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Translational genomics

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https://www.readbyqxmd.com/read/28430886/intrinsic-protein-disorder-reduces-small-scale-gene-duplicability
#1
Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein-protein interactions and are the target of post-translational modifications...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430547/enhancing-insights-into-pulmonary-vascular-disease-pvd-through-a-precision-medicine-approach-a-joint-nhlbi-cmref-workshop-report
#2
John H Newman, Stuart Rich, Steven H Abman, John H Alexander, John Barnard, Gerald J Beck, Raymond L Benza, Todd M Bull, Stephen Y Chan, Hyung J Chun, Declan Doogan, Jocelyn Dupuis, Serpil C Erzurum, Robert P Frantz, Mark Geraci, Hunter Gillies, Mark Gladwin, Michael P Gray, Anna R Hemnes, Roy S Herbst, Adrian F Hernandez, Nicholas S Hill, Evelyn M Horn, Kendall Hunter, Zhi-Cheng Jing, Roger Johns, Sanjay Kaul, Steven M Kawut, Tim Lahm, Jane A Leopold, Greg D Lewis, Stephen C Mathai, Vallerie V McLaughlin, Evangelos D Michelakis, Steven D Nathan, William Nichols, Grier Page, Marlene Rabinovitch, Jonathan Rich, Franz Rischard, Sharon Rounds, Sanjiv J Shah, Victor F Tapson, Naomi Lowy, Norman Stockbridge, Gail Weinmann, Lei Xiao
The Division of Lung Diseases of the National Heart, Lung and Blood Institute, (NHLBI) and the Cardiovascular Medical Education and Research Fund (CMREF), held a workshop to discuss to leverage of the anticipated scientific output from the recently launched "Redefining Pulmonary Hypertension (PH) through Pulmonary Vascular Disease Phenomics" (PVDOMICS) program. PVDOMICS is a protocol driven network to analyze PH patient populations to define novel pulmonary vascular disease (PVD) phenotypes. Basic, translational and clinical investigators, patient advocacy organizations, regulatory agencies, and pharmaceutical industry experts discussed the application of precision medicine to PVD clinical trials...
April 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28428978/20th-workshop-of-the-international-stroke-genetics-consortium-november-3-4-2016-milan-italy-2016-036-isgc-research-priorities
#3
Daniel Woo, Stephanie Debette, Christopher Anderson
OBJECTIVE: To develop a research priority list for the International Stroke Genetics Consortium (ISGC). BACKGROUND: Previously, stroke progress review groups and other activities provided an opportunity for members within the field to develop priorities for research. These filtered into larger categories which then published the top research priorities of their given field. However, these review groups are no longer forming and thus there has been no clear direction on what the research priorities and needs for stroke genetics research...
March 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28428832/a-meta-analysis-testing-eusocial-co-option-theories-in-termite-gut-physiology-and-symbiosis
#4
Michael E Scharf, Yunpeng Cai, Yijun Sun, Ruchira Sen, Rhitoban Raychoudhury, Drion G Boucias
The termite gut accomplishes key physiologic functions that underlie termite symbiosis and sociality. However, potential candidate functions of the host-symbiont holobiome have not yet been explored across seemingly divergent processes such as digestion, immunity, caste differentiation, and xenobiotic tolerance. This study took a meta-analysis approach for concurrently studying host and symbiont gut metatranscriptome responses of the lower termite Reticulitermes flavipes, which has ancestral characteristics and hosts a diverse mix of eukaryotic and bacterial symbionts...
2017: Communicative & Integrative Biology
https://www.readbyqxmd.com/read/28428795/non-canonical-translation-in-plant-rna-viruses
#5
REVIEW
Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427920/genome-improvement-of-the-acarbose-producer-actinoplanes-sp-se50-110-and-annotation-refinement-based-on-rna-seq-analysis
#6
Timo Wolf, Susanne Schneiker-Bekel, Armin Neshat, Vera Ortseifen, Daniel Wibberg, Till Zemke, Alfred Pühler, Jörn Kalinowski
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis is only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data...
