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https://www.readbyqxmd.com/read/28108990/geographic-heterogeneity-in-the-prevalence-of-human-papillomavirus-in-head-and-neck-cancer
#1
Devasena Anantharaman, Behnoush Abedi-Ardekani, Daniel C Beachler, Tarik Gheit, Andrew F Olshan, Kathy Wisniewski, Victor Wunsch-Filho, Tatiana N Toporcov, Eloiza H Tajara, José Eduardo Levi, Raquel A Moyses, Stefania Boccia, Gabriella Cadoni, Guido Rindi, Wolfgang Ahrens, Franco Merletti, David I Conway, Sylvia Wright, Christine Carreira, Helene Renard, Priscilia Chopard, Sandrine McKay-Chopin, Ghislaine Scelo, Massimo Tommasino, Paul Brennan, Gypsyamber D'Souza
Human papillomavirus (HPV) causes oropharyngeal squamous cell carcinoma (OPSCC), although strongly divergent results have been reported regarding the prevalence of HPV16 in different countries, whether this represents important differences in etiology remains unclear. Applying rigorous protocols for sample processing, we centrally evaluated 1420 head and neck tumors (533 oropharynx, 395 oral cavity and 482 larynx) from studies conducted in the US, Europe and Brazil for mucosal HPV DNA and p16(INK4a) expression to evaluate regional heterogeneity in the proportion of HPV16-associated OPSCC and other head and neck cancer, and to assess covariates associated with the risk of HPV16-positive OPSCC...
January 20, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28106918/divergent-cytosine-dna-methylation-patterns-in-single-cell-soybean-root-hairs
#2
Md Shakhawat Hossain, Taiji Kawakatsu, Kyung Do Kim, Zhang Ning, Cuong T Nguyen, Saad M Khan, Josef M Batek, Trupti Joshi, Jeremy Schmutz, Jane Grimwood, Robert J Schmitz, Dong Xu, Scott A Jackson, Joseph R Ecker, Gary Stacey
Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress...
January 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#3
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28104799/muscles-innervated-by-a-single-motor-neuron-exhibit-divergent-synaptic-properties-on-multiple-time-scales
#4
Dawn M Blitz, Amy E Pritchard, John K Latimer, Andrew T Wakefield
Adaptive changes in the output of neural circuits underlying rhythmic behaviors are relayed to muscles via motor neuron activity. Pre- and postsynaptic properties of neuromuscular junctions can impact the transformation from motor neuron activity to muscle response. Further, synaptic plasticity occurring on the time scale of inter-spike intervals can differ between multiple muscles innervated by the same motor neuron. In rhythmic behaviors, motor neuron bursts can elicit additional synaptic plasticity. However, it is unknown if plasticity regulated by the longer time scale of inter-burst intervals also differs between synapses from the same neuron, and whether any such distinctions occur across a physiological activity range...
January 19, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28104747/the-goddard-and-saturn-genes-are-essential-for-drosophila-male-fertility-and-may-have-arisen-de-novo
#5
Anna M Gubala, Jonathan F Schmitz, Michael J Kearns, Tery T Vinh, Erich Bornberg-Bauer, Mariana F Wolfner, Geoffrey D Findlay
New genes arise through a variety of mechanisms, including the duplication of existing genes and the de novo birth of genes from non-coding DNA sequences. While there are numerous examples of duplicated genes with important functional roles, the functions of de novo genes remain largely unexplored. Many newly evolved genes are expressed in the male reproductive tract, suggesting that these evolutionary innovations may provide advantages to males experiencing sexual selection. Using testis-specific RNA interference, we screened 11 putative de novo genes in Drosophila melanogaster for effects on male fertility and identified two, goddard and saturn, that are essential for spermatogenesis and sperm function...
January 19, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28103802/proteomics-informed-by-transcriptomics-for-characterising-active-transposable-elements-and-genome-annotation-in-aedes-aegypti
#6
Kevin Maringer, Amjad Yousuf, Kate J Heesom, Jun Fan, David Lee, Ana Fernandez-Sesma, Conrad Bessant, David A Matthews, Andrew D Davidson
BACKGROUND: Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step in the transmission of vector-borne viruses. However, up until now it has not been possible to study the overall proteome derived from an organism's mobile genetic elements, partly due to the highly divergent nature of TEs...
