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https://www.readbyqxmd.com/read/27910910/genome-wide-characterisation-and-expression-profile-of-the-grapevine-atl-ubiquitin-ligase-family-reveal-biotic-and-abiotic-stress-responsive-and-development-related-members
#1
Pietro Ariani, Alice Regaiolo, Arianna Lovato, Alejandro Giorgetti, Andrea Porceddu, Salvatore Camiolo, Darren Wong, Simone Castellarin, Elodie Vandelle, Annalisa Polverari
The Arabidopsis Tóxicos en Levadura (ATL) protein family is a class of E3 ubiquitin ligases with a characteristic RING-H2 Zn-finger structure that mediates diverse physiological processes and stress responses in plants. We carried out a genome-wide survey of grapevine (Vitis vinifera L.) ATL genes and retrieved 96 sequences containing the canonical ATL RING-H2 domain. We analysed their genomic organisation, gene structure and evolution, protein domains and phylogenetic relationships. Clustering revealed several clades, as already reported in Arabidopsis thaliana and rice (Oryza sativa), with an expanded subgroup of grapevine-specific genes...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27903804/structural-protein-vp2-of-african-horse-sickness-virus-is-not-essential-for-virus-replication-in-vitro
#2
René G P van Gennip, Sandra G P van de Water, Christiaan A Potgieter, Piet A van Rijn
: The Reoviridae family consists of non-enveloped multi-layered viruses with a double stranded RNA genome consisting of 9 to 12 genome segments. The Orbivirus genus of the Reoviridae family contains African horse sickness virus (AHSV), bluetongue virus and epizootic haemorrhagic disease virus causing notifiable diseases and are spread by biting Culicoides species. Here, we used reverse genetics for AHSV to study the role of outer capsid protein VP2 encoded by genome segment 2 (Seg-2)...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27899279/wormbase-parasite-a-comprehensive-resource-for-helminth-genomics
#3
Kevin L Howe, Bruce J Bolt, Myriam Shafie, Paul Kersey, Matthew Berriman
The number of publicly available parasitic worm genome sequences has increased dramatically in the past three years, and research interest in helminth functional genomics is now quickly gathering pace in response to the foundation that has been laid by these collective efforts. A systematic approach to the organisation, curation, analysis and presentation of these data is clearly vital for maximising the utility of these data to researchers. We have developed a portal called WormBase ParaSite (http://parasite...
November 26, 2016: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/27889532/characterisation-of-zbtb46-and-dc-script-znf366-in-rainbow-trout-transcription-factors-potentially-involved-in-dendritic-cell-maturation-and-activation-in-fish
#4
Jun Wang, Tiehui Wang, Ottavia Benedicenti, Catherine Collins, Kaiyu Wang, Christopher J Secombes, Jun Zou
ZBTB46 and DC-SCRIPT/ZNF366 are two zinc finger transcription factors that play important roles in regulating differentiation of dendritic cells in mammals. In this study, the ZBTB46 and DC-SCRIPT/ZNF366 homologues were identified in rainbow trout Oncorhynchus mykiss and their expression analysed in vivo and in vitro. As transcription factors, they are well conserved in sequence, genomic organisation and gene synteny. Their expression was differentially modulated by bacterial and viral PAMPs in the monocyte/macrophage like cell line RTS-11, in primary head kidney (HK) macrophages, and in HK macrophages cultured with IL-4/13A...
November 23, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27883255/genome-wide-association-of-functional-traits-linked-with-campylobacter-jejuni-survival-from-farm-to-fork
#5
Koji Yahara, Guillaume Méric, Aidan J Taylor, Stefan P W de Vries, Susan Murray, Ben Pascoe, Leonardos Mageiros, Alicia Torralbo, Ana Vidal, Anne Ridley, Sho Komukai, Helen Wimalarathna, Alison J Cody, Frances M Colles, Noel McCarthy, David Harris, James E Bray, Keith A Jolley, Martin C J Maiden, Stephen D Bentley, Julian Parkhill, Christopher D Bayliss, Andrew Grant, Duncan Maskell, Xavier Didelot, David J Kelly, Samuel K Sheppard
Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7,343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain...
November 24, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27861577/identifying-causal-genes-at-the-multiple-sclerosis-associated-region-6q23-using-capture-hi-c
#6
Paul Martin, Amanda McGovern, Jonathan Massey, Stefan Schoenfelder, Kate Duffus, Annie Yarwood, Anne Barton, Jane Worthington, Peter Fraser, Stephen Eyre, Gisela Orozco
BACKGROUND: The chromosomal region 6q23 has been found to be associated with multiple sclerosis (MS) predisposition through genome wide association studies (GWAS). There are four independent single nucleotide polymorphisms (SNPs) associated with MS in this region, which spans around 2.5 Mb. Most GWAS variants associated with complex traits, including these four MS associated SNPs, are non-coding and their function is currently unknown. However, GWAS variants have been found to be enriched in enhancers and there is evidence that they may be involved in transcriptional regulation of their distant target genes through long range chromatin looping...
