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Clinical genomics

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https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#1
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911167/recommendations-for-a-nomenclature-system-for-reporting-methylation-aberrations-in-imprinted-domains
#2
David Monk, Joannella Morales, Johan T den Dunnen, Silvia Russo, Franck Court, Dirk Prawitt, Thomas Eggermann, Jasmin Beygo, Karin Buiting, Zeynep Tümer
The analysis of DNA methylation has become routine in the pipeline for diagnosis of imprinting disorders, with many publications reporting aberrant methylation associated with imprinted differentially methylated regions (DMRs). However, comparisons between these studies are routinely hampered by the lack of consistency in reporting sites of methylation evaluated. To avoid confusion surrounding nomenclature, special care is needed to communicate results accurately, especially between scientists and other health care professionals...
December 2, 2016: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/27910939/real-time-pcr-based-serotyping-of-streptococcus-agalactiae
#3
Kathleen M Breeding, Bhavana Ragipani, Kun-Uk David Lee, Martin Malik, Tara M Randis, Adam J Ratner
Group B Streptococcus (GBS) is an encapsulated, gram-positive pathogen that is an important cause of neonatal invasive infections, including sepsis and meningitis. There are ten known GBS serotypes based on distinct capsule compositions (Ia, Ib, II-IX), and current candidate capsular polysaccharide conjugate vaccines target only a subset of these. Serotyping of GBS isolates is important for understanding local epidemiology and for monitoring for serotype replacement or capsular switching. However, serotyping generally requires either latex agglutination, multiplex PCR with analysis of band sizes, or analysis of whole genome sequences-all techniques that are either expensive or not widely available...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910897/genomic-variations-leading-to-alterations-in-cell-morphology-of-campylobacter-spp
#4
Diane Esson, Alison E Mather, Eoin Scanlan, Srishti Gupta, Stefan P W de Vries, David Bailey, Simon R Harris, Trevelyan J McKinley, Guillaume Méric, Sophia K Berry, Pietro Mastroeni, Samuel K Sheppard, Graham Christie, Nicholas R Thomson, Julian Parkhill, Duncan J Maskell, Andrew J Grant
Campylobacter jejuni, the most common cause of bacterial diarrhoeal disease, is normally helical. However, it can also adopt straight rod, elongated helical and coccoid forms. Studying how helical morphology is generated, and how it switches between its different forms, is an important objective for understanding this pathogen. Here, we aimed to determine the genetic factors involved in generating the helical shape of Campylobacter. A C. jejuni transposon (Tn) mutant library was screened for non-helical mutants with inconsistent results...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27910877/a-comprehensive-map-of-molecular-drug-targets
#5
Rita Santos, Oleg Ursu, Anna Gaulton, A Patrícia Bento, Ramesh S Donadi, Cristian G Bologa, Anneli Karlsson, Bissan Al-Lazikani, Anne Hersey, Tudor I Oprea, John P Overington
The success of mechanism-based drug discovery depends on the definition of the drug target. This definition becomes even more important as we try to link drug response to genetic variation, understand stratified clinical efficacy and safety, rationalize the differences between drugs in the same therapeutic class and predict drug utility in patient subgroups. However, drug targets are often poorly defined in the literature, both for launched drugs and for potential therapeutic agents in discovery and development...
December 2, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27910803/the-prognostic-and-predictive-value-of-tmprss2-erg-gene-fusion-and-erg-protein-expression-in-prostate-cancer-biopsies
#6
Kasper Drimer Berg
BACKGROUND: The clinical course of prostate carcinoma (PCa) is very heterogeneous. Consequently, a personalised approach for risk stratification and treatment planning is important. Recently, it has become evident that PCa, also at the genomic level, is heterogeneous. An early and common alteration is the gene fusion between the transmembrane protease serine 2 (TMPRSS2) gene and the v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) gene resulting in expression of the oncoprotein ERG...
