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Skin genomics

Pengfei Fan, Yang Liu, Zhechun Zhang, Chao Zhao, Cheng Li, Wulin Liu, Zhijin Liu, Ming Li
The white-cheeked macaque Macaca leucogenys is a recently described species that was only diagnosed based on photos, without any specimen measurements or molecular genetic diagnosis. Using extracted DNA from four newly collected skin specimens, we studied the genetic diversity and phylogenetic position of M. leucogenys using multilocus sequence data, including mitochondrial and Y chromosomal genes. Skin measurements of four individuals showed that the white-cheeked macaque is robust and larger than M. assamensis but is similar in body size to M...
October 18, 2016: Molecular Phylogenetics and Evolution
Shelby Calkins, M B Couger, Colin Jackson, Jordan Zandler, Garett C Hudgins, Radwa A Hanafy, Connie Budd, Donald P French, Wouter D Hoff, Noha Youssef
Staphylococcus hominis is a predominant member of the human skin microbiome. We here report on the genomic analysis of Staphylococcus hominis strain Hudgins that was isolated from the wrist area of human skin. The partial genome assembly of S. hominis Hudgins consists of 2,211,863 bp of DNA with 2174 protein-coding genes and 90 RNA genes. Based on the genomic analysis of KEGG pathways, the organism is expected to be a versatile heterotroph potentially capable of hydrolyzing the sugars glucose, fructose, mannose, and the amino acids alanine, aspartate, glutamate, glycine, threonine, cysteine, methionine, valine, isoleucine, leucine, lysine, arginine, phenylalanine, tyrosine, and tryptophan for energy production through aerobic respiration, with occasional lactate and acetate fermentation...
December 2016: Genomics Data
Riccardo Paolo Lia, Yasen Mutafchiev, Vincenzo Veneziano, Alessio Giannelli, Francesca Abramo, Mario Santoro, Maria Stefania Latrofa, Cinzia Cantacessi, Coralie Martin, Domenico Otranto, Andrea Bertuglia, Barbara Riccio
Equids can be infected by a range of skin-dwelling filarial nematodes, including four species of the genus Onchocerca. Current literature on equine onchocercosis is fragmentary and often limited to isolated case reports. The present study aimed to describe a clinical case of equine onchocercosis caused by Onchocerca boehmi (Supperer, 1953) (syn. Elaeophora boehmi) in an 8-year-old gelding Belgian show jumper from northern Italy. The horse was presented with a firm and painless mass on the proximal third of the right metacarpal region...
October 19, 2016: Parasitology Research
Ryosuke Kita, Hunter B Fraser
Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin...
October 2016: PLoS Genetics
Carmen Capel, Fernando J Yuste-Lisbona, Gloria López-Casado, Trinidad Angosto, Jesús Cuartero, Rafael Lozano, Juan Capel
QTL and codominant genetic markers for fruit cracking have been identified in a tomato genetic map derived from a RIL population, providing molecular tools for marker-assisted breeding of this trait. In tomato, as well as in other fleshy fruits, one of the main disorders that widely limit quality and production is fruit cracking or splitting of the epidermis that is observed on the fruit skin and flesh at any stage of fruit growth and maturation. To elucidate the genetic basis of fruit cracking, a quantitative trait loci (QTL) analysis was conducted in a recombinant inbred line (RIL) population derived from a cross between tomato (Solanum lycopersicum) and the wild-relative species S...
October 14, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Jia-Yun C Tsai, Jacelyn M S Loh, Fiona Clow, Natalie Lorenz, Thomas Proft
Group A Streptococcus (GAS), or Streptococcus pyogenes, is a human pathogen that causes diseases ranging from skin and soft tissue infections to severe invasive diseases, such as toxic shock syndrome. Each GAS strain carries a particular pilus type encoded in the variable fibronectin-binding, collagen-binding, T antigen (FCT) genomic region. Here we describe the functional analysis of the serotype M2 pilus encoded in the FCT-6 region. We found that, in contrast to other investigated GAS pili, the ancillary pilin 1 lacks adhesive properties...
October 14, 2016: Molecular Microbiology
L F S Batista, Y T Utsunomiya, T B F da Silva, R A Dias, T Y Tomokane, A D Pacheco, V L R da Matta, F T Silveira, M Marcondes, C M Nunes, M D Laurenti
A genome-wide association study (GWAS) could unravel the complexity of the cell-mediated immunity (CMI) to canine leishmaniasis (CanL). Thereby we committed to scan 110,165 single-nucleotide polymorphisms (SNPs) aiming to identify chromosomal regions associated to leishmanin skin test (LST), lymphocyte proliferation assay (LPA) and cytokines responses to further understanding the role played by the CMI in the outcome of the natural Leishmania infantum infection in 189 dogs. Based on LST and LPA, four CMI profiles were identified (LST-/LPA-, LST+/LPA-, LST-/LPA+ and LST+/LPA+), which were not associated to subclinical infected or diseased dogs...
