keyword
MENU ▼
Read by QxMD icon Read
search

genome organisation

keyword
https://www.readbyqxmd.com/read/29190361/shaping-epigenetic-memory-via-genomic-bookmarking
#1
Davide Michieletto, Michael Chiang, Davide Colì, Argyris Papantonis, Enzo Orlandini, Peter R Cook, Davide Marenduzzo
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors...
November 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29181457/comparison-of-real-time-quantitative-pcr-with-a-chairside-test-for-streptococcus-mutans-assessment
#2
Yihong Li, Prakaimuk Saraithong, Zhou Chen, Erica Leung, Komkham Pattanaporn, Ananda Dasanayake
OBJECTIVE: To compare two methods for Streptococcus mutans detection and quantification in the human oral cavity: a chairside commercial test and a molecular-based real-time quantitative polymerase chain reaction (qPCR) method. METHODS: A total of 688 whole saliva samples were collected from 344 children aged 3 and 5 and their biological mothers. Caries status was examined using a World Health Organisation survey method. S. mutans levels were measured using the Dentocult SM Strip mutans test and scored as colony forming units per millilitre of saliva...
2017: Chinese Journal of Dental Research
https://www.readbyqxmd.com/read/29158161/extension-of-the-transposable-bacterial-virus-family-two-genomic-organisations-among-phages-and-prophages-with-a-tn552-related-transposase
#3
Ariane Toussaint, Frédérique Van Gijsegem
Mu-like transposable phages and prophages have been isolated from, or predicted, in a wide range of bacterial phyla. However, related B3-like transposable phages, which differ in their genome organisation and the DDE transposase and transposition activator they code for have thus far been restricted to a very limited set of hosts. Through sequence similarity searches, we have now expanded the number of predicted B3-like prophages and uncovered a third genomic organisation. These new genomes, although only prophages, further illustrate the previously reported mosaicism existing in the proposed "Saltoviridae" family of Caudovirales, and further support the proposal to move morphology criteria (contractile vs...
November 17, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/29158132/deciphering-the-histone-code-to-build-the-genome-structure
#4
Kirti Prakash, David Fournier
Histones are punctuated with small chemical modifications that alter their interaction with DNA. One attractive hypothesis stipulates that certain combinations of these histone modifications may function, alone or together, as a part of a predictive histone code to provide ground rules for chromatin folding. We consider four features that relate histone modifications to chromatin folding: charge neutralisation, molecular specificity, robustness and evolvability. Next, we present evidence for the association among different histone modifications at various levels of chromatin organisation and show how these relationships relate to function such as transcription, replication and cell division...
November 17, 2017: Bio Systems
https://www.readbyqxmd.com/read/29148115/the-actionability-of-exome-sequencing-testing-results
#5
Tanya Stivers, Stefan Timmermans
Genomic tests such as exome sequencing have recently become an option for diagnosing patients. The tests allow clinical geneticists to sequence the majority of patients' disease causing genetic variants. As a new technology, exome sequencing confronts the question of what the benefit is of this increased genetic information. Against a narrow perspective of clinical utility that emphasises tangible improvements in a patient's disease management, professional organisations have argued that genomic sequencing should be considered beneficial if it helps families and society...
November 2017: Sociology of Health & Illness
https://www.readbyqxmd.com/read/29141034/structure-of-the-human-chromosome-interaction-network
#6
Sergio Sarnataro, Andrea M Chiariello, Andrea Esposito, Antonella Prisco, Mario Nicodemi
New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence...
2017: PloS One
https://www.readbyqxmd.com/read/29132315/comprehensive-genomic-analysis-of-the-cngc-gene-family-in-brassica-oleracea-novel-insights-into-synteny-structures-and-transcript-profiles
#7
Kaleem U Kakar, Zarqa Nawaz, Khadija Kakar, Essa Ali, Abdulwareth A Almoneafy, Raqeeb Ullah, Xue-Liang Ren, Qing-Yao Shu
BACKGROUND: The cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism. RESULTS: In present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29123645/beerdecoded-the-open-beer-metagenome-project
#8
Jonathan Sobel, Luc Henry, Nicolas Rotman, Gianpaolo Rando
Next generation sequencing has radically changed research in the life sciences, in both academic and corporate laboratories. The potential impact is tremendous, yet a majority of citizens have little or no understanding of the technological and ethical aspects of this widespread adoption. We designed BeerDeCoded as a pretext to discuss the societal issues related to genomic and metagenomic data with fellow citizens, while advancing scientific knowledge of the most popular beverage of all. In the spirit of citizen science, sample collection and DNA extraction were carried out with the participation of non-scientists in the community laboratory of Hackuarium, a not-for-profit organisation that supports unconventional research and promotes the public understanding of science...