December 2016: Danish Medical Journal
https://www.readbyqxmd.com/read/27910030/recurrent-cytogenetic-abnormalities-in-non-hodgkin-s-lymphoma-and-chronic-lymphocytic-leukemia
#7
Edmond S K Ma
Characteristic chromosomal translocations are found to be associated with subtypes of B-cell non-Hodgkin lymphoma (NHL), for example t(8;14)(q24;q32) and Burkitt lymphoma, t(14;18)(q32;q21) and follicular lymphoma, and t(11;14)(q13;q32) in mantle cell lymphoma. Only few recurrent cytogenetic aberrations have been identified in the T-cell NHL and the best known is the ALK gene translocation t(2;5)(p23;q35) in anaplastic large cell lymphoma. Since lymph node or other tissue is seldom submitted for conventional cytogenetics study, alternative approaches for translocation detection are polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909873/neutrophil-to-lymphocyte-ratio-associated-with-prognosis-of-lung-cancer
#8
V Bar-Ad, J Palmer, L Li, Y Lai, B Lu, R E Myers, Z Ye, R Axelrod, J M Johnson, M Werner-Wasik, S W Cowan, N R Evans, B T Hehn, C C Solomides, C Wang
PURPOSE: Many studies recently focus on complicated and expensive genomic tests, but the prognostic values of biochemical markers which are easily obtained in clinics are largely overlooked and without further exploration. This study assesses the association of neutrophil-lymphocyte-ratio (NLR) with prognosis of lung cancer patients. METHODS: In 1032 patients with histologically confirmed lung cancer, the association of pretreatment NLR values with overall survival (OS) was evaluated using a Cox proportional hazards model and the temporal relationship of longitudinal NLR was assessed using a mixed effects model...
December 1, 2016: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/27909331/dissecting-suicidality-using-a-combined-genomic-and-clinical-approach
#9
Alexander B Niculescu, Helen Le-Niculescu
No abstract text is available yet for this article.
January 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/27908990/draft-genome-sequences-of-campylobacter-jejuni-strains-that-cause-abortion-in-livestock
#10
Allison M Weis, Kristin A Clothier, Bihua C Huang, Nguyet Kong, Bart C Weimer
Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 Campylobacter jejuni genome sequences from isolates linked to abortion in livestock. These isolates are part of the 100K Pathogen Genome Project and are from clinical cases at the University of California (UC) Davis.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908989/draft-genome-sequence-of-the-yeast-saccharomyces-cerevisiae-guj105-from-gujarat-india
#11
Chandan Badapanda, Rajesh Detroja, Ankita Rathore
Here, we report the draft genome sequence of Saccharomyces cerevisiae strain GUJ105, isolated clinically. The size of the genome is approximately 11.5 Mb and contains 5,447 protein-coding genes.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908987/draft-genome-sequences-of-three-clinical-isolates-of-tannerella-forsythia-isolated-from-subgingival-plaque-from-periodontitis-patients-in-the-united-states
#12
Graham P Stafford, Roy R Chaudhuri, Violet Haraszthy, Valentin Friedrich, Christina Schäffer, Angela Ruscitto, Kiyonobu Honma, Ashu Sharma
We report the genome sequences of three clinical isolates of Tannerella forsythia from the subgingival plaque of periodontitis patients attending clinics at the School of Dental Medicine, University at Buffalo. The availability of these genome sequences will aid the understanding of the pathogenesis of periodontitis.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908827/different-routes-and-doses-influence-protection-in-pigs-immunised-with-the-naturally-attenuated-african-swine-fever-virus-isolate-ourt88-3
#13
Pedro J Sánchez-Cordón, Dave Chapman, Tamara Jabbar, Ana L Reis, Lynnette Goatley, Christopher L Netherton, Geraldine Taylor, Maria Montoya, Linda Dixon
This study compares different combinations of doses and routes of immunisation of pigs with low virulent African swine fever virus (ASFV) genotype I isolate OURT88/3, including the intramuscular and intranasal route, the latter not previously tested. Intranasal immunisations with low and moderate doses (10(3) and 10(4) TCID50) of OURT88/3 provided complete protection (100%) against challenge with virulent genotype I OURT88/1 isolate. Only mild and transient clinical reactions were observed in protected pigs...