January 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28100781/biogenesis-of-a-mitochondrial-outer-membrane-protein-in-trypanosoma-brucei-targeting-signal-and-dependence-on-an-unique-biogenesis-factor
#7
Julia Bruggisser, Sandro K Aumlser, Jan Mani, Andre Schneider
The mitochondrial outer membrane (OM) contains single and multiple membrane-spanning proteins which need to contain signals that ensure correct targeting and insertion into the OM. The biogenesis of such proteins has so far essentially only been studied in yeast and related organisms. Here we show that POMP10, an OM protein of the early diverging protozoan Trypanosoma brucei, is signal-anchored. Transgenic cells expressing variants of POMP10 fused to GFP demonstrate that the N-terminal membrane-spanning domain flanked by a few positively charged or neutral residues is both necessary and sufficient for mitochondrial targeting...
January 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28100025/sex-biased-transcriptome-divergence-along-a-latitudinal-gradient
#8
Scott L Allen, Russell Bonduriansky, Carla Sgro, Stephen F Chenoweth
Although not all sex-dependent gene expression is adaptive, it is likely an important genomic mechanism that allows each sex to independently adapt to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex-differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28100017/subspecies-delineation-amid-phenotypic-geographic-and-genetic-discordance-in-a-songbird
#9
Jennifer Walsh, Irby J Lovette, Virginia Winder, Chris S Elphick, Brian J Olsen, W Gregory Shriver, Adrienne I Kovach
Understanding the processes that drive divergence within and among species is a long-standing goal in evolutionary biology. Traditional approaches to assessing differentiation rely on phenotypes to identify intra- and interspecific variation, but many species express subtle morphological gradients in which boundaries among forms are unclear. This intraspecific variation may be driven by differential adaptation to local conditions and may thereby reflect the evolutionary potential within a species. Here, we combine genetic and morphological data to evaluate intraspecific variation within the Nelson's (Ammodramus nelsoni) and saltmarsh (A...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099447/genome-wide-immune-modulation-of-tlr3-mediated-inflammation-in-intestinal-epithelial-cells-differs-between-single-and-multi-strain-probiotic-combination
#10
Chad W MacPherson, Padmaja Shastri, Olivier Mathieu, Thomas A Tompkins, Pierre Burguière
Genome-wide transcriptional analysis in intestinal epithelial cells (IEC) can aid in elucidating the impact of single versus multi-strain probiotic combinations on immunological and cellular mechanisms of action. In this study we used human expression microarray chips in an in vitro intestinal epithelial cell model to investigate the impact of three probiotic bacteria, Lactobacillus helveticus R0052 (Lh-R0052), Bifidobacterium longum subsp. infantis R0033 (Bl-R0033) and Bifidobacterium bifidum R0071 (Bb-R0071) individually and in combination, and of a surface-layer protein (SLP) purified from Lh-R0052, on HT-29 cells' transcriptional profile to poly(I:C)-induced inflammation...
2017: PloS One
https://www.readbyqxmd.com/read/28098160/a-zip6-zip10-heteromer-controls-ncam1-phosphorylation-and-integration-into-focal-adhesion-complexes-during-epithelial-to-mesenchymal-transition
#11
Dylan Brethour, Mohadeseh Mehrabian, Declan Williams, Xinzhu Wang, Farinaz Ghodrati, Sepehr Ehsani, Elizabeth A Rubie, James R Woodgett, Jean Sevalle, Zhengrui Xi, Ekaterina Rogaeva, Gerold Schmitt-Ulms
The prion protein (PrP) evolved from the subbranch of ZIP metal ion transporters comprising ZIPs 5, 6 and 10, raising the prospect that the study of these ZIPs may reveal insights relevant for understanding the function of PrP. Building on data which suggested PrP and ZIP6 are critical during epithelial-to-mesenchymal transition (EMT), we investigated ZIP6 in an EMT paradigm using ZIP6 knockout cells, mass spectrometry and bioinformatic methods. Reminiscent of PrP, ZIP6 levels are five-fold upregulated during EMT and the protein forms a complex with NCAM1...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#12
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28096378/biosynthesis-of-the-microtubule-destabilizing-diterpene-pseudolaric-acid-b-from-golden-larch-involves-an-unusual-diterpene-synthase
#13
Sibongile Mafu, Prema Sambandaswami Karunanithi, Teresa Ann Palazzo, Bronwyn Lee Harrod, Selina Marakana Rodriguez, Iris Natalie Mollhoff, Terrence Edward O'Brien, Shen Tong, Oliver Fiehn, Dean J Tantillo, Jörg Bohlmann, Philipp Zerbe
The diversity of small molecules formed via plant diterpene metabolism offers a rich source of known and potentially new biopharmaceuticals. Among these, the microtubule-destabilizing activity of pseudolaric acid B (PAB) holds promise for new anticancer agents. PAB is found, perhaps uniquely, in the coniferous tree golden larch (Pseudolarix amabilis, Pxa). Here we describe the discovery and mechanistic analysis of golden larch terpene synthase 8 (PxaTPS8), an unusual diterpene synthase (diTPS) that catalyzes the first committed step in PAB biosynthesis...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28095782/genome-scale-transcriptional-study-of-hybrid-effects-and-regulatory-divergence-in-an-f1-hybrid-ruellia-wild-petunias-acanthaceae-and-its-parents
#14
Yongbin Zhuang, Erin A Tripp
BACKGROUND: New combinations of divergent genomes can give rise to novel genetic functions in resulting hybrid progeny. Such functions may yield opportunities for ecological divergence, contributing ultimately to reproductive isolation and evolutionary longevity of nascent hybrid lineages. In plants, the degree to which transgressive genotypes contribute to floral novelty remains a question of key interest. Here, we generated an F1 hybrid plant between the red-flowered Ruellia elegans and yellow flowered R...
