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Translational genomics

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https://www.readbyqxmd.com/read/29353304/unraveling-the-heterogeneity-of-igm-monoclonal-gammopathies-a-gene-mutational-and-gene-expression-study
#1
Cristina Jiménez, María Isabel Prieto-Conde, María García-Álvarez, Miguel Alcoceba, Fernando Escalante, María Del Carmen Chillón, Alfonso García de Coca, Ana Balanzategui, Alberto Cantalapiedra, Carlos Aguilar, Rocío Corral, Tomás González-López, Luis A Marín, Abelardo Bárez, Noemí Puig, Aránzazu García-Mateo, Norma C Gutiérrez, María Eugenia Sarasquete, Marcos González, Ramón García-Sanz
Immunoglobulin M (IgM) monoclonal gammopathies show considerable variability, involving three different stages of presentation: IgM monoclonal gammopathy of undetermined significance (IgM-MGUS), asymptomatic Waldenström's macroglobulinemia (AWM), and symptomatic WM (SWM). Despite recent findings about the genomic and transcriptomic characteristics of such disorders, we know little about the causes of this clinical heterogeneity or the mechanisms involved in the progression from indolent to symptomatic forms...
January 20, 2018: Annals of Hematology
https://www.readbyqxmd.com/read/29351515/understanding-key-mechanisms-of-exercise-induced-cardiac-protection-to-mitigate-disease-current-knowledge-and-emerging-concepts
#2
Bianca C Bernardo, Jenny Y Y Ooi, Kate L Weeks, Natalie L Patterson, Julie R McMullen
The benefits of exercise on the heart are well recognized, and clinical studies have demonstrated that exercise is an intervention that can improve cardiac function in heart failure patients. This has led to significant research into understanding the key mechanisms responsible for exercise-induced cardiac protection. Here, we summarize molecular mechanisms that regulate exercise-induced cardiac myocyte growth and proliferation. We discuss in detail the effects of exercise on other cardiac cells, organelles, and systems that have received less or little attention and require further investigation...
January 1, 2018: Physiological Reviews
https://www.readbyqxmd.com/read/29350227/albusnodin-an-acetylated-lasso-peptide-from-streptomyces-albus
#3
Chuhan Zong, Wai Ling Cheung-Lee, Hader E Elashal, Monika Raj, A James Link
We describe a lasso peptide, albusnodin, that is post-translationally modified with an acetyl group, the first example of a lasso peptide with this modification. Using heterologous expression, we further show that the acetyltransferase colocalized with the albusnodin gene cluster is required for the biosynthesis of this lasso peptide. This type of lasso peptide is widespread in Actinobacteria with 44 examples found in currently sequenced genomes.
January 19, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29345920/acetylation-by-eis-and-deacetylation-by-rv1151c-of-mycobacterium-tuberculosis-hupb-biochemical-and-structural-insight
#4
Keith D Green, Tapan Biswas, Allan H Pang, Melisa J Willby, Matthew S Reed, Olga Stuchlik, Jan Pohl, James E Posey, Oleg V Tsodikov, Sylvie Garneau-Tsodikova
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29344971/clear-cell-carcinomas-of-the-ovary-and-kidney-clarity-through-genomics
#5
REVIEW
Jennifer X Ji, Yi Kan Wang, Dawn R Cochrane, David G Huntsman
Clear cell ovarian carcinoma (CCOC) and clear cell renal cell carcinoma (ccRCC) both feature clear cytoplasm due to the accumulation of cytoplasmic glycogen. Genomic studies have demonstrated several mutational similarities between these two diseases including frequent alterations in the chromatin remodeling SWI/SNF and cellular proliferation PI3K/mTOR pathways, as well as a shared hypoxia-like mRNA expression signature. Although many targeted treatment options have been approved for advance stage ccRCC, CCOC patients are still treated with conventional platinum and taxane chemotherapy, to which they are resistant...
January 17, 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29344903/nuclear-genes-involved-in-mitochondrial-diseases-caused-by-instability-of-mitochondrial-dna
#6
REVIEW
Joanna Rusecka, Magdalena Kaliszewska, Ewa Bartnik, Katarzyna Tońska
Mitochondrial diseases are defined by a respiratory chain dysfunction and in most of the cases manifest as multisystem disorders with predominant expression in muscles and nerves and may be caused by mutations in mitochondrial (mtDNA) or nuclear (nDNA) genomes. Most of the proteins involved in respiratory chain function are nuclear encoded, although 13 subunits of respiratory chain complexes (together with 2 rRNAs and 22 tRNAs necessary for their translation) encoded by mtDNA are essential for cell function...
