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Skin genomics

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https://www.readbyqxmd.com/read/28431039/genomic-data-for-78-chickens-from-14-populations
#1
Diyan Li, Tiandong Che, Binlong Chen, Shilin Tian, Xuming Zhou, Guolong Zhang, Miao Li, Uma Gaur, Yan Li, Majing Luo, Long Zhang, Zhongxian Xu, Xiaoling Zhao, Huadong Yin, Yan Wang, Long Jin, Qianzi Tang, Huailiang Xu, Mingyao Yang, Rongjia Zhou, Ruiqiang Li, Qing Zhu, Mingzhou Li
Background: Since the domestication of the red jungle fowls ( Gallus gallus ) (dating back to ∼10,000 B.P.) in Asia, domestic chickens ( Gallus gallus domesticus ) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production and skin color. Population genomic variations through diversifying selection have not been fully investigated...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430587/parkin-regulates-translesion-dna-synthesis-in-response-to-uv-radiation
#2
Xuefei Zhu, Xiaolu Ma, Yingfeng Tu, Min Huang, Hongmei Liu, Fengli Wang, Juanjuan Gong, Jiuqiang Wang, Xiaoling Li, Qian Chen, Hongyan Shen, Shu Zhu, Yun Wang, Yang Liu, Caixia Guo, Tie-Shan Tang
Deficiency of Parkin is a major cause of early-onset Parkinson's disease (PD). Notably, PD patients also exhibit a significantly higher risk in melanoma and other skin tumors, while the mechanism remains largely unknown. In this study, we show that depletion of Parkin causes compromised cell viability and genome stability after ultraviolet (UV) radiation. We demonstrate that Parkin promotes efficient Rad18-dependent proliferating cell nuclear antigen (PCNA) monoubiquitination by facilitating the formation of Replication protein A (RPA)-coated ssDNA upon UV radiation...
April 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/28427244/whole-genome-expression-analyses-of-type-2-diabetes-in-human-skin-reveal-altered-immune-function-and-burden-of-infection
#3
Chun Wu, Xiaopan Chen, Jing Shu, Chun-Ting Lee
Skin disorders are among most common complications associated with type 2 diabetes mellitus (T2DM). Although T2DM patients are known to have increased risk of infections and other T2DM-related skin disorders, their molecular mechanisms are largely unknown. This study aims to identify dysregulated genes and gene networks that are associated with T2DM in human skin. We compared the expression profiles of 56,318 transcribed genes on 74 T2DM cases and 148 gender- age-, and race-matched non-diabetes controls from the Genotype-Tissue Expression (GTEx) database...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426749/molecular-characterization-tissue-tropism-and-genetic-variability-of-the-novel-mupapillomavirus-type-hpv204-and-phylogenetically-related-types-hpv1-and-hpv63
#4
Anja Šterbenc, Lea Hošnjak, Diego Chouhy, Elisa M Bolatti, Anja Oštrbenk, Katja Seme, Boštjan J Kocjan, Boštjan Luzar, Adriana A Giri, Mario Poljak
HPV204 is the only newly identified Mupapillomavirus (Mu-PV) type in more than a decade. To comprehensively characterize HPV204, we performed a detailed molecular analysis of the viral genome and evaluated its clinical relevance in comparison to the other Mu-PVs, HPV1 and HPV63. The 7,227-bp long genome of HPV204 exhibits typical genomic organization of Mu-PVs with eight open reading frames (ORFs) (E6, E7, E1, E2, E8, E4, L2, and L1). We developed three type-specific quantitative real-time PCRs and used them to test a representative collection (n = 1,006) of various HPV-associated benign and malignant neoplasms, as well as samples of clinically normal cutaneous, mucosal, and mucocutaneous origins...