2016: PloS One
https://www.readbyqxmd.com/read/27859262/functional-and-prognostic-significance-of-the-genomic-amplification-of-frizzled-receptor-6-fzd6-in-breast-cancer
#7
Gabriele Corda, Gianluca Sala, Rossano Lattanzio, Manuela Iezzi, Michele Sallese, Giorgia Fragassi, Alessia Lamolinara, Hasan Mirza, Daniela Barcaroli, Sibylle Ermler, Elisabete Silva, Hemad Yasaei, Robert F Newbold, Paola Vagnarelli, Marcella Mottolese, Pier Giorgio Natali, Letizia Perracchio, Jelmar Quist, Anita Grigoriadis, Pierfrancesco Marra, Andrew N Tutt, Mauro Piantelli, Stefano Iacobelli, Vincenzo De Laurenzi, Arturo Sala
Frizzled receptors mediate Wnt ligands' signalling, which is crucially involved in regulating tissue development, differentiation and is often deregulated in cancer. In this study we found that the Wnt receptor frizzled 6 (FZD6) is frequently amplified in breast cancer, with an increased incidence in the triple negative breast cancer (TNBC) subtype. Ablation of FZD6 gene expression in mammary cancer cell lines: a) inhibited motility and invasion b) induced a more symmetric shape of organoid 3D cultures c) inhibited bone and liver metastasis in vivo...
November 9, 2016: Journal of Pathology
https://www.readbyqxmd.com/read/27827988/the-european-classical-swine-fever-virus-database-blueprint-for-a-pathogen-specific-sequence-database-with-integrated-sequence-analysis-tools
#8
Alexander Postel, Stefanie Schmeiser, Bernd Zimmermann, Paul Becher
Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world's largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis...
November 7, 2016: Viruses
https://www.readbyqxmd.com/read/27816910/progressive-and-biased-divergent-evolution-underpins-the-origin-and-diversification-of-peridinin-dinoflagellate-plastids
#9
Richard G Dorrell, Christen M Klinger, Robert J Newby, Erin R Butterfield, Elisabeth Richardson, Joel B Dacks, Christopher J Howe, R Ellen R Nisbet, Chris Bowler
Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organisation of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons...
November 4, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27816794/investigating-the-cell-biology-of-plant-infection-by-the-rice-blast-fungus-magnaporthe-oryzae
#10
REVIEW
Xia Yan, Nicholas J Talbot
Rice blast disease is a major constraint on worldwide rice production and understanding the biology of plant infection is a priority for development of new disease control strategies. Recent advances in live cell imaging, coupled with tractability of both host and pathogen to molecular genetics and genomics, has made the rice blast pathosystem an important model for understanding plant disease. Here we review recent advances in understanding the cell biology of plant infection and, in particular, the remarkable ability of the rice blast fungus to invade plant tissue and manipulate the host plant using a battery of secreted effector proteins...
November 3, 2016: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/27807005/inappropriate-expression-of-the-translation-elongation-factor-1a-disrupts-genome-stability-and-metabolism
#11
Daniel J Tarrant, Mariarita Stirpe, Michelle Rowe, Mark J Howard, Tobias von der Haar, Campbell W Gourlay
The translation elongation factor eEF1A is one of the most abundant proteins found within cells and its role within protein synthesis is well documented. Levels of eEF1A are tightly controlled, with inappropriate expression linked to oncogenesis. However the mechanisms by which increased eEF1A expression alter cell behaviour are unknown. Our analyses in yeast suggest that elevation of eEF1A levels lead to stabilisation of the spindle pole body and changes in nuclear organisation. Elevation of eEF1A2 also leads to altered nuclear morphology in cultured human cells suggesting a conserved role in maintaining genome stability...
November 2, 2016: Journal of Cell Science
https://www.readbyqxmd.com/read/27805827/nrf2-activation-as-a-key-event-triggered-by-skin-sensitisers-the-development-of-the-stable-keratinosens-reporter-gene-assay
#12
REVIEW
Andreas Natsch, Roger Emter
The 21st century paradigm for toxicology and the adverse outcome pathway concept envisage a future toxicology largely based on mechanistic in vitro assays and relying mainly on cellular models. In the skin sensitisation field, this concept was not intuitive at the beginning. Given the high structural diversity of skin sensitising molecules, classical receptor binding as the molecular initiating event in a cell-based assay could be excluded from the start, leaving the question of how cells could sense potential skin sensitising chemicals and be able to differentiate them from non-sensitisers...
October 2016: Alternatives to Laboratory Animals: ATLA
https://www.readbyqxmd.com/read/27797076/resolving-the-genomic-localization-of-the-kollerin-cohesin-loader-complex
#13
Kerstin S Wendt
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27775198/mapping-the-triticum-aestivum-proteome
#14
Owen Duncan, Josua Trösch, Ricarda Fenske, Nicolas L Taylor, A Harvey Millar
Yield and quality improvement of bread wheat (Triticum aestivum) is a focus in efforts to meet new demands from population growth and changing human diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome...
October 24, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27766952/the-third-international-genomic-medicine-conference-3rd-igmc-2015-overall-activities-and-outcome-highlights
#15
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
https://www.readbyqxmd.com/read/27766357/klebsiella-phages-representing-a-novel-clade-of-viruses-with-an-unknown-dna-modification-and-biotechnologically-interesting-enzymes
#16
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
https://www.readbyqxmd.com/read/27739501/the-bornavirus-derived-human-protein-ebln1-promotes-efficient-cell-cycle-transit-microtubule-organisation-and-genome-stability
#17
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
https://www.readbyqxmd.com/read/27738453/effects-of-dna-supercoiling-on-chromatin-architecture
#18
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
https://www.readbyqxmd.com/read/27729393/ultrastructural-organisation-of-hcv-from-the-bloodstream-of-infected-patients-revealed-by-electron-microscopy-after-specific-immunocapture
#19
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
https://www.readbyqxmd.com/read/27722995/training-genetic-counsellors-to-deliver-an-innovative-therapeutic-intervention-their-views-and-experience-of-facilitating-multi-family-discussion-groups
#20
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
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