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Genetic markers

Maria Martinez-Lage, Felix Sahm
The updated 2016 WHO classification of Central Nervous System tumors introduced a novel concept of neuropathology diagnostics. Molecular parameters are now included into the definition of several entities. This evolution from a previously purely histology-based classification to an integrated approach of histology and genetic characteristics has implications in daily diagnostic and clinical practice. Both the spectrum of diagnostic workup demanded from the neuropathologist and the range of relevant markers to be considered by clinicians and clinical investigators have increased...
February 2018: Seminars in Neurology
Sofía I Deperi, Martín E Tagliotti, M Cecilia Bedogni, Norma C Manrique-Carpintero, Joseph Coombs, Ruofang Zhang, David Douches, Marcelo A Huarte
The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis...
2018: PloS One
James R Smith, Jaboury Ghazoul, David F R P Burslem, Akira Itoh, Eyen Khoo, Soon Leong Lee, Colin R Maycock, Satoshi Nanami, Kevin Kit Siong Ng, Chris J Kettle
Documenting the scale and intensity of fine-scale spatial genetic structure (FSGS), and the processes that shape it, is relevant to the sustainable management of genetic resources in timber tree species, particularly where logging or fragmentation might disrupt gene flow. In this study we assessed patterns of FSGS in three species of Dipterocarpaceae (Parashorea tomentella, Shorea leprosula and Shorea parvifolia) across four different tropical rain forests in Malaysia using nuclear microsatellite markers. Topographic heterogeneity varied across the sites...
2018: PloS One
Yi Pang, Yunfeng Guan, Xing Jin, Hongmei Shen, Lixiang Liu, Qingzhen Jia, Fangang Meng, Xiaoye Zhang
Thyroid-stimulating hormone (TSH) is secreted by the pituitary gland and promotes thyroid growth and function, with increased TSH levels typically associated with hypothyroidism. By consulting the literature, we found that the TSHR, PAX8, and PDE4B genes are associated with thyroid function. Recently, copy number variations (CNVs) have been used as genetic markers to investigate inter-individual variation. Therefore, we investigated the relationship between the TSHR, PAX8, and PDE4B gene CNVs and TSH abnormalities, by calculating variations in gene copy number...
March 15, 2018: Biological Trace Element Research
Maliha Khan, Rabbia Siddiqi, Kiran Naqvi
Mixed phenotype acute leukemia (MPAL) is an uncommon diagnosis, representing only about 2-5% of acute leukemia cases. The blast cells of MPAL express multilineage immunophenotypic markers and may have a shared B/T/myeloid phenotype. Due to historical ambiguity in the diagnosis of MPAL, the genetics and clinical features of this disease remain poorly characterized. Based on the 2008 and 2016 World Health Organization classifications, myeloid lineage is best determined by presence of myeloperoxidase, while B and T lymphoid lineages are demonstrated by CD19 and cytoplasmic CD3 expression...
March 15, 2018: Annals of Hematology
Neshat Golikhajeh, Bahram Naseri, Jabraeil Razmjou, Reza Hosseini, Marzieh Asadi Aghbolaghi
In order to understand the population genetic diversity and structure of Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae), a serious pest of sugar beet in Iran and the world, we genotyped 133 individuals from seven regions in Iran using four microsatellite loci. Significant difference was seen between the observed and expected heterozygosity in all loci. A lower observed heterozygosity than expected heterozygosity indicated a low heterozygosity in these populations. The value of F showed a high genetic differentiation, so that the mean of Fst was 0...
March 13, 2018: Journal of Economic Entomology
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Junya Kitadani, Toshiyasu Ojima, Hiromitsu Iwamoto, Hirotaka Tabata, Mikihito Nakamori, Masaki Nakamura, Keiji Hayata, Masahiro Katsuda, Masayasu Miyajima, Hiroki Yamaue
Clinical application of dendritic cell (DC) vaccine therapy is hindered by the need for a large quantity of DCs generated from peripheral blood monocytes of the patient. We investigated whether genetically modified human induced pluripotent stem cell (iPSC)-derived dendritic cells (hiPSDCs) expressing carcinoembryonic antigen (CEA) could induce CEA-specific cytotoxic T cells in a human model and whether genetically modified mouse iPSDCs (miPSDCs) expressing CEA showed an actual antitumor effect using a CEA transgenic mouse model...
