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genome organisation

Muhammad Abu-Elmagd, Mourad Assidi, Ashraf Dallol, Abdelbaset Buhmeida, Peter Natesan Pushparaj, Gauthaman Kalamegam, Emad Al-Hamzi, Jerry W Shay, Stephen W Scherer, Ashok Agarwal, Bruce Budowle, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Mohammed Al-Qahtani
The Third International Genomic Medicine Conference (3(rd) IGMC) was organised by the Centre of Excellence in Genomic Medicine Research (CEGMR) at the King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia (KSA). This conference is a continuation of a series of meetings, which began with the first International Genomic Medicine Conference (1(st) IGMC, 2011) followed by the second International Genomic Medicine Conference (2(nd) IGMC, 2013). The 3(rd) IGMC meeting presented as a timely opportunity to bring scientists from across the world to gather, discuss, and exchange recent advances in the field of genomics and genetics in general as well as practical information on using these new technologies in different basic and clinical applications...
October 17, 2016: BMC Genomics
Barbara Maciejewska, Bartosz Roszniowski, Akbar Espaillat, Agata Kęsik-Szeloch, Grazyna Majkowska-Skrobek, Andrew M Kropinski, Yves Briers, Felipe Cava, Rob Lavigne, Zuzanna Drulis-Kawa
Lytic bacteriophages and phage-encoded endolysins (peptidoglycan hydrolases) provide a source for the development of novel antimicrobial strategies. In the present study, we focus on the closely related (96 % DNA sequence identity) environmental myoviruses vB_KpnM_KP15 (KP15) and vB_KpnM_KP27 (KP27) infecting multidrug-resistant Klebsiella pneumoniae and Klebsiella oxytoca strains. Their genome organisation and evolutionary relationship are compared to Enterobacter phage phiEap-3 and Klebsiella phages Matisse and Miro...
October 21, 2016: Applied Microbiology and Biotechnology
Katie N Myers, Giancarlo Barone, Anil Ganesh, Christopher J Staples, Anna E Howard, Ryan D Beveridge, Sarah Maslen, J Mark Skehel, Spencer J Collis
It was recently discovered that vertebrate genomes contain multiple endogenised nucleotide sequences derived from the non-retroviral RNA bornavirus. Strikingly, some of these elements have been evolutionary maintained as open reading frames in host genomes for over 40 million years, suggesting that some endogenised bornavirus-derived elements (EBL) might encode functional proteins. EBLN1 is one such element established through endogenisation of the bornavirus N gene (BDV N). Here, we functionally characterise human EBLN1 as a novel regulator of genome stability...
October 14, 2016: Scientific Reports
Samuel Corless, Nick Gilbert
Disruptions in chromatin structure are necessary for the regulation of eukaryotic genomes, from remodelling of nucleosomes at the base pair level through to large-scale chromatin domains that are hundreds of kilobases in size. RNA polymerase is a powerful motor which, prevented from turning with the tight helical pitch of the DNA, generates over-wound DNA ahead of itself and under-wound DNA behind. Mounting evidence supports a central role for transcription-dependent DNA supercoiling in disrupting chromatin structure at all scales...
2016: Biophysical Reviews
Eric Piver, Audrey Boyer, Julien Gaillard, Anne Bull, Elodie Beaumont, Philippe Roingeard, Jean-Christophe Meunier
OBJECTIVE: HCV particles are associated with very low-density lipoprotein components in chronically infected patients. These hybrid particles, or 'lipo-viro particles' (LVPs), are rich in triglycerides, and contain the viral RNA, the capsid protein, E1E2 envelope glycoproteins and apolipoproteins B and E. However, their specific ultrastructural organisation has yet to be determined. We developed a strategy for the preparation of any viral sample that preserves the native structure of the LVPs, facilitating their precise morphological characterisation...
October 11, 2016: Gut
Ivan Eisler, Frances Flinter, Jo Grey, Suzanne Hutchison, Carole Jackson, Louise Longworth, Rhona MacLeod, Marion McAllister, Alison Metcalfe, Christine Patch, Buddug Cope, Glenn Robert, Emma Rowland, Fiona Ulph
Innovations in clinical genetics have increased diagnosis, treatment and prognosis of inherited genetic conditions (IGCs). This has led to an increased number of families seeking genetic testing and / or genetic counselling and increased the clinical load for genetic counsellors (GCs). Keeping pace with biomedical discoveries, interventions are required to support families to understand, communicate and cope with their Inherited Genetic Condition. The Socio-Psychological Research in Genomics (SPRinG) collaborative have developed a new intervention, based on multi-family discussion groups (MFDGs), to support families affected by IGCs and train GCs in its delivery...