2017: PloS One
https://www.readbyqxmd.com/read/28420421/analysis-of-100-000-human-cancer-genomes-reveals-the-landscape-of-tumor-mutational-burden
#5
Zachary R Chalmers, Caitlin F Connelly, David Fabrizio, Laurie Gay, Siraj M Ali, Riley Ennis, Alexa Schrock, Brittany Campbell, Adam Shlien, Juliann Chmielecki, Franklin Huang, Yuting He, James Sun, Uri Tabori, Mark Kennedy, Daniel S Lieber, Steven Roels, Jared White, Geoffrey A Otto, Jeffrey S Ross, Levi Garraway, Vincent A Miller, Phillip J Stephens, Garrett M Frampton
BACKGROUND: High tumor mutational burden (TMB) is an emerging biomarker of sensitivity to immune checkpoint inhibitors and has been shown to be more significantly associated with response to PD-1 and PD-L1 blockade immunotherapy than PD-1 or PD-L1 expression, as measured by immunohistochemistry (IHC). The distribution of TMB and the subset of patients with high TMB has not been well characterized in the majority of cancer types. METHODS: In this study, we compare TMB measured by a targeted comprehensive genomic profiling (CGP) assay to TMB measured by exome sequencing and simulate the expected variance in TMB when sequencing less than the whole exome...
April 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28419202/genomic-characterization-of-usa300-mrsa-to-evaluate-intraclass-transmission-and-recurrence-of-ssti-among-high-risk-military-trainees
#6
Eugene V Millar, Gregory K Rice, Emad M Elassal, Carey D Schlett, Jason W Bennett, Cassie L Redden, Deepika Mor, Natasha N Law, David R Tribble, Theron Hamilton, Michael W Ellis, Kimberly A Bishop-Lilly
Background.: Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. Methods.: We conducted a prospective case-control study of SSTI among US Army Infantry trainees at Fort Benning, GA from July 2012-December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates...
April 17, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28414762/transcriptional-networks-are-associated-with-resistance-to-mycobacterium-tuberculosis-infection
#7
Chetan Seshadri, Nafiseh Sedaghat, Monica Campo, Glenna Peterson, Richard D Wells, Gregory S Olson, David R Sherman, Catherine M Stein, Harriet Mayanja-Kizza, Ali Shojaie, W Henry Boom, Thomas R Hawn
RATIONALE: Understanding mechanisms of resistance to M. tuberculosis (M.tb) infection in humans could identify novel therapeutic strategies as it has for other infectious diseases, such as HIV. OBJECTIVES: To compare the early transcriptional response of M.tb-infected monocytes between Ugandan household contacts of tuberculosis patients who demonstrate clinical resistance to M.tb infection (cases) and matched controls with latent tuberculosis infection. METHODS: Cases (n = 10) and controls (n = 18) were selected from a long-term household contact study in which cases did not convert their tuberculin skin test (TST) or develop tuberculosis over two years of follow up...
2017: PloS One
https://www.readbyqxmd.com/read/28414163/droplet-digital-pcr-ddpcr-vs-quantitative-real-time-pcr-qpcr-approach-for-detection-and-quantification-of-merkel-cell-polyomavirus-mcpyv-dna-in-formalin-fixed-paraffin-embedded-ffpe-cutaneous-biopsies
#8
Rosaria Arvia, Mauro Sollai, Federica Pierucci, Carmelo Urso, Daniela Massi, Krystyna Zakrzewska
BACKGROUND: Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. OBJECTIVE: To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples...