October 10, 2016: Infection and Immunity
Epameinondas Gousopoulos, Steven T Proulx, Samia B Bachmann, Jeannette Scholl, Dimitris Dionyssiou, Efterpi Demiri, Cornelia Halin, Lothar C Dieterich, Michael Detmar
Secondary lymphedema is a common postcancer treatment complication, but the underlying pathological processes are poorly understood and no curative treatment exists. To investigate lymphedema pathomechanisms, a top-down approach was applied, using genomic data and validating the role of a single target. RNA sequencing of lymphedematous mouse skin indicated upregulation of many T cell-related networks, and indeed depletion of CD4(+) cells attenuated lymphedema. The significant upregulation of Foxp3, a transcription factor specifically expressed by regulatory T cells (Tregs), along with other Treg-related genes, implied a potential role of Tregs in lymphedema...
October 6, 2016: JCI Insight
Susanne Stemmler, Sabine Hoffjan
Atopic dermatitis (AD) is a common and complex skin disease associated with both genetic and environmental factors. Loss-of-function mutations in the filaggrin gene, encoding a structural protein with an important role in epidermal barrier function, constitutes a well recognised susceptibility locus for AD. Further, genome-wide association studies (GWAS), including large meta-analyses, have discovered 38 additional susceptibility loci with genome-wide significance. However, the reported variations only explain a fraction of the overall heritability of AD...
October 7, 2016: Molecular and Cellular Probes
Ying Jin, Genevieve Andersen, Daniel Yorgov, Tracey M Ferrara, Songtao Ben, Kelly M Brownson, Paulene J Holland, Stanca A Birlea, Janet Siebert, Anke Hartmann, Anne Lienert, Nanja van Geel, Jo Lambert, Rosalie M Luiten, Albert Wolkerstorfer, J P Wietze van der Veen, Dorothy C Bennett, Alain Taïeb, Khaled Ezzedine, E Helen Kemp, David J Gawkrodger, Anthony P Weetman, Sulev Kõks, Ele Prans, Külli Kingo, Maire Karelson, Margaret R Wallace, Wayne T McCormack, Andreas Overbeck, Silvia Moretti, Roberta Colucci, Mauro Picardo, Nanette B Silverberg, Mats Olsson, Yan Valle, Igor Korobko, Markus Böhm, Henry W Lim, Iltefat Hamzavi, Li Zhou, Qing-Sheng Mi, Pamela R Fain, Stephanie A Santorico, Richard A Spritz
Vitiligo is an autoimmune disease in which depigmented skin results from the destruction of melanocytes, with epidemiological association with other autoimmune diseases. In previous linkage and genome-wide association studies (GWAS1 and GWAS2), we identified 27 vitiligo susceptibility loci in patients of European ancestry. We carried out a third GWAS (GWAS3) in European-ancestry subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication...
October 10, 2016: Nature Genetics
Inmaculada Moreno, Francisco M Codoñer, Felipe Vilella, Diana Valbuena, Juan F Martinez-Blanch, Jorge Jimenez-Almazán, Roberto Alonso, Pilar Alamá, Jose Remohí, Antonio Pellicer, Daniel Ramon, Carlos Simon
BACKGROUND: Bacterial cells in the human body account for 1-3% of total body weight and are at least equal in number to human cells. Recent research has focused on understanding how the different bacterial communities in the body (eg, gut, respiratory, skin, and vaginal microbiomes) predispose to health and disease. The microbiota of the reproductive tract has been inferred from the vaginal bacterial communities, and the uterus has been classically considered a sterile cavity. However, while the vaginal microbiota has been investigated in depth, there is a paucity of consistent data regarding the existence of an endometrial microbiota and its possible impact in reproductive function...
October 4, 2016: American Journal of Obstetrics and Gynecology
Peng Mao, John J Wyrick, Steven A Roberts, Michael J Smerdon
UV radiation induces photolesions that distort the DNA double helix and, if not repaired, can cause severe biological consequences, including mutagenesis or cell death. In eukaryotes, both the formation and repair of UV damage occur in the context of chromatin, in which genomic DNA is packaged with histones into nucleosomes and higher-order chromatin structures. Here, we review how chromatin impacts the formation of UV photoproducts in eukaryotic cells. We describe the initial discovery that nucleosomes and other DNA-binding proteins induce characteristic 'photofootprints' during the formation of UV photoproducts...
September 26, 2016: Photochemistry and Photobiology
Koki Fujimori, Toshiki Tezuka, Hiroyuki Ishiura, Jun Mitsui, Koichiro Doi, Jun Yoshimura, Hirobumi Tada, Takuya Matsumoto, Miho Isoda, Ryota Hashimoto, Nubutaka Hattori, Takuya Takahashi, Shinichi Morishita, Shoji Tsuji, Wado Akamatsu, Hideyuki Okano
Patient-specific induced pluripotent stem cells (iPSCs) facilitate understanding of the etiology of diseases, discovery of new drugs and development of novel therapeutic interventions. A frequently used starting source of cells for generating iPSCs has been dermal fibroblasts (DFs) isolated from skin biopsies. However, there are also numerous repositories containing lymphoblastoid B-cell lines (LCLs) generated from a variety of patients. To date, this rich bioresource of LCLs has been underused for generating iPSCs, and its use would greatly expand the range of targeted diseases that could be studied by using patient-specific iPSCs...