October 10, 2016: Journal of Genetic Counseling
Stephen D Thorpe, Myriam Charpentier
The last decade has seen rapid advances in our understanding of the proteins of the nuclear envelope, which have multiple roles including positioning the nucleus, maintaining its structural organisation, and in events ranging from mitosis and meiosis to chromatin positioning and gene expression. Diverse new and stimulating results relating to nuclear organisation and genome function from across kingdoms were presented in a session stream entitled "Dynamic Organisation of the Nucleus" at this year's Society of Experimental Biology (SEB) meeting in Brighton, UK (July 2016)...
October 7, 2016: Nucleus
Igor E Agranovski, Evgeny V Usachev, Elina Agranovski, Olga V Usacheva
AIMS: A portable bioaerosol monitor is highly demanded technology in many areas including air quality control, occupational exposure assessment and health risk evaluation, environmental studies and, especially, in defence and bio-terrorism applications. Our recent groundwork allowed us to formulate the concept of a portable bioaerosol monitor, which ought to be light, user friendly, reliable and capable of detecting airborne pathogens within 1 -1.5 hours at the spot. METHODS AND RESULTS: Conceptually, the event of bioaerosol concentration burst is determined by triggers, commencing representative air sampling with sequential real-time PCR confirmation of the targeted microorganism presence in the air...
October 6, 2016: Journal of Applied Microbiology
Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to 'jump' around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterised domain organisation. For the past 30 years, model organisms have been used to define L1s as 6-8kb sequences containing a 5'-UTR, two open reading frames working harmoniously in cis, and a 3'-UTR with a polyA tail...
October 3, 2016: Genome Biology and Evolution
Gunnar Völkel, Sebastian Wiese, Karlheinz Holzmann, Johann M Kraus, Fabian Schneider, Matthias Görlach, Hans A Kestler
MOTIVATION: Core service units have become an organisational hallmark in many research institutions world wide. Such service cores provide complex state-of-the-art technologies and expertise to the research community. Typically, a user delivers material or raw data to a core. The core defines work packages for ensuing analysis and returns results back to the user. This core activity can be quite complex and time consuming and usually does not communicate itself to the outside. Naturally, the user is highly interested to follow the progress of a project once handed over to the core unit...
2016: PloS One
Elsie Jacobson, Jo K Perry, David S Long, Mark H Vickers, Justin M O'Sullivan
Immune cells react to a wide range of environments, both chemical and physical. While the former has been extensively studied, there is growing evidence that physical and in particular mechanical forces also affect immune cell behavior and development. In order to elicit a response that affects immune cell behavior or development, environmental signals must often reach the nucleus. Chemical and mechanical signals can initiate signal transduction pathways, but mechanical forces may also have a more direct route to the nucleus, altering nuclear shape via mechanotransduction...
September 27, 2016: Nucleus
Yang Hu, Wenyang Zhou, Jun Ren, Lixiang Dong, Yadong Wang, Shuilin Jin, Liang Cheng
Increasing evidences indicated that function annotation of human genome in molecular level and phenotype level is very important for systematic analysis of genes. In this study, we presented a framework named Gene2Function to annotate Gene Reference into Functions (GeneRIFs), in which each functional description of GeneRIFs could be annotated by a text mining tool Open Biomedical Annotator (OBA), and each Entrez gene could be mapped to Human Genome Organisation Gene Nomenclature Committee (HGNC) gene symbol...
2016: BioMed Research International
Benjamin M Skinner, Emma E P Johnson
Studies of chromosome and genome biology often focus on condensed chromatin in the form of chromosomes and neglect the non-dividing cells. Even when interphase nuclei are considered, they are often then treated as interchangeable round objects. However, different cell types can have very different nuclear shapes, and these shapes have impacts on cellular function; indeed, many pathologies are linked with alterations to nuclear shape. In this review, we describe some of the nuclear morphologies beyond the spherical and ovoid...
