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https://www.readbyqxmd.com/read/28445833/phytochrome-diversification-in-cyanobacteria-and-eukaryotic-algae
#1
REVIEW
Nathan C Rockwell, J Clark Lagarias
Phytochromes control almost every aspect of plant biology, including germination, growth, development, and flowering, in response to red and far-red light. These photoreceptors thus hold considerable promise for engineering crop plant responses to light. Recently, structural research has shed new light on how phytochromes work. Genomic and transcriptomic studies have improved our understanding of phytochrome loss, retention, and diversification during evolution. We are also beginning to understand phytochrome function in cyanobacteria and eukaryotic algae...
April 22, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#2
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28444928/antiinflammatory-activity-of-cinnamon-cinnamomum-zeylanicum-bark-essential-oil-in-a-human-skin-disease-model
#3
Xuesheng Han, Tory L Parker
The effect of cinnamon (Cinnamomum zeylanicum) bark essential oil (CBEO) on human skin cells has not been elucidated. Therefore, we investigated the activity of a commercially available CBEO in a validated human dermal fibroblast system, a model of chronic inflammation and fibrosis. We first evaluated the impact of CBEO on 17 protein biomarkers that play critical roles in inflammation and tissue remodeling. The impact of CBEO on genome-wide gene expression was also evaluated. CBEO showed strong anti-proliferative effects on skin cells and significantly inhibited the production of several inflammatory biomarkers, including vascular cell adhesion molecule-1, intercellular cell adhesion molecule-1, monocyte chemoattractant protein-1, interferon gamma-induced protein 10, interferon-inducible T-cell alpha chemoattractant, and monokine induced by gamma interferon...
April 26, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/28444740/chronic-lymphocytic-leukaemia-genomics-and-the-precision-medicine-era
#4
REVIEW
Hussein Ghamlouch, Florence Nguyen-Khac, Olivier A Bernard
Massive genomic analyses have underscored the diversity of chronic lymphocytic leukaemia (CLL) between patients. Genetic heterogeneity of tumour clones within a patient may fuel tumour evolution. Several recurrently deregulated intra-cellular pathways are candidates for targeted therapies that are very promising and are dramatically changing clinical patients' perspectives. In this review we present an overview of the genetic and epigenetic features of CLL and their clinical and biological implications.
April 25, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28444381/evidence-for-very-recent-positive-selection-in-mongolians
#5
Kazuhiro Nakayama, Jun Ohashi, Kazuhisa Watanabe, Lkagvasuren Munkhtulga, Sadahiko Iwamoto
Mongols, the founders of the largest continental empire in history, successfully adapted to the harsh environments of Inner Asia through nomadic pastoralism. Considerable interest exists in ascertaining whether genetic adaptation also contributed to the Mongols' success, and dissecting the genome diversity of present-day populations in Mongolia can help address this question. To this end, we determined the genotypes of nearly 2.4 million single nucleotide polymorphisms (SNPs) of 96 unrelated Mongolian individuals in Ulaanbaatar city, and performed genome-wide scans for population-specific positive selection...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444293/regulation-of-hematopoiesis-and-immune-responses-by-long-noncoding-rnas
#6
Wooseok Seo, Ichiro Taniuchi
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of noncoding RNAs...