March 15, 2018: Scientific Reports
Tim Beissinger, Jochen Kruppa, David Cavero, Ngoc-Thuy Ha, Malena Erbe, Henner Simianer
Important traits in agricultural, natural, and human populations are increasingly being shown to be under the control of many genes that individually contribute only a small proportion of genetic variation. However, the majority of modern tools in quantitative and population genetics, including genome wide association studies and selection mapping protocols, are designed to identify individual genes with large effects. We have developed an approach to identify traits that have been under selection and are controlled by large numbers of loci...
March 15, 2018: Genetics
Else M Balke, Eric V Balti, Bart Van der Auwera, Ilse Weets, Olivier Costa, Simke Demeester, Pascale Abrams, Kristina Casteels, Marina Coeckelberghs, Sylvie Tenoutasse, Bart Keymeulen, Daniel G Pipeleers, Frans K Gorus
OBJECTIVE: We investigated the effect of HLA class I risk alleles on disease progression in various phases of subclinical islet autoimmunity in first-degree relatives of patients with type 1 diabetes. RESEARCH DESIGN AND METHODS: A registry-based group of siblings/offspring (aged 0-39 years) was monitored from single- to multiple-autoantibody positivity ( n = 267) and from multiple-autoantibody positivity to clinical onset ( n = 252) according to HLA-DQ , -A*24 , -B*18 and -B*39 status...
March 15, 2018: Diabetes Care
Holger Winkels, Erik Ehinger, Melanie Vassallo, Konrad Buscher, Huy Dinh, Kouji Kobiyama, Anouk Hamers, Clément Cochain, Ehsan Vafadarnejad, Antoine-Emmanuel Saliba, Alma Zernecke, Akula Pramod, Amlan Ghosh, Nathaly Anto Michel, Natalie Hoppe, Ingo Hilgendorf, Andreas Zirlik, Catherine Hedrick, Klaus Ley, Dennis Wolf
<u>Rationale:</u> Atherosclerosis is a chronic inflammatory disease that is driven by the interplay of pro- and anti-inflammatory leukocytes in the aorta. Yet, the phenotypic and transcriptional diversity of aortic leukocytes is only poorly understood. <u>Objective:</u> We characterized leukocytes from healthy and atherosclerotic mouse aortas in-depth by single cell RNA-sequencing (scRNAseq) and mass cytometry (CyTOF) to define an atlas of the immune cell landscape in atherosclerosis...
March 15, 2018: Circulation Research
Krzysztof Karpowicz, Katarzyna Krych, Małgorzata Karpowicz, Witold Nowak, Piotr Gronek
The map of candidate genes that can potentially affect physical fitness becomes larger every year, and they are associated with such aspects as respiratory and cardiovascular stability; body build and composition - especially muscle mass and strength; carbohydrate and lipid metabolism; response to training; and exercise intolerance.The aim of this study was to analyze the relationship between the CA repeat polymorphism of the P1 promoter of the IGF1 gene and the structure of motor skills in the two groups of Polish young athletes in 2011-2013...
March 15, 2018: Acta Biochimica Polonica
Jacobus H Visser, Nigel C Bennett, Bettine Jansen van Vuuren
The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis)...
2018: PloS One
Yan Li, Zhirong Zhang, Junbo Yang, Guanghui Lv
Fritillaria spp. constitute important traditional Chinese medicinal plants. Xinjiang is one of two diversity hotspots in China in which eight Fritillaria species occur, two of which are endemic to the region. Furthermore, the phylogenetic relationships of Xinjiang Fritillaria species (including F. yuminensis) within the genus are unclear. In the present study, we sequenced the chloroplast (cp) genomes of seven Fritillaria species in Xinjiang using the Illumina HiSeq platform, with the aim of assessing the global structural patterns of the seven cp genomes and identifying highly variable cp DNA sequences...