January 17, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28095348/immune-transcriptome-reveals-the-mincle-c-type-lectin-receptor-acts-as-a-partial-replacement-for-tlr4-in-lipopolysaccharide-mediated-inflammatory-response-in-barramundi-lates-calcarifer
#15
Emmanuelle Zoccola, Stuart Kellie, Andrew C Barnes
Fish represent the most diverse and abundant extant vertebrate infraclass. They are also one of the earliest divergent phyla with adaptive immunity based on antigen recognition by MHC and immunoglobulin. The aquaculture industry, which currently provides more than half of the fish for human consumption globally, has successfully exploited the adaptive immune system of fish through mass vaccination programs. However, vaccination against highly diverse antigens, mostly carbohydrates, such as capsular polysaccharides and lipopolysaccharide (LPS) is challenging...
January 14, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28095328/an-integrated-proteomic-and-transcriptomic-analysis-of-perivitelline-fluid-proteins-in-a-freshwater-gastropod-laying-aerial-eggs
#16
Huawei Mu, Jin Sun, Horacio Heras, Ka Hou Chu, Jian-Wen Qiu
: Proteins of the egg perivitelline fluid (PVF) that surrounds the embryo are critical for embryonic development in many animals, but little is known about their identities. Using an integrated proteomic and transcriptomic approach, we identified 64 proteins from the PVF of Pomacea maculata - a freshwater snail adopting aerial oviposition. Proteins were classified into eight functional groups: major multifunctional perivitellin subunits, immune response, energy metabolism, protein degradation, oxidation-reduction, signaling and binding, transcription and translation, and others...
January 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28092920/evolutionary-genomics-of-the-cold-adapted-diatom-fragilariopsis-cylindrus
#17
Thomas Mock, Robert P Otillar, Jan Strauss, Mark McMullan, Pirita Paajanen, Jeremy Schmutz, Asaf Salamov, Remo Sanges, Andrew Toseland, Ben J Ward, Andrew E Allen, Christopher L Dupont, Stephan Frickenhaus, Florian Maumus, Alaguraj Veluchamy, Taoyang Wu, Kerrie W Barry, Angela Falciatore, Maria I Ferrante, Antonio E Fortunato, Gernot Glöckner, Ansgar Gruber, Rachel Hipkin, Michael G Janech, Peter G Kroth, Florian Leese, Erika A Lindquist, Barbara R Lyon, Joel Martin, Christoph Mayer, Micaela Parker, Hadi Quesneville, James A Raymond, Christiane Uhlig, Ruben E Valas, Klaus U Valentin, Alexandra Z Worden, E Virginia Armbrust, Matthew D Clark, Chris Bowler, Beverley R Green, Vincent Moulton, Cock van Oosterhout, Igor V Grigoriev
The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms...
January 16, 2017: Nature
https://www.readbyqxmd.com/read/28091568/identification-of-misexpressed-genetic-elements-in-hybrids-between-drosophila-related-species
#18
Hélène Lopez-Maestre, Elias A G Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron, Claudia M A Carareto, Cristina Vieira
Crosses between close species can lead to genomic disorders, often considered to be the cause of hybrid incompatibility, one of the initial steps in the speciation process. How these incompatibilities are established and what are their causes remain unclear. To understand the initiation of hybrid incompatibility, we performed reciprocal crosses between two species of Drosophila (D. mojavensis and D. arizonae) that diverged less than 1 Mya. We performed a genome-wide transcriptomic analysis on ovaries from parental lines and on hybrids from reciprocal crosses...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28087637/retinoic-acid-receptor-regulation-of-epimorphic-and-homeostatic-regeneration-in-the-axolotl
#19
Matthew Nguyen, Pankhuri Singhal, Judith Piet, Sandra J Shefelbine, Malcolm Maden, S Randal Voss, James R Monaghan
Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs...
January 13, 2017: Development
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#20
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
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