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Translational genomics

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https://www.readbyqxmd.com/read/28225828/systematic-analysis-of-non-structural-protein-features-for-the-prediction-of-ptm-function-potential-by-artificial-neural-networks
#1
Henry M Dewhurst, Matthew P Torres
Post-translational modifications (PTMs) provide an extensible framework for regulation of protein behavior beyond the diversity represented within the genome alone. While the rate of identification of PTMs has rapidly increased in recent years, our knowledge of PTM functionality encompasses less than 5% of this data. We previously developed SAPH-ire (Structural Analysis of PTM Hotspots) for the prioritization of eukaryotic PTMs based on function potential of discrete modified alignment positions (MAPs) in a set of 8 protein families...
2017: PloS One
https://www.readbyqxmd.com/read/28223918/rpph1-upregulates-cdc42-expression-and-promotes-hippocampal-neuron-dendritic-spine-formation-by-competing-with-mir-330-5p
#2
Yifei Cai, Ziling Sun, Huizhen Jia, Hongxue Luo, Xiaoyang Ye, Qi Wu, Yi Xiong, Wei Zhang, Jun Wan
Alzheimer's disease (AD) is a heterogeneous neurodegenerative disease. Recent studies employing microRNA-seq and genome-wide sequencing have identified some non-coding RNAs that are influentially involved in AD pathogenesis. Non-coding RNAs can compete with other endogenous RNAs by microRNA response elements (MREs) and manipulate biological processes, such as tumorigenesis. However, only a few non-coding RNAs have been reported in the pathogenesis of AD. In this study, we constructed the first competing endogenous RNA (ceRNA) network leveraging whole transcriptome sequencing and a previously studied microRNA-seq of APPswe/PS1ΔE9 transgenic mice...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28222748/identification-of-host-cellular-proteins-that-interact-with-the-m-protein-of-a-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-vaccine-strain
#3
Qian Wang, Yanwei Li, Hong Dong, Li Wang, Jinmei Peng, Tongqing An, Xufu Yang, Zhijun Tian, Xuehui Cai
BACKGROUND: The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. METHODS: Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb)...
February 22, 2017: Virology Journal
https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#4
EDITORIAL
Hikmet Budak, Baohong Zhang
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms...
February 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28220193/hsa-mir-4485-regulates-mitochondrial-functions-and-inhibits-the-tumorigenicity-of-breast-cancer-cells
#5
Lakshmi Sripada, Kritarth Singh, Anastasiya V Lipatova, Aru Singh, Paresh Prajapati, Dhanendra Tomar, Khyati Bhatelia, Milton Roy, Rochika Singh, Madan M Godbole, Peter M Chumakov, Rajesh Singh
The modulation of mitochondrial functions is important for maintaining cellular homeostasis. Mitochondria essentially depend on the import of RNAs and proteins encoded by the nuclear genome. MicroRNAs encoded in the nucleus can translocate to mitochondria and target the genome, affecting mitochondrial function. Here, we analyzed the role of miR-4485 in the regulation of mitochondrial functions. We showed that miR-4485 translocated to mitochondria where its levels varied in response to different stress conditions...