2018: PloS One
Sunirmal Sheet, Kuntal Ghosh, Satabdi Acharya, Kwang-Pyo Kim, Yang Soo Lee
Apart from being fed to silkworms in sericulture, the ecologically important Mulberry plant has been used for traditional medicine in Asian countries as well as in manufacturing wine, food, and beverages. Germplasm analysis among Mulberry cultivars originating from South Korea is crucial in the plant breeding program for cultivar development. Hence, the genetic deviations and relations among 8 Morus alba plants, and one Morus lhou plant, of different cultivars collected from South Korea were investigated using 10 random amplified polymorphic DNA (RAPD) and 10 inter-simple sequence repeat (ISSR) markers in the present study...
March 15, 2018: Plants (Basel, Switzerland)
Frederic Strobl, Anita Anderl, Ernst Hk Stelzer
Diploid transgenic organisms are either hemi- or homozygous. Genetic assays are, therefore, required to identify the genotype. Our AGameOfClones vector concept uses two clearly distinguishable transformation markers embedded in interweaved, but incompatible Lox site pairs. Cre-mediated recombination leads to hemizygous individuals that carry only one marker. In the following generation, heterozygous descendants are identified by the presence of both markers and produce homozygous progeny that are selected by the lack of one marker...
March 15, 2018: ELife
Michael A Taylor, Jong W Yu, Thomas L Howell, Stephen H Jones
Vibrio parahaemolyticus is the leading cause of seafood-borne human infections in the United States, and many of these illnesses are associated with consumption of raw molluscan shellfish. V. parahaemolyticus levels in shellfish vary temporally and spatially with environmental conditions in and around production areas. The objective of this study was to study the potential for reducing levels of V. parahaemolyticus in live oysters by relaying them during higher-risk warm weather to a site with elevated salinity and consistently low V...
March 15, 2018: Journal of Food Protection
Francesco Caso, Marco Tasso, Pasquale Ambrosino, Matteo Nicola, Dario Di Minno, Roberta Lupoli, Livio Criscuolo, Paolo Caso, Francesco Ursini, Antonio Del Puente, Raffaele Scarpa, Luisa Costa, Rosario Peluso
BACKGROUND: Psoriatic arthritis is a chronic inflammatory arthropathy that affects 14%-30% of patients with skin and/or nail psoriasis and leading to severe physical limitations and disability. It has been included in the group of spondyloarthropathy with which it shares clinical, radiologic, and serologic features in addition to familial and genetic relationship. Beyond skin and joint involvement, psoriatic arthritis is characterized by a high prevalence of extra-articular manifestation and comorbidities, such as autoimmune, infectious and neoplastic diseases...
March 13, 2018: Reviews on Recent Clinical Trials
Karl Payne, Rachel Spruce, Andrew Beggs, Neil Sharma, Anthony Kong, Timothy Martin, Satyesh Parmar, Prav Praveen, Paul Nankivell, Hisham Mehanna
The use of circulating biochemical molecular markers in head and neck cancer holds the promise of improved diagnostics, treatment planning, and posttreatment surveillance. In this review, we provide an introduction for the head and neck surgeon of the basic science, current evidence, and future applications of circulating tumor DNA (ctDNA) as a biomarker and liquid biopsy to detect tumor genetic heterogeneity in patients with head and neck squamous cell carcinoma (HNSCC).
March 15, 2018: Head & Neck
Antonio Fadda, Davide Gentilini, Loredana Moi, Ludovic Barault, Vera Piera Leoni, Pia Sulas, Luigi Zorcolo, Angelo Restivo, Francesco Cabras, Federica Fortunato, Cesare Zavattari, Liliana Varesco, Viviana Gismondi, Maria Rosaria De Miglio, Antonio Mario Scanu, Federica Colombi, Pasquale Lombardi, Ivana Sarotto, Eleonora Loi, Francesco Leone, Silvia Giordano, Federica Di Nicolantonio, Amedeo Columbano, Patrizia Zavattari
Colorectal cancer (CRC) develops through the accumulation of both genetic and epigenetic alterations. However, while the former are already used as prognostic and predictive biomarkers, the latter are less well characterized. Here, performing global methylation analysis on both CRCs and adenomas by Illumina Infinium HumanMethylation450 Bead Chips, we identified a panel of 74 altered CpG islands, demonstrating that the earliest methylation alterations affect genes coding for proteins involved in the crosstalk between cell and surrounding environment...
March 15, 2018: International Journal of Cancer. Journal International du Cancer
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