April 22, 2017: International Immunology
https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#7
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28443631/a-peripheral-epigenetic-signature-of-immune-system-genes-is-linked-to-neocortical-thickness-and-memory
#8
Virginie Freytag, Tania Carrillo-Roa, Annette Milnik, Philipp G Sämann, Vanja Vukojevic, David Coynel, Philippe Demougin, Tobias Egli, Leo Gschwind, Frank Jessen, Eva Loos, Wolfgang Maier, Steffi G Riedel-Heller, Martin Scherer, Christian Vogler, Michael Wagner, Elisabeth B Binder, Dominique J-F de Quervain, Andreas Papassotiropoulos
Increasing age is tightly linked to decreased thickness of the human neocortex. The biological mechanisms that mediate this effect are hitherto unknown. The DNA methylome, as part of the epigenome, contributes significantly to age-related phenotypic changes. Here, we identify an epigenetic signature that is associated with cortical thickness (P=3.86 × 10(-8)) and memory performance in 533 healthy young adults. The epigenetic effect on cortical thickness was replicated in a sample comprising 596 participants with major depressive disorder and healthy controls...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28443625/genome-wide-meta-analysis-of-241-258-adults-accounting-for-smoking-behaviour-identifies-novel-loci-for-obesity-traits
#9
Anne E Justice, Thomas W Winkler, Mary F Feitosa, Misa Graff, Virginia A Fisher, Kristin Young, Llilda Barata, Xuan Deng, Jacek Czajkowski, David Hadley, Julius S Ngwa, Tarunveer S Ahluwalia, Audrey Y Chu, Nancy L Heard-Costa, Elise Lim, Jeremiah Perez, John D Eicher, Zoltán Kutalik, Luting Xue, Anubha Mahajan, Frida Renström, Joseph Wu, Qibin Qi, Shafqat Ahmad, Tamuno Alfred, Najaf Amin, Lawrence F Bielak, Amelie Bonnefond, Jennifer Bragg, Gemma Cadby, Martina Chittani, Scott Coggeshall, Tanguy Corre, Nese Direk, Joel Eriksson, Krista Fischer, Mathias Gorski, Marie Neergaard Harder, Momoko Horikoshi, Tao Huang, Jennifer E Huffman, Anne U Jackson, Johanne Marie Justesen, Stavroula Kanoni, Leena Kinnunen, Marcus E Kleber, Pirjo Komulainen, Meena Kumari, Unhee Lim, Jian'an Luan, Leo-Pekka Lyytikäinen, Massimo Mangino, Ani Manichaikul, Jonathan Marten, Rita P S Middelberg, Martina Müller-Nurasyid, Pau Navarro, Louis Pérusse, Natalia Pervjakova, Cinzia Sarti, Albert Vernon Smith, Jennifer A Smith, Alena Stančáková, Rona J Strawbridge, Heather M Stringham, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Stella Trompet, Sander W van der Laan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Sailaja L Vedantam, Niek Verweij, Jacqueline M Vink, Veronique Vitart, Ying Wu, Loic Yengo, Weihua Zhang, Jing Hua Zhao, Martina E Zimmermann, Niha Zubair, Gonçalo R Abecasis, Linda S Adair, Saima Afaq, Uzma Afzal, Stephan J L Bakker, Traci M Bartz, John Beilby, Richard N Bergman, Sven Bergmann, Reiner Biffar, John Blangero, Eric Boerwinkle, Lori L Bonnycastle, Erwin Bottinger, Daniele Braga, Brendan M Buckley, Steve Buyske, Harry Campbell, John C Chambers, Francis S Collins, Joanne E Curran, Gert J de Borst, Anton J M de Craen, Eco J C de Geus, George Dedoussis, Graciela E Delgado, Hester M den Ruijter, Gudny Eiriksdottir, Anna L Eriksson, Tõnu Esko, Jessica D Faul, Ian Ford, Terrence Forrester, Karl Gertow, Bruna Gigante, Nicola Glorioso, Jian Gong, Harald Grallert, Tanja B Grammer, Niels Grarup, Saskia Haitjema, Göran Hallmans, Anders Hamsten, Torben Hansen, Tamara B Harris, Catharina A Hartman, Maija Hassinen, Nicholas D Hastie, Andrew C Heath, Dena Hernandez, Lucia Hindorff, Lynne J Hocking, Mette Hollensted, Oddgeir L Holmen, Georg Homuth, Jouke Jan Hottenga, Jie Huang, Joseph Hung, Nina Hutri-Kähönen, Erik Ingelsson, Alan L James, John-Olov Jansson, Marjo-Riitta Jarvelin, Min A Jhun, Marit E Jørgensen, Markus Juonala, Mika