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https://www.readbyqxmd.com/read/29141036/the-disjunct-pattern-of-the-neotropical-harvestman-discocyrtus-dilatatus-gonyleptidae-explained-by-climate-driven-range-shifts-in-the-quaternary-paleodistributional-and-molecular-evidence
#1
Julia Vergara, Luis E Acosta, Raúl E González-Ittig, Luis M Vaschetto, Cristina N Gardenal
The disjunct distribution of the harvestman Discocyrtus dilatatus (Opiliones, Gonyleptidae) is used as a case study to test the hypothesis of a trans-Chaco Pleistocene paleobridge during range expansion stages. This would have temporarily connected humid regions ('Mesopotamia' in northeastern Argentina, and the 'Yungas' in the northwest, NWA) in the subtropical and temperate South American lowlands. The present study combines two independent approaches: paleodistributional reconstruction, using the Species Distribution Modeling method MaxEnt and projection onto Quaternary paleoclimates (6 kya, 21 kya, 130 kya), and phylogeographic analyses based on the cytochrome oxidase subunit I molecular marker...
2017: PloS One
https://www.readbyqxmd.com/read/29140792/a-bayesian-hierarchical-model-for-identifying-significant-polygenic-effects-while-controlling-for-confounding-and-repeated-measures
#2
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29140770/specificity-and-genetic-diversity-of-xylose-fermenting-scheffersomyces-yeasts-associated-with-small-blue-stag-beetles-of-the-genus-platycerus-in-east-asia
#3
Masahiko Tanahashi, Jong-Kuk Kim, Kana Watanabe, Takema Fukatsu, Kôhei Kubota
Among insect-fungus relationships, xylose-fermenting Scheffersomyces yeasts are well known for their potential in utilizing wood hemicelluloses and their association with various wood-feeding insects. However, their specificity to host insects or strain-level diversity within host species has not been clearly elucidated. In the insect family Lucanidae, larvae usually feed on decaying wood, and adult females consistently possess a fungus-storage organ, called the mycangium, near the abdominal tip. Here the authors investigated host-symbiont relationships between Scheffersomyces yeast symbionts and small blue stag beetles of the genus Platycerus (Coleoptera: Lucanidae) in East Asia by using intergenic spacer (IGS) region as a genetic marker...
November 9, 2017: Mycologia
https://www.readbyqxmd.com/read/29140561/interaction-among-smoking-status-single-nucleotide-polymorphisms-and-markers-of-systemic-inflammation-in-healthy-individuals
#4
Thitiya Luetragoon, Lars Erik Rutqvist, Orathai Tangvarasittichai, Bengt-Åke Andersson, Sture Löfgren, Kanchana Usuwanthim, Nongnit Laytragoon Lewin
Cigarette smoke contains toxic and carcinogenic substances that contribute to the development of cancer and various diseases. Genetic variation might be important because not all smokers develop smoking-related disease. The current study addressed the possible interactions among selected single nucleotide polymorphisms (SNPs) in genes related to systemic inflammation, smoking status, the levels of circulating immune response cells and plasma biomarkers of systemic inflammation. Sixty-four healthy blood donors were recruited, of whom 31 were current smokers and 33 were never-users of tobacco products, references...
November 15, 2017: Immunology
https://www.readbyqxmd.com/read/29139642/matrilineal-heritage-in-southern-iberia-reveals-deep-genetic-links-between-continents
#5
Candela L Hernández, Rosario Calderón
Within the Mediterranean Basin, the Iberian Peninsula has been a focus of attraction for several cultures and civilizations from its prehistory and history, making it a target territory for studying human migration patterns and peopling processes using a wide and heterogeneous spectrum of genomic markers. While its Cantabrian fringe represents the most regularly analysed area in terms of its mitochondrial diversity, the absence of monographic surveys on the maternal genetic composition of southern Iberians (i...