September 8, 2016: Chromosoma
Jacques D Ibaba, Mark D Laing, Augustine Gubba
Pepo aphid-borne yellows virus (PABYV) has been proposed as a putative representative of a new species in the genus Polerovirus in the family Luteoviridae. The genomes of two South African (SA) isolates of cucurbit-infecting PABYV were described in this record. Total RNA, extracted from a pattypan (Cucurbita pepo L.) and a baby marrow (C. pepo L.) leaf samples, was subjected to next-generation sequencing (NGS) on the HiSeq Illumina platform. Sanger sequencing was subsequently used to authenticate the integrity of PABYV's genome generated from de novo assembly of the NGS data...
September 13, 2016: Virus Genes
Marcela Rosato, Aleš Kovařík, Ricardo Garilleti, Josep A Rosselló
Genes encoding ribosomal RNA (rDNA) are universal key constituents of eukaryotic genomes, and the nuclear genome harbours hundreds to several thousand copies of each species. Knowledge about the number of rDNA loci and gene copy number provides information for comparative studies of organismal and molecular evolution at various phylogenetic levels. With the exception of seed plants, the range of 45S rDNA locus (encoding 18S, 5.8S and 26S rRNA) and gene copy number variation within key evolutionary plant groups is largely unknown...
2016: PloS One
Salma Jamal, Sonam Arora, Vinod Scaria
BACKGROUND: The dynamic and differential regulation and expression of genes is majorly governed by the complex interactions of a subset of biomolecules in the cell operating at multiple levels starting from genome organisation to protein post-translational regulation. The regulatory layer contributed by the epigenetic layer has been one of the favourite areas of interest recently. This layer of regulation as we know today largely comprises of DNA modifications, histone modifications and noncoding RNA regulation and the interplay between each of these major components...
2016: PloS One
Joëlle Goüy de Bellocq, Jana Těšíková, Yonas Meheretu, Dagmar Čížková, Anna Bryjová, Herwig Leirs, Josef Bryja
Hantaviruses, well-known human pathogens, have only recently been identified on the African continent. Tigray virus (TIGV) was found in Ethiopia in 2012 in a Murinae species, Stenocephalemys albipes, but the genetic data obtained at that time were too limited to correctly assess its phylogenetic position within the hantavirus tree. We used high throughput sequencing to determine the complete genome of TIGV, which showed a typical hantavirus organisation. The large (L), medium (M), and small (S) genome segments were found to be 6532, 3594 and 1908 nucleotides long, respectively, and the 5' and 3' termini for all three segments were predicted to form the panhandle-like structure typical for bunyaviruses...
September 9, 2016: Infection, Genetics and Evolution
Nourdine Hamdane, Michel G Tremblay, Stefan Dillinger, Victor Y Stefanovsky, Attila Németh, Tom Moss
The nucleolus is the site of ribosome biogenesis and forms around the actively transcribed ribosomal RNA (rRNA) genes. However, the nucleolus is also implicated in cell cycle regulation, tumour suppression and chromosome segregation and nucleolar disfunction is linked to a wide range of human diseases. Interestingly, the nucleolus is also required for genome reprogramming and the establishment of heterochromatin in the mammalian embryo. Mammalian oocytes contain a subnuclear structure that is believed to be the precursor of the functional nucleolus, the Nucleolar Precursor Body (NPB)...
September 7, 2016: Gene
Richard Schilsky, Will Davies
The Worldwide Innovative Networking (WIN) consortium is an alliance of academic institutions, pharmaceutical partners, representatives from technology companies and charitable/health payer organisations from across the globe. For the last six years, the consortium's aims have been to foster communication and collaboration between members, encourage dialogue in an open forum, and deliver clinical trial results that improve the care and outcomes of patients with cancer using the latest advances in genomic-based medicine...
2016: Ecancermedicalscience
David Dickerson, Marek Gierliński, Vijender Singh, Etsushi Kitamura, Graeme Ball, Tomoyuki U Tanaka, Tom Owen-Hughes
BACKGROUND: Genomes of eukaryotes exist as chromatin, and it is known that different chromatin states can influence gene regulation. Chromatin is not a static structure, but is known to be dynamic and vary between cells. In order to monitor the organisation of chromatin in live cells we have engineered fluorescent fusion proteins which recognize specific operator sequences to tag pairs of syntenic gene loci. The separation of these loci was then tracked in three dimensions over time using fluorescence microscopy...
2016: BMC Cell Biology
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