Kähönen, Magnus Karlsson, Heikki A Koistinen, Ivana Kolcic, Genovefa Kolovou, Charles Kooperberg, Bernhard K Krämer, Johanna Kuusisto, Kirsti Kvaløy, Timo A Lakka, Claudia Langenberg, Lenore J Launer, Karin Leander, Nanette R Lee, Lars Lind, Cecilia M Lindgren, Allan Linneberg, Stephane Lobbens, Marie Loh, Mattias Lorentzon, Robert Luben, Gitta Lubke, Anja Ludolph-Donislawski, Sara Lupoli, Pamela A F Madden, Reija Männikkö, Pedro Marques-Vidal, Nicholas G Martin, Colin A McKenzie, Barbara McKnight, Dan Mellström, Cristina Menni, Grant W Montgomery, Aw Bill Musk, Narisu Narisu, Matthias Nauck, Ilja M Nolte, Albertine J Oldehinkel, Matthias Olden, Ken K Ong, Sandosh Padmanabhan, Patricia A Peyser, Charlotta Pisinger, David J Porteous, Olli T Raitakari, Tuomo Rankinen, D C Rao, Laura J Rasmussen-Torvik, Rajesh Rawal, Treva Rice, Paul M Ridker, Lynda M Rose, Stephanie A Bien, Igor Rudan, Serena Sanna, Mark A Sarzynski, Naveed Sattar, Kai Savonen, David Schlessinger, Salome Scholtens, Claudia Schurmann, Robert A Scott, Bengt Sennblad, Marten A Siemelink, Günther Silbernagel, P Eline Slagboom, Harold Snieder, Jan A Staessen, David J Stott, Morris A Swertz, Amy J Swift, Kent D Taylor, Bamidele O Tayo, Barbara Thorand, Dorothee Thuillier, Jaakko Tuomilehto, Andre G Uitterlinden, Liesbeth Vandenput, Marie-Claude Vohl, Henry Völzke, Judith M Vonk, Gérard Waeber, Melanie Waldenberger, R G J Westendorp, Sarah Wild, Gonneke Willemsen, Bruce H R Wolffenbuttel, Andrew Wong, Alan F Wright, Wei Zhao, M Carola Zillikens, Damiano Baldassarre, Beverley Balkau, Stefania Bandinelli, Carsten A Böger, Dorret I Boomsma, Claude Bouchard, Marcel Bruinenberg, Daniel I Chasman, Yii-DerIda Chen, Peter S Chines, Richard S Cooper, Francesco Cucca, Daniele Cusi, Ulf de Faire, Luigi Ferrucci, Paul W Franks, Philippe Froguel, Penny Gordon-Larsen, Hans-Jörgen Grabe, Vilmundur Gudnason, Christopher A Haiman, Caroline Hayward, Kristian Hveem, Andrew D Johnson, J Wouter Jukema, Sharon L R Kardia, Mika Kivimaki, Jaspal S Kooner, Diana Kuh, Markku Laakso, Terho Lehtimäki, Loic Le Marchand, Winfried März, Mark I McCarthy, Andres Metspalu, Andrew P Morris, Claes Ohlsson, Lyle J Palmer, Gerard Pasterkamp, Oluf Pedersen, Annette Peters, Ulrike Peters, Ozren Polasek, Bruce M Psaty, Lu Qi, Rainer Rauramaa, Blair H Smith, Thorkild I A Sørensen, Konstantin Strauch, Henning Tiemeier, Elena Tremoli, Pim van der Harst, Henrik Vestergaard, Peter Vollenweider, Nicholas J Wareham, David R Weir, John B Whitfield, James F Wilson, Jessica Tyrrell, Timothy M Frayling, Inês Barroso, Michael Boehnke, Panagiotis Deloukas, Caroline S Fox, Joel N Hirschhorn, David J Hunter, Tim D Spector, David P Strachan, Cornelia M van Duijn, Iris M Heid, Karen L Mohlke, Jonathan Marchini, Ruth J F Loos, Tuomas O Kilpeläinen, Ching-Ti Liu, Ingrid B Borecki, Kari E North, L Adrienne Cupples
Few genome-wide association studies (GWAS) account for environmental exposures, like smoking, potentially impacting the overall trait variance when investigating the genetic contribution to obesity-related traits. Here, we use GWAS data from 51,080 current smokers and 190,178 nonsmokers (87% European descent) to identify loci influencing BMI and central adiposity, measured as waist circumference and waist-to-hip ratio both adjusted for BMI. We identify 23 novel genetic loci, and 9 loci with convincing evidence of gene-smoking interaction (GxSMK) on obesity-related traits...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28443113/barcode-system-for-genetic-identification-of-soybean-glycine-max-l-merrill-cultivars-using-indel-markers-specific-to-dense-variation-blocks
#10
Hwang-Bae Sohn, Su-Jeong Kim, Tae-Young Hwang, Hyang-Mi Park, Yu-Young Lee, Kesavan Markkandan, Dongwoo Lee, Sunghoon Lee, Su-Young Hong, Yun-Ho Song, Bon-Cheol Koo, Yul-Ho Kim