February 20, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28220131/plant-stress-responses-and-phenotypic-plasticity-in-the-epigenomics-era-perspectives-on-the-grapevine-scenario-a-model-for-perennial-crop-plants
#6
Ana M Fortes, Philippe Gallusci
Epigenetic marks include Histone Post-Translational Modifications and DNA methylation which are known to participate in the programming of gene expression in plants and animals. These epigenetic marks may be subjected to dynamic changes in response to endogenous and/or external stimuli and can have an impact on phenotypic plasticity. Studying how plant genomes can be epigenetically shaped under stressed conditions has become an essential issue in order to better understand the molecular mechanisms underlying plant stress responses and enabling epigenetic in addition to genetic factors to be considered when breeding crop plants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220104/systems-biology-derived-discoveries-of-intrinsic-clocks
#7
REVIEW
Arthur Millius, Hiroki R Ueda
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28219341/integrating-genetic-maps-in-bambara-groundnut-vigna-subterranea-l-verdc-and-their-syntenic-relationships-among-closely-related-legumes
#8
Wai Kuan Ho, Hui Hui Chai, Presidor Kendabie, Nariman Salih Ahmad, Jaeyres Jani, Festo Massawe, Andrzej Kilian, Sean Mayes
BACKGROUND: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata)...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28218713/transgene-expression-and-host-cell-responses-to-replication-defective-single-cycle-and-replication-competent-adenovirus-vectors
#9
Catherine M Crosby, Michael A Barry
Most adenovirus (Ad) vectors are E1 gene deleted replication defective (RD-Ad) vectors that deliver one transgene to the cell and all expression is based on that one gene. In contrast, E1-intact replication-competent Ad (RC-Ad) vectors replicate their DNA and their transgenes up to 10,000-fold, amplifying transgene expression markedly higher than RD-Ad vectors. While RC-Ad are more potent, they run the real risk of causing adenovirus infections in vector recipients and those that administer them. To gain the benefits of transgene amplification, but avoid the risk of Ad infections, we developed "single cycle" Ad (SC-Ad) vectors...
February 18, 2017: Genes
https://www.readbyqxmd.com/read/28217095/endogenous-protein-interactome-of-human-udp-glucuronosyltransferases-exposed-by-untargeted-proteomics
#10
Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock, Chantal Guillemette
The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, transcriptional, post-transcriptional and post-translational levels. However, the UGT protein interaction network, which is likely to influence glucuronidation, has received little attention...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28217082/genomic-editing-of-non-coding-rna-genes-with-crispr-cas9-ushers-in-a-potential-novel-approach-to-study-and-treat-schizophrenia
#11
REVIEW
Chuanjun Zhuo, Weihong Hou, Lirong Hu, Chongguang Lin, Ce Chen, Xiaodong Lin
Schizophrenia is a genetically related mental illness, in which the majority of genetic alterations occur in the non-coding regions of the human genome. In the past decade, a growing number of regulatory non-coding RNAs (ncRNAs) including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been identified to be strongly associated with schizophrenia. However, the studies of these ncRNAs in the pathophysiology of schizophrenia and the reverting of their genetic defects in restoration of the normal phenotype have been hampered by insufficient technology to manipulate these ncRNA genes effectively as well as a lack of appropriate animal models...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28216628/genome-wide-primary-transcriptome-analysis-of-h2-producing-archaeon-thermococcus-onnurineus-na1
#12
Suhyung Cho, Min-Sik Kim, Yujin Jeong, Bo-Rahm Lee, Jung-Hyun Lee, Sung Gyun Kang, Byung-Kwan Cho
In spite of their pivotal roles in transcriptional and post-transcriptional processes, the regulatory elements of archaeal genomes are not yet fully understood. Here, we determine the primary transcriptome of the H2-producing archaeon Thermococcus onnurineus NA1. We identified 1,082 purine-rich transcription initiation sites along with well-conserved TATA box, A-rich B recognition element (BRE), and promoter proximal element (PPE) motif in promoter regions, a high pyrimidine nucleotide content (T/C) at the -1 position, and Shine-Dalgarno (SD) motifs (GGDGRD) in 5' untranslated regions (5' UTRs)...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216108/crispr-enabled-trackable-genome-engineering-for-isopropanol-production-in-escherichia-coli
#13
Liya Liang, Rongming Liu, Andrew D Garst, Thomas Lee, Violeta Sànchez I Nogué, Gregg T Beckham, Ryan T Gill
Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and testing of production strains. Here, we report on the use of such capabilities to construct and test 903 different variants of the isopropanol production pathway in Escherichia coli. We first constructed variants to explore the effect of codon optimization, copy number, and translation initiation rates on isopropanol production...