April 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28413781/sequencing-and-de-novo-transcriptome-assembly-of-the-chinese-giant-salamander-andrias-davidianus
#9
Yong Huang, Xiao Chan Gao, Jian Li Xiong, Hong Tao Ren, Xi Hong Sun
Next-generation technologies for determination of genomics and transcriptomics composition have a wide range of applications. Andrias davidianus, has become an endangered amphibian species of salamander endemic in China. However, there is a lack of the molecular information. In this study, we obtained the RNA-Seq data from a pool of A. davidianus tissue including spleen, liver, muscle, kidney, skin, testis, gut and heart using Illumina HiSeq 2500 platform. A total of 15,398,997,600 bp were obtained, corresponding to 102,659,984 raw reads...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28411854/the-molecular-revolution-in-cutaneous-biology-chromosomal-territories-higher-order-chromatin-remodeling-and-the-control-of%C3%A2-gene-expression-in-keratinocytes
#10
REVIEW
Vladimir A Botchkarev
Three-dimensional organization of transcription in the nucleus and mechanisms controlling the global chromatin folding, including spatial interactions between the genes, noncoding genome elements, and epigenetic and transcription machinery, are essential for establishing lineage-specific gene expression programs during cell differentiation. Spatial chromatin interactions in the nucleus involving gene promoters and distal regulatory elements are currently considered major forces that drive cell differentiation and genome evolution in general, and such interactions are substantially reorganized during many pathological conditions...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411853/the-molecular-revolution-in-cutaneous-biology-the-era-of-global-transcriptional-analysis
#11
REVIEW
Andrew Johnston, Mrinal K Sarkar, Antonia Vrana, Lam C Tsoi, Johann E Gudjonsson
In the 3 decades since the discovery of the polymerase chain reaction, a progression of remarkable technical advances has driven great strides in our understanding of molecular biology such that now we are able to study at once the entire and complete set of RNA transcripts that are produced by the genome. In this review, we describe the milestones that have led to this era of global transcriptional analysis, how these approaches have been extended towards skin disease, and their future directions.
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411843/the-molecular-revolution-in-cutaneous-biology-emerging-landscape-in-genomic-dermatology-new-mechanistic-ideas-gene-editing-and-therapeutic-breakthroughs
#12
REVIEW
Matthias Titeux, Araksya Izmiryan, Alain Hovnanian
Stunning technological advances in genomics have led to spectacular breakthroughs in the understanding of the underlying defects, biological pathways and therapeutic targets of skin diseases leading to new therapeutic interventions. Next-generation sequencing has revolutionized the identification of disease-causing genes and has a profound impact in deciphering gene and protein signatures in rare and frequent skin diseases. Gene addition strategies have shown efficacy in junctional EB and in recessive dystrophic EB (RDEB)...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411841/the-molecular-revolution-in-cutaneous-biology-the-era-of-genome-wide-association-studies-and-statistical-big%C3%A2-data-and-computational-topics
#13
REVIEW
Hima Anbunathan, Anne M Bowcock
The investigation of biological systems involving all organs of the body including the skin is in era of big data. This requires heavy-duty computational tools, and novel statistical methods. Microarrays have allowed the interrogation of thousands of common genetic markers in thousands of individuals from the same population (termed genome wide association studies or GWAS) to reveal common variation associated with disease or phenotype. These markers are usually single nucleotide polymorphisms (SNPs) that are relatively common in the population...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28411840/the-molecular-revolution-in-cutaneous-biology-noncoding-rnas-new-molecular-players-in-dermatology-and-cutaneous-biology
#14
REVIEW
Natalia V Botchkareva
Progress in genome sequencing achieved during the last two decades revealed that only about 2% of the genome codes for proteins, while the largest genome fraction is encoding thousands of non-coding RNAs. Non-coding RNAs play indispensable roles in regulating the activity and stability of the genome. Recent research in the area of the non-coding transcriptome signified the crucial roles for RNA regulatory networks in the normal development and their implications in a variety of pathological conditions. Here, recent advances in our understanding of non-coding RNA-mediated regulation of skin development and homeostasis are highlighted, focusing mainly on the regulatory roles of miRNAs and lncRNAs...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28408691/whole-genome-sequence-of-staphylococcus-hominis-strain-j31-isolated-from-healthy-human-skin
#15
Rosanna Coates-Brown, Malcolm J Horsburgh
We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.
April 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28407719/anti-inflammatory-activity-of-clove-eugenia-caryophyllata-essential-oil-in-human-dermal-fibroblasts
#16
Xuesheng Han, Tory L Parker
CONTEXT: Clove (Eugenia caryophyllata Thunb. [Myrtaceae]) essential oil (CEO) has been shown to possess antimicrobial, antifungal, antiviral, antioxidant, anti-inflammatory and anticancer properties. However, few studies have focused on its topical use. OBJECTIVE: We investigated the biological activity of a commercially available CEO in a human skin disease model. MATERIALS AND METHODS: We evaluated the effect of CEO on 17 protein biomarkers that play critical roles in inflammation and tissue remodelling in a validated human dermal fibroblast system, which was designed to model chronic inflammation and fibrosis...