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28442708/the-complete-12%C3%A2-mb-genome-and-transcriptome-of-nonomuraea-gerenzanensis-with-new-insights-into-its-duplicated-magic-rna-polymerase
#11
Valeria D'Argenio, Mauro Petrillo, Daniela Pasanisi, Caterina Pagliarulo, Roberta Colicchio, Adelfia Talà, Maria Stella de Biase, Mario Zanfardino, Emanuela Scolamiero, Chiara Pagliuca, Antonio Gaballo, Annunziata Gaetana Cicatiello, Piergiuseppe Cantiello, Irene Postiglione, Barbara Naso, Angelo Boccia, Miriana Durante, Luca Cozzuto, Paola Salvatore, Giovanni Paolella, Francesco Salvatore, Pietro Alifano
In contrast to the widely accepted consensus of the existence of a single RNA polymerase in bacteria, several actinomycetes have been recently shown to possess two forms of RNA polymerases due the to co-existence of two rpoB paralogs in their genome. However, the biological significance of the rpoB duplication is obscure. In this study we have determined the genome sequence of the lipoglycopeptide antibiotic A40926 producer Nonomuraea gerenzanensis ATCC 39727, an actinomycete with a large genome and two rpoB genes, i...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/28442608/unexpected-relations-of-historical-anthrax-strain
#12
M H Antwerpen, J W Sahl, D Birdsell, T Pearson, M J Pearce, C Redmond, H Meyer, P S Keim
In 1998, it was claimed that an 80-year-old glass tube intentionally filled with Bacillus anthracis and embedded in a sugar lump as a WWI biological weapon still contained viable spores. Today, genome sequencing of three colonies isolated in 1998 and subjected to phylogenetic analysis surprisingly identified a well-known B. anthracis reference strain isolated in the United States in 1981, pointing to accidental laboratory contamination.IMPORTANCE Next-generation sequencing and subsequent phylogenetic analyses are useful and reliable tools for the classification of recent and historical samples...
April 25, 2017: MBio
https://www.readbyqxmd.com/read/28442506/genome-wide-association-studies-of-chemotherapeutic-toxicities-genomics-of-inequality
#13
Brandon Mapes, Omar El Charif, Shereen Al-Sawwaf, M Eileen Dolan
With an estimated global population of cancer survivors exceeding 32 million and growing, there is a heightened awareness of the long-term toxicities resulting from cancer treatments and their impact on quality of life. Unexplained heterogeneity in the persistence and development of toxicities, as well as an incomplete understanding of their mechanisms have generated a growing need for the identification of predictive pharmacogenomic markers. Early studies addressing this need used a candidate gene approach; however, over the last decade, unbiased and comprehensive genome-wide association studies (GWAS) have provided markers of phenotypic risk and potential targets to explore the mechanistic and regulatory pathways of biological functions associated with chemotherapeutic toxicity...
April 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28441662/buffalo-leukemia-inhibitory-factor-induces-differentiation-and-dome-like-secondary-structures-in-cos-1-cells
#14
Gurjeet Kaur, Syed Azmal Ali, Shikha Pachauri, Dhruba Malakar, Jai K Kaushik, Ashok K Mohanty, Sudarshan Kumar
This study aimed to understand the molecular characteristics of buffalo leukemia inhibitory factor (BuLIF) and the generation of a stably transfected COS-1_BuLIF cell line for its functional characterization. Cumulus cells, isolated from oocytes, were separated, and total cDNA was prepared. The BuLIF gene was ligated into the cloning vector pJET1.2/blunt and expression vector pAcGFP-N1 which was transfected into COS-1 cells and confirmed by qRT-PCR and Western blot. BuLIF was immunoprecipitated and evaluated through a MTT assay...