November 28, 2016: Antiviral Research
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#14
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27908669/cellular-responses-to-replication-stress-implications-in-cancer-biology-and-therapy
#15
REVIEW
Hui-Ju Hsieh, Guang Peng
DNA replication is essential for cell proliferation. Any obstacles during replication cause replication stress, which may lead to genomic instability and cancer formation. In this review, we summarize the physiological DNA replication process and the normal cellular response to replication stress. We also outline specialized therapies in clinical trials based on current knowledge and future perspectives in the field.
November 22, 2016: DNA Repair
https://www.readbyqxmd.com/read/27908228/detection-of-mutations-in-mitochondrial-dna-by-droplet-digital-pcr
#16
J K Sofronova, Y Y Ilinsky, K E Orishchenko, E G Chupakhin, E A Lunev, I O Mazunin
Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy - a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-to-date methods that have not yet been introduced as routine clinical assays...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906881/stem-cells-and-clinical-practice-new-advances-and-challenges-at-the-time-of-emerging-problems-with-induced-pluripotent-stem-cell-therapies
#17
Mariusz Z Ratajczak, Kamila Bujko, Wojciech Wojakowski
Humans, like other species that reproduce sexually, originate from a fertilized oocyte (zygote), which is a totipotent stem cell giving rise to an adult organism. During the process of embryogenesis, stem cells at different levels of the developmental hierarchy establish all 3 germ layers and give rise to tissue‑committed stem cells, which are responsible for rejuvenation of a given tissue or organ. The robustness of the stem cell compartment is one of the major factors that directly impact life quality as well as lifespan...
November 10, 2016: Polskie Archiwum Medycyny Wewnętrznej
https://www.readbyqxmd.com/read/27906774/lessons-from-characterization-and-treatment-of-the-autoinflammatory-syndromes
#18
Ivona Aksentijevich, Michael F McDermott
PURPOSE OF REVIEW: The list of genes associated with systemic inflammatory diseases has been steadily growing because of the explosion of new genomic technologies. Significant advances in the past year have deepened our understanding of the molecular mechanisms linked to inflammation and elucidated insights on the efficacy of specific therapies for these and related conditions. We review the molecular pathogenesis of four recently characterized monogenic autoinflammatory diseases: haploinsufficiency of A20, otulipenia, a severe form of pyrin-associated disease, and a monogenic form of systemic juvenile idiopathic arthritis...
November 30, 2016: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/27906711/polycystic-ovary-syndrome-in-adolescent-girls
#19
Natalie Hecht Baldauff, Selma Feldman Witchel
PURPOSE OF REVIEW: Polycystic ovary syndrome (PCOS) is a common heterogeneous disorder that appears to have its origins during the peripubertal years. The diagnostic conundrum is that the typical clinical features, irregular menses and acne, occur during normal female puberty. Understanding the physiologic origins and molecular basis of the dysregulated hypothalamic-pituitary-gonadal axis in PCOS is fundamental to interrupting the distinctive vicious cycle of hyperandrogenism and chronic anovulation...
November 30, 2016: Current Opinion in Endocrinology, Diabetes, and Obesity
https://www.readbyqxmd.com/read/27906186/preimplantation-factor-is-an-anti-apoptotic-effector-in-human-trophoblasts-involving-p53-signaling-pathway
#20
Hadia Moindjie, Esther Dos Santos, Rita-Josiane Gouesse, Nelly Swierkowski-Blanchard, Valérie Serazin, Eytan R Barnea, François Vialard, Marie-Noëlle Dieudonné
From the earliest stages of gestation, embryonic-maternal interaction has a key role in a successful pregnancy. Various factors present during gestation may significantly influence this type of juxta/paracrine interaction. PreImplantation Factor (PIF) is a recently identified factor with activity at the fetomaternal interface. PIF is secreted by viable embryos and directly controls placental development by increasing the invasive capacity of human extravillous trophoblasts (EVTs). To further specify PIF's role in the human placenta, we analyzed the genome-wide expression profile of the EVT in the presence of a synthetic PIF analog (sPIF)...
December 1, 2016: Cell Death & Disease
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