April 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28427349/genome-wide-survey-of-mirnas-and-their-evolutionary-history-in-the-ascidian-halocynthia-roretzi
#7
Kai Wang, Christelle Dantec, Patrick Lemaire, Takeshi A Onuma, Hiroki Nishida
BACKGROUND: miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied. RESULTS: We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28426554/barking-up-the-right-tree-advancing-our-understanding-and-treatment-of-lymphoma-with-a-spontaneous-canine-model
#8
Dania Villarnovo, Angela L McCleary-Wheeler, Kristy L Richards
PURPOSE OF REVIEW: Spontaneous lymphoma in pet dogs is increasingly recognized as an ideal model for studying the disease in humans and for developing new targeted therapeutics for patients. Increasing interest by funding agencies, the private sector, and multidisciplinary academic collaborations between different disciplines and sectors now enables large knowledge gaps to be addressed and provides additional proof-of-concept examples to showcase the significance of the canine model. RECENT FINDINGS: The current review addresses the rationale for a canine lymphoma model including the valuable role it can play in drug development, serving as a link between mouse xenograft models and human clinical trials and the infrastructure that is now in place to facilitate these studies...
April 19, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28425876/characterization-of-the-translation-elongation-factor-1-%C3%AE-gene-in-a-wide-range-of-pathogenic-aspergillus-species
#9
Sadegh Nouripour-Sisakht, Bahram Ahmadi, Koichi Makimura, Sybren de Hoog, Yoshiko Umeda, Mohamed Mahdi Alshahni, Hossein Mirhendi
PURPOSE: We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species. METHODOLOGY: Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains. RESULTS: Analysis of TEF-1α sequences indicated a mean similarity of 92...
April 21, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28424941/isolation-and-complete-genome-sequence-of-a-novel-pseudoalteromonas-phage-ph357-from-the-yangtze-river-estuary
#10
Zheng Gong, Min Wang, Qingwei Yang, Zhongshi Li, Jun Xia, Yu Gao, Yong Jiang, Xue Meng, Zhaoyang Liu, Ding Yang, Fangfei Zhang, Hongbing Shao, Duobing Wang
Phage PH357, a novel lytic Pseudoalteromonas lipolytica phage belonging to the Myoviridae family was isolated from the Yangtze River estuary. The microbiological characterization demonstrated that phage PH357 is stable from -20 to 60 °C and the optimal pH 7. The one-step growth curve showed a latent period of 20 min, a rise period of 20 min, and the average burst size was about 85 virions per cell. Complete genome of phage PH357 was determined. Genome of phage PH357 consisted of a linear, double-stranded 136,203 bp DNA molecule with 34...
April 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28423787/it-infrastructure-of-an-oncological-trial-where-xenografts-inform-individual-second-line-treatment-decision
#11
Doris Lindoerfer, Ulrich Mansmann
Translational clinical research is often characterized by a unidirectional information flow from clinical to molecular data by using phenotypes to elucidate molecular disease processes. Here we present the RESIST study which uses xenograft information for individual treatment decisions after resistance to a specific anticancer treatment establishing a bidirectional information flow between patient and molecular biology. The paper discusses the specific challenges related to the IT infrastructure for such bidirectional translational projects and proposes solutions...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423538/gene-regulatory-pattern-analysis-reveals-essential-role-of-core-transcriptional-factors-activation-in-triple-negative-breast-cancer
#12
Li Min, Cheng Zhang, Like Qu, Jialiang Huang, Lan Jiang, Jiafei Liu, Luca Pinello, Guo-Cheng Yuan, Chengchao Shou
BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype. Genome-scale molecular characteristics and regulatory mechanisms that distinguish TNBC from other subtypes remain incompletely characterized. RESULTS: By combining gene expression analysis and PANDA network, we defined three different TF regulatory patterns. A core TNBC-Specific TF Activation Driven Pattern (TNBCac) was specifically identified in TNBC by computational analysis...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423517/next-generation-sequencing-of-extraskeletal-myxoid-chondrosarcoma
#13
Elizabeth J Davis, Yi-Mi Wu, Dan Robinson, Scott M Schuetze, Laurence H Baker, Jyoti Athanikar, Xuhong Cao, Lakshmi P Kunju, Arul M Chinnaiyan, Rashmi Chugh
Extraskeletal myxoid chondrosarcoma (EMC) is an indolent translocation-associated soft tissue sarcoma with a high propensity for metastases. Using a clinical sequencing approach, we genomically profiled patients with metastatic EMC to elucidate the molecular biology and identify potentially actionable mutations. We also evaluated potential predictive factors of benefit to sunitinib, a multi-targeted tyrosine kinase inhibitor with reported activity in a subset of EMC patients. Between January 31, 2012 and April 15, 2016, six patients with EMC participated in the clinical sequencing research study...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#14
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422758/first-in-human-trial-of-multikinase-vegf-inhibitor-regorafenib-and-anti-egfr-antibody-cetuximab-in-advanced-cancer-patients
#15
Vivek Subbiah, Muhammad Rizwan Khawaja, David S Hong, Behrang Amini, Jiang Yungfang, Hui Liu, Adrienne Johnson, Alexa B Schrock, Siraj M Ali, James X Sun, David Fabrizio, Sarina Piha-Paul, Siqing Fu, Apostolia M Tsimberidou, Aung Naing, Filip Janku, Daniel D Karp, Michael Overman, Cathy Eng, Scott Kopetz, Funda Meric-Bernstam, Gerald S Falchook
BACKGROUND: The combination of multikinase VEGF inhibitor regorafenib and anti-EGFR antibody cetuximab overcomes intrinsic and acquired resistance in both EGFR-sensitive and EGFR-resistant preclinical models of colorectal cancer (CRC). METHODS: Utilizing a standard 3+3 design, a phase I study was designed to determine safety, maximum tolerated dose (MTD), and dose-limiting toxicities (DLTs) of the regorafenib plus cetuximab combination among patients with advanced cancer including CRC...