January 17, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29344895/bioinformatics-approaches-to-predict-drug-responses-from-genomic-sequencing
#7
Neel S Madhukar, Olivier Elemento
Fulfilling the promises of precision medicine will depend on our ability to create patient-specific treatment regimens. Therefore, being able to translate genomic sequencing into predicting how a patient will respond to a given drug is critical. In this chapter, we review common bioinformatics approaches that aim to use sequencing data to predict sample-specific drug susceptibility. First, we explain the importance of customized drug regimens to the future of medical care. Second, we discuss the different public databases and community efforts that can be leveraged to develop new methods for identifying new predictive biomarkers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344885/microrna-networks-in-breast-cancer-cells
#8
Andliena Tahiri, Miriam R Aure, Vessela N Kristensen
A variety of molecular techniques can be used in order to unravel the molecular composition of cells. In particular, the microarray technology has been used to identify novel biomarkers that may be useful in the diagnosis, prognosis, or treatment of cancer. The microarray technology is ideal for biomarker discovery as it allows for the screening of a large number of molecules at once. In this review, we focus on microRNAs (miRNAs) which are key molecules in cells and regulate gene expression post-transcriptionally...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29344651/identification-of-genes-and-pathways-in-the-synovia-of-women-with-osteoarthritis-by-bioinformatics-analysis
#9
Bobin Mi, Guohui Liu, Wu Zhou, Huijuan Lv, Yi Liu, Jing Liu
Osteoarthritis (OA) has a high prevalence in female patients and sex may be a key factor affecting the progression of OA. The aim of the present study was to identify genetic signatures in the synovial membranes of female patients with OA and to elucidate the potential associated molecular mechanisms. The gene expression profiles of the GSE55457 and GSE55584 datasets were obtained from the Gene Expression Omnibus database. Data of two synovial membranes from normal female individuals (GSM1337306 and GSM1337310) and two synovial membranes from female patients affected by OA (GSM1337327 and GSM1337330) were obtained from the dataset GSE55457, and those of three synovial membranes from female patients affected by OA (GSM1339628, GSM1339629 and GSM1339632) were obtained from the dataset GSE55584...
January 15, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29342113/mitochondria-oxidative-stress-and-the-kynurenine-system-with-a-focus-on-ageing-and-neuroprotection
#10
REVIEW
Katalin Sas, Elza Szabó, László Vécsei
In this review, the potential causes of ageing are discussed. We seek to gain insight into the main physiological functions of mitochondria and discuss alterations in their function and the genome, which are supposed to be the central mechanisms in senescence. We conclude by presenting the potential modulating role of the kynurenine pathway in the ageing processes. Mitochondrial dynamics are supposed to have important physiological roles in maintaining cell homeostasis. During ageing, a decrease in mitochondrial dynamics was reported, potentially compromising the function of mitochondria...
January 17, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29341488/gene-gene-interaction-between-msx1-and-tp63-in-asian-case-parent-trios-with-nonsyndromic-cleft-lip-with-or-without-cleft-palate
#11
Dongjing Liu, Holger Schwender, Mengying Wang, Hong Wang, Ping Wang, Hongping Zhu, Zhibo Zhou, Jing Li, Tao Wu, Terri H Beaty
BACKGROUND: Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P)...
January 17, 2018: Birth Defects Research
https://www.readbyqxmd.com/read/29340235/evidence-based-design-and-evaluation-of-a-whole-genome-sequencing-clinical-report-for-the-reference-microbiology-laboratory
#12
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L Gardy
Background: Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics-including clinicians, laboratorians, epidemiologists, and researchers-is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain...
2018: PeerJ
https://www.readbyqxmd.com/read/29340217/translational-cross-activation-of-the-encapsidated-rna-of-potexviruses
#13
M V Arkhipenko, N A Nikitin, E K Donchenko, O V Karpova, J G Atabekov
We had shown the genomic RNA of potexviruses potato virus X and the alternanthera mosaic virus to be inaccessible in vitro to ribosomes while in intact virion form, but the RNAs can be translationally activated following the binding of movement protein 1 (MP1) to virus particles. Here, we present the results of the follow-up study targeting two more potexvirus species - the Narcissus mosaic virus and the Potato aucuba mosaic virus. We found encapsidated potexviral RNA to share common translational features in vitro and the MP1 to be potent over homological virions of its "own" species and over heterological virions of other species, as well exhibiting selective specificity...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29340096/crispr-cas9-mediated-reversibly-immortalized-mouse-bone-marrow-stromal-stem-cells-bmscs-retain-multipotent-features-of-mesenchymal-stem-cells-mscs
#14