2017: F1000Research
https://www.readbyqxmd.com/read/29123641/systematically-linking-transmart-galaxy-and-ega-for-reusing-human-translational-research-data
#9
Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J Dylan Spalding, Sanne Abeln
The availability of high-throughput molecular profiling techniques has provided more accurate and informative data for regular clinical studies. Nevertheless, complex computational workflows are required to interpret these data. Over the past years, the data volume has been growing explosively, requiring robust human data management to organise and integrate the data efficiently. For this reason, we set up an ELIXIR implementation study, together with the Translational research IT (TraIT) programme, to design a data ecosystem that is able to link raw and interpreted data...
2017: F1000Research
https://www.readbyqxmd.com/read/29121649/spatiotemporal-dynamics-of-hsv-genome-nuclear-entry-and-compaction-state-transitions-using-bioorthogonal-chemistry-and-super-resolution-microscopy
#10
Eiki Sekine, Nora Schmidt, David Gaboriau, Peter O'Hare
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes...
November 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29094240/complete-genome-sequence-of-a-novel-bromovirus-infecting-elderberry-sambucus-nigra-l-in-the-czech-republic
#11
Dana Šafářová, Thierry Candresse, Milan Navrátil
The genus Bromovirus currently contains six species whose members have relatively narrow host ranges. In the present work, a new bromovirus infecting elderberry (Sambucus nigra L.) is reported. dsRNA was purified and sequenced by next-generation sequencing, and with minimal additional completion by Sanger sequencing, the full tripartite genome was obtained. RNA1 is 3241 nt long and contains ORF1 (1a protein), RNA2 is 2810 nt long and contains ORF2 (2a protein), and RNA3 is 2244 nt long and contains ORF3a (movement protein) and ORF3b (coat protein, CP), separated by an intercistronic poly(A) stretch...
November 1, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29080858/tailored-first-line-and-second-line-cdk4-targeting-treatment-combinations-in-mouse-models-of-pancreatic-cancer
#12
Angela Chou, Danielle Froio, Adnan M Nagrial, Ashleigh Parkin, Kendelle J Murphy, Venessa T Chin, Dalia Wohl, Angela Steinmann, Rhys Stark, Alison Drury, Stacey N Walters, Claire Vennin, Andrew Burgess, Mark Pinese, Lorraine A Chantrill, Mark J Cowley, Timothy J Molloy, Nicola Waddell, Amber Johns, Sean M Grimmond, David K Chang, Andrew V Biankin, Owen J Sansom, Jennifer P Morton, Shane T Grey, Thomas R Cox, John Turchini, Jaswinder Samra, Stephen J Clarke, Paul Timpson, Anthony J Gill, Marina Pajic
OBJECTIVE: Extensive molecular heterogeneity of pancreatic ductal adenocarcinoma (PDA), few effective therapies and high mortality make this disease a prime model for advancing development of tailored therapies. The p16-cyclin D-cyclin-dependent kinase 4/6-retinoblastoma (RB) protein (CDK4) pathway, regulator of cell proliferation, is deregulated in PDA. Our aim was to develop a novel personalised treatment strategy for PDA based on targeting CDK4. DESIGN: Sensitivity to potent CDK4/6 inhibitor PD-0332991 (palbociclib) was correlated to protein and genomic data in 19 primary patient-derived PDA lines to identify biomarkers of response...
October 28, 2017: Gut
https://www.readbyqxmd.com/read/29074984/alf-a-strategy-for-identification-of-unauthorized-gmos-in-complex-mixtures-by-a-gw-ngs-method-and-dedicated-bioinformatics-analysis
#13
Alexandra Bogožalec Košir, Alfred J Arulandhu, Marleen M Voorhuijzen, Hongmei Xiao, Rico Hagelaar, Martijn Staats, Adalberto Costessi, Jana Žel, Esther J Kok, Jeroen P van Dijk
The majority of feed products in industrialised countries contains materials derived from genetically modified organisms (GMOs). In parallel, the number of reports of unauthorised GMOs (UGMOs) is gradually increasing. There is a lack of specific detection methods for UGMOs, due to the absence of detailed sequence information and reference materials. In this research, an adapted genome walking approach was developed, called ALF: Amplification of Linearly-enriched Fragments. Coupling of ALF to NGS aims for simultaneous detection and identification of all GMOs, including UGMOs, in one sample, in a single analysis...
October 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29063999/backbone-1-h-13-c-and-15-n-resonance-assignments-of-the-ob-domain-of-the-single-stranded-dna-binding-protein-hssb2-nabp1-obfc2a-and-chemical-shift-mapping-of-the-dna-binding-interface
#14
Ruvini Kariawasam, Maddison Knight, Roland Gamsjaeger, Liza Cubeddu
Single stranded DNA-binding proteins (SSBs) are essential for the maintenance of genome integrity and are required in in all known cellular organisms. Over the last 10 years, the role of two new human SSBs, hSSB1 (NABP2/OBFC2B) and hSSB2 (NABP1/OBFC2A), has been described and characterised in various important DNA repair processes. Both these proteins are made up of a conserved oligonucleotide-binding (OB) fold that is responsible for ssDNA recognition as well a unique flexible carboxy-terminal extension involved in protein-protein interactions...