April 26, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28441462/transcriptomic-profiling-of-a-chicken-lung-epithelial-cell-line-clec213-reveals-a-mitochondrial-respiratory-chain-activity-boost-during-influenza-virus-infection
#15
Léa Meyer, Olivier Leymarie, Christophe Chevalier, Evelyne Esnault, Marco Moroldo, Bruno Da Costa, Sonia Georgeault, Philippe Roingeard, Bernard Delmas, Pascale Quéré, Ronan Le Goffic
Avian Influenza virus (AIV) is a major concern for the global poultry industry. Since 2012, several countries have reported AIV outbreaks among domestic poultry. These outbreaks had tremendous impact on poultry production and socio-economic repercussion on farmers. In addition, the constant emergence of highly pathogenic AIV also poses a significant risk to human health. In this study, we used a chicken lung epithelial cell line (CLEC213) to gain a better understanding of the molecular consequences of low pathogenic AIV infection in their natural host...
2017: PloS One
https://www.readbyqxmd.com/read/28441456/genome-wide-association-study-of-facial-morphology-reveals-novel-associations-with-frem1-and-park2
#16
Myoung Keun Lee, John R Shaffer, Elizabeth J Leslie, Ekaterina Orlova, Jenna C Carlson, Eleanor Feingold, Mary L Marazita, Seth M Weinberg
Several studies have now shown evidence of association between common genetic variants and quantitative facial traits in humans. The reported associations generally involve simple univariate measures and likely represent only a small fraction of the genetic loci influencing facial morphology. In this study, we applied factor analysis to a set of 276 facial linear distances derived from 3D facial surface images of 2187 unrelated individuals of European ancestry. We retained 23 facial factors, which we then tested for genetic associations using a genome-wide panel of 10,677,593 single nucleotide polymorphisms (SNPs)...
2017: PloS One
https://www.readbyqxmd.com/read/28441401/ancient-genes-establish-stress-induced-mutation-as-a-hallmark-of-cancer
#17
Luis Cisneros, Kimberly J Bussey, Adam J Orr, Milica Miočević, Charles H Lineweaver, Paul Davies
Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes...
2017: PloS One
https://www.readbyqxmd.com/read/28441108/novel-clades-of-the-hu-ihf-superfamily-point-to-unexpected-roles-in-the-eukaryotic-centrosome-chromosome-partitioning-and-biological-conflicts
#18
A Maxwell Burroughs, Gurmeet Kaur, Dapeng Zhang, L Aravind
The HU superfamily of proteins, with a unique DNA-binding mode, has been extensively studied as the primary chromosome-packaging protein of the bacterial superkingdom. Representatives also play a role in DNA-structuring during recombination events and in eukaryotic organellar genome maintenance. However, beyond these well-studied roles, little is understood of the functional diversification of this large superfamily. Using sensitive sequence and structure analysis methods we identify multiple novel clades of the HU superfamily...
April 25, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28441061/precisely-where-are-we-going-charting-the-new-terrain-of-precision-prevention
#19
Karen M Meagher, Michelle L McGowan, Richard A Settersten, Jennifer R Fishman, Eric T Juengst
In addition to genetic data, precision medicine research gathers information about three factors that modulate gene expression: lifestyles, environments, and communities. The relevant research tools-epidemiology, environmental assessment, and socioeconomic analysis-are those of public health sciences rather than molecular biology. Because these methods are designed to support inferences and interventions addressing population health, the aspirations of this research are expanding from individualized treatment toward precision prevention in public health...
April 24, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28441042/aberrantly-expressed-long-noncoding-rnas-in-recurrent-implantation-failure-a-microarray-related-study
#20
Li-Juan Fan, Hong-Jing Han, Jing Guan, Xiao-Wei Zhang, Qing-Hua Cui, Huan Shen, Cheng Shi
Long noncoding RNAs (lncRNAs) are a class of noncoding RNAs longer than 200 nucleotides. They were long regarded as transcription noise for their low expression and non-protein coding features. Recent published reports indicate that lncRNAs are involved in virtually every aspect of human biology. We aimed to profile the endometrial lncRNA expression pattern in women with recurrent implantation failure (RIF) and predict the function of the genes of the dysregulated lncRNA transcripts. Endometrial samples (24) were collected during window of implantation (14 RIF women and 10 women who conceived after embryo transfer)...
April 25, 2017: Systems Biology in Reproductive Medicine
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