Xue Hu, Li Li, Xinyi Yu, Ruyi Zhang, Shujuan Yan, Zongyue Zeng, Yi Shu, Chen Zhao, Xingye Wu, Jiayan Lei, Yasha Li, Wenwen Zhang, Chao Yang, Ke Wu, Ying Wu, Liping An, Shifeng Huang, Xiaojuan Ji, Cheng Gong, Chengfu Yuan, Linghuan Zhang, Wei Liu, Bo Huang, Yixiao Feng, Bo Zhang, Rex C Haydon, Hue H Luu, Russell R Reid, Michael J Lee, Jennifer Moriatis Wolf, Zebo Yu, Tong-Chuan He
Mesenchymal stem cells (MSCs) are multipotent non-hematopoietic progenitor cells that can undergo self-renewal and differentiate into multi-lineages. Bone marrow stromal stem cells (BMSCs) represent one of the most commonly-used MSCs. In order to overcome the technical challenge of maintaining primary BMSCs in long-term culture, here we seek to establish reversibly immortalized mouse BMSCs (imBMSCs). By exploiting CRISPR/Cas9-based homology-directed-repair (HDR) mechanism, we target SV40T to mouse Rosa26 locus and efficiently immortalize mouse BMSCs (i...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339647/proceedings-of-the-11th-congress-of-the-international-society-of-nutrigenetics-and-nutrigenomics-isnn-2017
#15
William T Barrington, Anna C Salvador, Jaana A Hartiala, Raffaele De Caterina, Martin Kohlmeier, J Alfredo Martinez, Carin B Kreutzer, David Heber, Aldons J Lusis, Zhaoping Li, Hooman Allayee
The International Society of Nutrigenetics and Nutrigenomics (ISNN) held its 11th annual Congress in Los Angeles, California, between September 16 and 19, 2017. In addition to 2 keynote lectures, 4 plenary sessions included presentations by internationally renowned speakers on cutting-edge areas of research and new discoveries in genetics/genomics, the microbiome, and nutrition. Scientific topics included multi-omics approaches; diet and the microbiome; cancer, longevity, and metabolism; moving the field forward; and translational/educational aspects and the future of medicine...
January 17, 2018: Journal of Nutrigenetics and Nutrigenomics
https://www.readbyqxmd.com/read/29339407/genomic-identification-and-functional-characterization-of-essential-genes-in-caenorhabditis-elegans
#16
Zhaozhao Qin, Robert Johnsen, Shicheng Yu, Jeffrey Shih-Chieh Chu, David Baillie, Nansheng Chen
Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of C. elegans totalling approximately 14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins...
January 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29338766/identification-of-differentially-expressed-genes-and-pathways-for-intramuscular-fat-metabolism-between-breast-and-thigh-tissues-of-chickens
#17
Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu, Jie Wen
BACKGROUND: Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a systematic identification of differentially expressed genes (DEGs) and molecular regulatory mechanism related to IMF metabolism between Beijing-you chicken breast and thigh at 42 and 90 days of age was performed. RESULTS: IMF contents, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, The results showed that both IMF contents in breast at 42 and 90 d were significantly lower (P < 0...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29337910/network-based-methods-for-identifying-key-active-proteins-in-the-extracellular-electron-transfer-process-in-shewanella-oneidensis-mr-1
#18
Dewu Ding, Xiao Sun
Shewanella oneidensis MR-1 can transfer electrons from the intracellular environment to the extracellular space of the cells to reduce the extracellular insoluble electron acceptors (Extracellular Electron Transfer, EET). Benefiting from this EET capability, Shewanella has been widely used in different areas, such as energy production, wastewater treatment, and bioremediation. Genome-wide proteomics data was used to determine the active proteins involved in activating the EET process. We identified 1012 proteins with decreased expression and 811 proteins with increased expression when the EET process changed from inactivation to activation...
January 16, 2018: Genes
https://www.readbyqxmd.com/read/29337437/canonical-signaling-and-nuclear-activity-of-mtor-a-teamwork-effort-to-regulate-metabolism-and-cell-growth
#19
REVIEW
Vincent Giguère
Mechanistic (or mammalian) target of rapamycin (mTOR) is a kinase that regulates almost all functions related to cell growth and metabolism in response to extra- and intracellular stimuli such as availability of nutrients, presence of growth factors or the energy status of the cell. As part of two distinct protein complexes, mTORC1 and mTORC2, the kinase has been shown to influence cell growth and proliferation by controlling ribosome biogenesis, mRNA translation, carbohydrate and lipid metabolism, protein degradation, autophagy as well as microtubule and actin dynamics...
January 16, 2018: FEBS Journal
https://www.readbyqxmd.com/read/29337163/utility-of-ultra-deep-sequencing-for-detection-of-varicella-zoster-virus-antiviral-resistance-mutations
#20
Mélanie Mercier-Darty, David Boutolleau, Raphaël Lepeule, Christophe Rodriguez, Sonia Burrel
We report the first application of ultra-deep sequencing (UDS) to varicella-zoster virus (VZV) genotypic antiviral testing in a case of acyclovir-resistant VZV infection initially detected by Sanger sequencing within a deeply immunocompromised heart transplant recipient. As added-value compared to Sanger analysis, UDS revealed complex dynamics of viral population under antiviral pressure. Varicella-zoster virus (VZV) is a ubiquitous human herpesvirus affecting populations worldwide. VZV is commonly acquired in youth whose primary infection usually manifests as benign varicella (chickenpox)...
January 11, 2018: Antiviral Research
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