October 24, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29062388/highlights-from-the-win-2017-symposium-26-27-june-2017-paris-france-expediting-global-innovation-in-precision-cancer-medicine
#15
Will Davies
The Worldwide Innovative Networking (WIN) symposium brings together representatives from academic institutions, pharmaceutical partners, technology companies and charitable organisations from across the globe for an annual summit, discussing ongoing research and the latest developments in precision medicine. Now, in its seventh year, the aims of the WIN consortium's annual meeting, to foster communication and collaboration between members and deliver clinical trial results that improve the care and outcomes of patients are presented in open dialogue to encourage debate and discussion...
2017: Ecancermedicalscience
https://www.readbyqxmd.com/read/29037147/de-novo-assembly-of-genomes-from-long-sequence-reads-reveals-uncharted-territories-of-propionibacterium-freudenreichii
#16
Paulina Deptula, Pia K Laine, Richard J Roberts, Olli-Pekka Smolander, Helena Vihinen, Vieno Piironen, Lars Paulin, Eija Jokitalo, Kirsi Savijoki, Petri Auvinen, Pekka Varmanen
BACKGROUND: Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species. RESULTS: We used the PacBio RS II sequencing platform to generate complete genomes of 20 P...
October 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28978305/implementing-non-invasive-prenatal-testing-into-publicly-funded-antenatal-screening-services-for-down-syndrome-and-other-conditions-in-aotearoa-new-zealand
#17
Sara Filoche, Fiona Cram, Bev Lawton, Angela Beard, Peter Stone
BACKGROUND: Non-invasive prenatal testing (NIPT) is a relatively new screen for congenital conditions - specifically, common fetal aneuploidies including Down Syndrome. The test is based on isolating freely circulating fragments of fetal-placental DNA that is present in the mother's blood. NIPT has a superior clinical performance compared to current screening, and has been available privately in Aotearoa New Zealand for the last 4 years. MAIN ISSUE: The proposed implementation of NIPT as a publicly funded service may widen the inequity in access to optional antenatal screening that already exists in this country...
October 4, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/28902917/hsp70-j-protein-machinery-from-glossina-morsitans-morsitans-vector-of-african-trypanosomiasis
#18
Stephen J Bentley, Aileen Boshoff
Tsetse flies (Glossina spp.) are the sole vectors of the protozoan parasites of the genus Trypanosoma, the causative agents of African Trypanosomiasis. Species of Glossina differ in vector competence and Glossina morsitans morsitans is associated with transmission of Trypanosoma brucei rhodesiense, which causes an acute and often fatal form of African Trypanosomiasis. Heat shock proteins are evolutionarily conserved proteins that play critical roles in proteostasis. The activity of heat shock protein 70 (Hsp70) is regulated by interactions with its J-protein (Hsp40) co-chaperones...
2017: PloS One
https://www.readbyqxmd.com/read/28898293/the-vibrio-cholerae-var-regulon-encodes-a-metallo-%C3%AE-lactamase-and-an-antibiotic-efflux-pump-which-are-regulated-by-varr-a-lysr-type-transcription-factor
#19
Hong-Ting Victor Lin, Teresa Massam-Wu, Chen-Ping Lin, Yen-Jen Anna Wang, Yu-Chi Shen, Wen-Jung Lu, Pang-Hung Hsu, Yu-Hou Chen, Maria Ines Borges-Walmsley, Adrian Robert Walmsley
The genome sequence of V. cholerae O1 Biovar Eltor strain N16961 has revealed a putative antibiotic resistance (var) regulon that is predicted to encode a transcriptional activator (VarR), which is divergently transcribed relative to the putative resistance genes for both a metallo-β-lactamase (VarG) and an antibiotic efflux-pump (VarABCDEF). We sought to test whether these genes could confer antibiotic resistance and are organised as a regulon under the control of VarR. VarG was overexpressed and purified and shown to have β-lactamase activity against penicillins, cephalosporins and carbapenems, having the highest activity against meropenem...
2017: PloS One
https://www.readbyqxmd.com/read/28893199/comprehensive-survey-and-evolutionary-analysis-of-genome-wide-mirna-genes-from-ten-diploid-oryza-species
#20
Showkat Ahmad Ganie, Ananda Bhusan Debnath, Abubakar Mohammad Gumi, Tapan Kumar Mondal
BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT: All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species...
September 11, 2017: BMC Genomics
keyword
keyword
64990
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"