December 2017: Pharmaceutical Biology
https://www.readbyqxmd.com/read/28407332/transcriptome-analysis-of-severely-active-chronic-spontaneous-urticaria-shows-an-overall-immunological-skin-involvement
#17
A Giménez-Arnau, L Curto-Barredo, L Nonell, E Puigdecanet, J Yelamos, R Gimeno, S Rüberg, L Santamaria-Babi, R M Pujol
BACKGROUND: The knowledge about chronic spontaneous urticaria (CSU) phenotypes is based on its clinical characteristics, associated comorbidities, course of the disease and its response to the available effective drugs. Genotype expression and its further correlation with CSU phenotypes are still unknown. We describe the cutaneous transcriptome of patients suffering a severely active CSU refractory to antihistamine treatment. METHODS: Through the bioinformatic analysis of the whole Human Genome with Oligo Microarrays and Quantitative real-time polymerase chain reaction (qPCR), relevant genes expressed in non-lesional [NLS-CSU] and lesional skin [LS-CSU]) and peripheral blood were identified in 20 patients suffering from severely active CSU and 10 healthy controls (HCs) RESULTS: From 39 genes differentially expressed in NLS-CSU when compared with HCs, 31 (79...
April 13, 2017: Allergy
https://www.readbyqxmd.com/read/28403479/the-gard-platform-for-potency-assessment-of-skin-sensitizing-chemicals
#18
Kathrin S Zeller, Andy Forreryd, Tim Lindberg, Robin Gradin, Aakash Chawade, Malin Lindstedt
Contact allergy induced by certain chemicals is a common health concern, and several alternative methods have been developed to fulfill the requirements of European legislation with regard to hazard assessment of potential skin sensitizers. However, validated methods, which provide information about the potency of skin sensitizers, are still lacking. The cell-based assay Genomic Allergen Rapid Detection (GARD), targeting key event 3, dendritic cell activation, of the skin sensitizer AOP, uses gene expression profiling and a machine learning approach for the prediction of chemicals as sensitizers or non-sensitizers...
April 12, 2017: ALTEX
https://www.readbyqxmd.com/read/28401320/the-virulence-factors-of-group-a-streptococcus-strains-isolated-from-invasive-and-non-invasive-infections-in-polish-and-german-centres-2009-2011
#19
M Strus, P B Heczko, E Golińska, A Tomusiak, A Chmielarczyk, M Dorycka, M van der Linden, A Samet, A Piórkowska
Streptococcus pyogenes (GAS) is one of the major human pathogenic bacteria that cause a wide range of diseases. Currently, increased incidence of streptococcal invasive infections is observed worldwide. In this study, we focused on the prevalence of genes encoding superantigens and type M proteins in the population of GAS strains from invasive versus non-invasive infections. We tested 253 GAS strains: 48 strains from patients with invasive infections (18 from wound/deep skin localization, 30 from women in labour) and 205 strains from non-invasive forms (147 from common infections of the upper respiratory, 49 from the vagina of females with genital tract infections and 9 from non-invasive wound and superficial skin infections)...
April 11, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28399906/target-organs-for-lymphocystis-disease-virus-replication-in-gilthead-seabream-sparus-aurata
#20
Estefania J Valverde, Juan J Borrego, M Carmen Sarasquete, Juan B Ortiz-Delgado, Dolores Castro
The lymphocystis disease (LCD), the main viral pathology described in cultured gilthead seabream (Sparus aurata), is a self-limiting condition characterized by the appearance of hypertrophied fibroblasts (named lymphocysts) in the connective tissue of fish, primarily in the skin and fins. The causative agent of the disease is the Lymphocystis disease virus (LCDV), a member of the Iridoviridae family. In the present study, LCDV genome and transcripts were detected by real-time PCR in caudal fin, as well as in several internal organs, such as intestine, liver, spleen, kidney and brain, from asymptomatic, diseased and recovered gilthead seabream juveniles...
April 11, 2017: Veterinary Research
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