October 3, 2016: Molecular Brain
Guo-Dong Li, Dong Wang, Deng-Feng Zhang, Qun Xiang, Jia-Qi Feng, Xiao-An Li, Yu-Ye Li, Yong-Gang Yao
BACKGROUND: Previous genome-wide association study (GWAS) identified two new leprosy associated loci (1p31.3 [rs3762318] and 6q24.3 [rs2275606]). However, there were insufficient validations in independent populations. OBJECTIVE: To validate the association and to map the potentially causal variants/genes underlying the association between the confirmed GWAS hit and leprosy. METHODS: We genotyped 10 variants in the regions encompassing the two loci in 1110 Han Chinese subjects with and without leprosy, followed by expression quantitative trait loci (eQTL), mRNA expression profiling, and network analysis...
September 28, 2016: Journal of Dermatological Science
Andrei Kuzminov
As the ratio of the copy number of the most replicated to the unreplicated regions in the same chromosome, the definition of chromosomal replication complexity (CRC) appears to leave little room for variation, being either two during S-phase or one otherwise. However, bacteria dividing faster than they replicate their chromosome spike CRC to four and even eight. A recent experimental inquiry about the limits of CRC in Escherichia coli revealed two major reasons to avoid elevating it further: (i) increased chromosomal fragmentation and (ii) complications with subsequent double-strand break repair...
October 2016: PLoS Genetics
L Hua, W Y Zheng, H Xia, P Zhou
Comprehensive multi-omics data analyses have become an important means for understanding cancer incidence and progression largely driven by the availability of high-throughput sequencing technologies for genomes, proteomes, and transcriptomes. However, how tumor cells from the site of origin of the cancer begin to grow in other sites of the body is very poorly understood. In order to examine potential connections between different cancers and to gain an insight into the metastatic process, we conducted a multi-omics data analysis using data deposited in The Cancer Genome Atlas database...
August 19, 2016: Genetics and Molecular Research: GMR
Ana M Misic, Christine L Cain, Daniel O Morris, Shelley C Rankin, Daniel P Beiting
Staphylococcus species are a leading cause of skin and soft tissue infections in humans and animals, and the antibiotics used to treat these infections are often the same. Methicillin- and multidrug-resistant staphylococcal infections are becoming more common in human and veterinary medicine. From a "One Health" perspective, this overlap in antibiotic use and resistance raises concerns over the potential spread of antibiotic resistance genes. Whole-genome sequencing and comparative genomics analysis revealed that Staphylococcus species use divergent pathways to synthesize isoprenoids...
September 2016: MSphere
Amelia K Smit, David Espinoza, Ainsley J Newson, Rachael L Morton, Georgina Fenton, Lucinda Freeman, Kate Dunlop, Phyllis N Butow, Matthew H Law, Michael G Kimlin, Louise A Keogh, Suzanne J Dobbinson, Judy Kirk, Peter A Kanetsky, Graham J Mann, Anne E Cust
BACKGROUND: Communication of personalised melanoma genomic risk information may improve melanoma prevention behaviours. METHODS: We evaluated the feasibility and acceptability of communicating personalised genomic risk of melanoma to the public, and its preliminary impact on behaviours and psychosocial outcomes. 118 people aged 22-69 years provided a saliva sample and were randomised to the control (non-personalised educational materials), or intervention (personalised booklet presenting melanoma genomic risk as absolute and relative risks and a risk category based on variants in 21 genes, telephone-based genetic counselling, and non-personalised educational materials)...
October 4, 2016: Cancer Epidemiology, Biomarkers & Prevention
Arvis Sulovari, Yolanda H Chen, James J Hudziak, Dawei Li
Genetic variants with extreme allele frequency differences (EAFD) may underlie some human health disparities across populations. To identify EAFD loci, we systematically analyzed and characterized 81 million genomic variants from 2504 unrelated individuals of 26 world populations (phase III of the 1000 Genomes Project). Our analyses revealed a total of 434 genes, 15 pathways, and 18 diseases and traits influenced by EAFD variants from five continental populations. They included known EAFD genes, such as LCT (lactose tolerance), SLC24A5 (skin pigmentation), and EDAR (hair morphology)...
October 3, 2016: Human Genetics
T J Poorten, E B Rosenblum
In the past century, recently emerged infectious diseases have become major drivers of species decline and extinction. The fungal disease chytridiomycosis has devastated many amphibian populations and exacerbated the amphibian conservation crisis. Biologists are beginning to understand what host traits contribute to disease susceptibility, but more work is needed to determine why some species succumb to chytridiomycosis while others do not. We conducted an integrative laboratory experiment to examine how two toad species respond to infection with the pathogen Batrachochytrium dendrobatidis in a controlled environment...
October 1, 2016: Molecular Ecology
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