared in combination with CD3...
May 2018: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29678151/analysis-of-human-es-cell-differentiation-establishes-that-the-dominant-isoforms-of-the-lncrnas-rmst-and-firre-are-circular
#17
Osagie G Izuogu, Abd A Alhasan, Carla Mellough, Joseph Collin, Richard Gallon, Jonathon Hyslop, Francesco K Mastrorosa, Ingrid Ehrmann, Majlinda Lako, David J Elliott, Mauro Santibanez-Koref, Michael S Jackson
BACKGROUND: Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. RESULTS: A transcriptome-wide increase in circRNA expression, size, and exon count was observed, with circRNA levels reaching a plateau by day 45...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29678149/comparative-mitochondrial-genomics-of-cryptophyte-algae-gene-shuffling-and-dynamic-mobile-genetic-elements
#18
Jong Im Kim, Hwan Su Yoon, Gangman Yi, Woongghi Shin, John M Archibald
BACKGROUND: Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS: To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax...
April 20, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29678141/evolving-in-the-highlands-the-case-of-the-neotropical-lerma-live-bearing-poeciliopsis-infans-woolman-1894-cyprinodontiformes-poeciliidae-in-central-mexico
#19
Rosa Gabriela Beltrán-López, Omar Domínguez-Domínguez, Rodolfo Pérez-Rodríguez, Kyle Piller, Ignacio Doadrio
BACKGROUND: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7...
April 20, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29677702/is-the-pelvis-sexually-dimorphic-in-turtles
#20
Gerardo A Cordero
Variation in the pelvis is intrinsically linked to life history evolution. This is perhaps best exemplified by sexually dimorphic pelvic variation in bipedal primates. Yet, whether this trend is applicable to other taxa is unclear. Using turtle anatomy as a model, I tested the hypothesis that the pelvis is also sexually dimorphic in egg-laying tetrapods. I sampled a natural turtle population with female-biased sexual size dimorphism (i.e. larger females). I show that the area of the egg canal (pelvic aperture) is greater in females...
April 20, 2018: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
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