February 16, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28213978/estrogens-and-androgens-inhibit-association-of-rankl-with-the-pre-osteoblast-membrane-through-post-translational-mechanisms
#14
Anthony Martin, Jiali Yu, Jian Xiong, Aysha B Khalid, Benita Katzenellenbogen, Sung Hoon Kim, John A Katzenellenbogen, Suchinda Malaivijitnond, Yankel Gabet, Susan A Krum, Baruch Frenkel
We have recently demonstrated that RUNX2 promoted, and 17-β-Estradiol (E2) diminished, association of RANKL with the cell membrane in pre-osteoblast cultures. Here we show that, similar to E2, dihydrotestosterone (DHT) diminishes association of RANKL and transiently transfected GFP-RANKL with the pre-osteoblast membrane without decreasing total RANKL mRNA or protein levels. Diminution of membrane-associated RANKL was accompanied with marked suppression of osteoclast differentiation from co-cultured pre-osteoclasts, even though DHT increased, not decreased, RANKL concentrations in pre-osteoblast conditioned media...
February 18, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28213379/slowed-decay-of-mrnas-enhances-platelet-specific-translation
#15
Eric W Mills, Rachel Green, Nicholas T Ingolia
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28212969/lessons-learned-when-introducing-pharmacogenomic-panel-testing-into-clinical-practice
#16
Marc B Rosenman, Brian Decker, Kenneth D Levy, Ann M Holmes, Victoria M Pratt, Michael T Eadon
OBJECTIVES: Implementing new programs to support precision medicine in clinical settings is a complex endeavor. We describe challenges and potential solutions based on the Indiana GENomics Implementation: an Opportunity for the Underserved (INGenious) program at Eskenazi Health-one of six sites supported by the Implementing GeNomics In pracTicE network grant of the National Institutes of Health/National Human Genome Research Institute. INGenious is an implementation of a panel of genomic tests...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212892/atf2-a-paradigm-of-the-multifaceted-regulation-of-transcription-factors-in-biology-and-disease
#17
REVIEW
Gregory Watson, Ze'ev Ronai, Eric Lau
Stringent transcriptional regulation is crucial for normal cellular biology and organismal development. Perturbations in the proper regulation of transcription factors can result in numerous pathologies, including cancer. Thus, understanding how transcription factors are regulated and how they are dysregulated in disease states is key to the therapeutic targeting of these factors and/or the pathways that they regulate. Activating transcription factor 2 (ATF2) has been studied in a number of developmental and pathological conditions...
February 14, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28212842/pathophysiological-consequences-of-receptor-mistraffic-tales-from-the-platelet-p2y12-receptor
#18
Margaret R Cunningham, Riyaad Aungraheeta, Stuart J Mundell
Genetic variations in G protein-coupled receptor (GPCR) genes can disrupt receptor function in a wide variety of human genetic diseases, including platelet bleeding disorders. Platelets are critical for haemostasis with inappropriate platelet activation leading to the development of arterial thrombosis, which can result in heart attack and stroke whilst decreased platelet activity is associated with an increased risk of bleeding. GPCRs expressed on the surface of platelets play key roles in regulating platelet activity and therefore function...
February 14, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28212627/genome-wide-identification-of-direct-hbx-genomic-targets
#19
Francesca Guerrieri, Laura Belloni, Daniel D'Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, Cecilia Scisciani, Oceane Floriot, Fabien Zoulim, Anna Tramontano, Massimo Levrero
BACKGROUND: The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modulate histone post-translational modifications and to regulate viral cccDNA transcription and cellular gene expression. Aiming to identify genes and non-coding RNAs (ncRNAs) directly targeted by HBx, we performed a chromatin immunoprecipitation sequencing (ChIP-Seq) to analyse HBV recruitment on host cell chromatin in cells replicating HBV...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#20
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
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