April 20, 2017: JCI Insight
https://www.readbyqxmd.com/read/28420742/synergistic-internal-ribosome-entry-site-microrna-based-approach-for-flavivirus-attenuation-and-live-vaccine-development
#16
Konstantin A Tsetsarkin, Guangping Liu, Evgeniya Volkova, Alexander G Pletnev
The recent emergence of Zika virus underscores the need for new strategies for a rapid development of safe flavivirus vaccines. Using another flavivirus (Langat virus [LGTV]) that belongs to the group of tick-borne flaviviruses as a model, we describe a dual strategy for virus attenuation which synergistically accesses the specificity of microRNA (miRNA) genome targeting and the effectiveness of internal ribosome entry site (IRES) insertion. To increase the stability and immunogenicity of bicistronic LGTVs, we developed a novel approach in which the capsid (C) protein gene was relocated into the 3' noncoding region (NCR) and expressed under translational control from an IRES...
April 18, 2017: MBio
https://www.readbyqxmd.com/read/28420614/applications-of-genome-editing-tools-in-precision-medicine-research
#17
Li Shuang, Yang Yuanyuan, Qiu Yan, Chen Yanhao, Xu Luwei, Ding Qiurong
The emergence of genome editing tools, such as the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, has enabled researchers to achieve somatic and germline genomic manipulations in cell lines and model organisms. Within a couple of years, genome editing is now being rapidly developed for multiple applications and widely used in biomedical researches, including creation of disease models with desired genetic mutations, screening in a high-throughput manner for drug resistance genes, and making appropriate editions to genes in vivo for disease treatment...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28420414/integrated-genomic-analysis-of-mitochondrial-rna-processing-in-human-cancers
#18
Youssef Idaghdour, Alan Hodgkinson
BACKGROUND: The mitochondrial genome is transcribed as continuous polycistrons of RNA containing multiple genes. As a consequence, post-transcriptional events are critical for the regulation of gene expression and therefore all aspects of mitochondrial function. One particularly important process is the m(1)A/m(1)G RNA methylation of the ninth position of different mitochondrial tRNAs, which allows efficient processing of mitochondrial mRNAs and protein translation, and de-regulation of genes involved in these processes has been associated with altered mitochondrial function...
April 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28419908/editorial-overview-characterizing-the-cancer-genome-mechanistic-insights-and-translational-opportunities
#19
EDITORIAL
Olivier Delattre, Carol J Bult
No abstract text is available yet for this article.
April 15, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28417974/the-e-coli-molecular-phenotype-under-different-growth-conditions
#20
Mehmet U Caglar, John R Houser, Craig S Barnhart, Daniel R Boutz, Sean M Carroll, Aurko Dasgupta, Walter F Lenoir, Bartram L Smith, Viswanadham Sridhara, Dariya K Sydykova, Drew Vander Wood, Christopher J Marx, Edward M Marcotte, Jeffrey E Barrick, Claus O Wilke
Modern systems biology requires extensive, carefully curated measurements of cellular components in response to different environmental conditions. While high-throughput methods have made transcriptomics and proteomics datasets widely accessible and relatively economical to generate, systematic measurements of both mRNA and protein abundances under a wide range of different conditions are still relatively rare. Here we present a detailed, genome-wide transcriptomics and proteomics dataset of E. coli grown under 34 different conditions...
April 18, 2017: Scientific Reports
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