March 2017: Collegium Antropologicum
https://www.readbyqxmd.com/read/29139263/-next-generation-sequencing-and-transcriptome-analysis-of-root-bark-from-paeonia-suffruticosa-cv-feng-dan
#6
Dong-Mei Xie, Nian-Jun Yu, Lu-Qi Huang, Dai-Yin Peng, Cong-Bin Liu, Yue-Jian Zhu, Hao Huang
Moutan Cortex is an important traditional Chinese medicine, "Fengdan Pi" was known as Dao-di herbs from the root bark of Paeonia suffruticosa cv. Feng Dan for its extracted various active components. However, the genetic basis for their activity is virtually unknown. The transcriptome of the root bark from "Fengdan" was sequenced using the Illumina HiSeq 4000 sequencing platform. The clean reads were then de novo assembled into 72 997 unigenes. Among them, the number of unigenes which could been annotated by dataset Nr and GO was 41 139 and 34 592...
August 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29139039/genetic-screening-and-molecular-characterization-of-met-alterations-in-non-small-cell-lung-cancer
#7
M Saigi, A McLeer-Florin, E Pros, E Nadal, E Brambilla, M Sanchez-Cespedes
PURPOSE: Aberrant activation of MET as a result of exon 14-skipping (METex14) mutations or gene amplification is an oncogenic mechanism in non-small cell lung carcinoma (NSCLC) and a potential therapeutic target. The purpose of this study was to characterize MET alterations in a cohort of NSCLC patients treated with surgery. METHODS AND PATIENTS: 157 NSCLCs of various histopathologies, including pulmonary sarcomatoid carcinomas (PSC), were tested for MET alterations...
November 14, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/29138903/next-generation-sequencing-to-identify-candidate-genes-and-develop-diagnostic-markers-for-a-novel-phytophthora-resistance-gene-rpshc18-in-soybean
#8
Chao Zhong, Suli Sun, Yinping Li, Canxing Duan, Zhendong Zhu
A novel Phytophthora sojae resistance gene RpsHC18 was identified and finely mapped on soybean chromosome 3. Two NBS-LRR candidate genes were identified and two diagnostic markers of RpsHC18 were developed. Phytophthora root rot caused by Phytophthora sojae is a destructive disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Phytophthora-resistant Rps genes. The soybean cultivar Huachun 18 has a broad and distinct resistance spectrum to 12 P. sojae isolates...
November 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29138689/clarifying-sub-genomic-positions-of-qtls-for-flowering-habit-and-fruit-quality-in-u-s-strawberry-fragaria%C3%A3-ananassa-breeding-populations-using-pedigree-based-qtl-analysis
#9
Sujeet Verma, Jason D Zurn, Natalia Salinas, Megan M Mathey, Beatrice Denoyes, James F Hancock, Chad E Finn, Nahla V Bassil, Vance M Whitaker
The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29138254/estimating-realized-heritability-in-panmictic-populations
#10
Milan Lstibůrek, Václav Bittner, Gary R Hodge, Jan Picek, Trudy F C Mackay
Narrow sense heritability (h(2) ) is a key concept in quantitative genetics, as it expresses the proportion of the observed phenotypic variation that is transmissible from parents to offspring. h(2) determines the resemblance among relatives and the rate of response to artificial and natural selection. Classical methods for estimating h(2) use random samples of individuals with known relatedness, as well as response to artificial selection, when it is called realized heritability. Here, we present a method for estimating realized h(2) based on a simple assessment of a random-mating population with no artificial manipulation of the population structure, and derive standard errors of the estimates...
November 14, 2017: Genetics
https://www.readbyqxmd.com/read/29137279/implications-of-mutational-spectrum-in-myelodysplastic-syndromes-based-on-targeted-next-generation-sequencing
#11
Yuanyuan Xu, Yan Li, Qingyu Xu, Yuelong Chen, Na Lv, Yu Jing, Liping Dou, Jian Bo, Guangyuan Hou, Jing Guo, Xiuli Wang, Lili Wang, Yonghui Li, Chongjian Chen, Li Yu
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137267/tumacrophage-macrophages-transformed-into-tumor-stem-like-cells-by-virulent-genetic-material-from-tumor-cells
#12
Yizhuang Zhang, Na Zhou, Xiuyan Yu, Xuehui Zhang, Shanxin Li, Zhen Lei, Ruobi Hu, Hui Li, Yiqing Mao, Xi Wang, Jinshu Zhang, Yuan Li, Hongyan Guo, David M Irwin, Gang Niu, Huanran Tan
Tumor-associated macrophages are regarded as tumor-enhancers as they have key roles in the subversion of adaptive immunity and in inflammatory circuits that promote tumor progression. Here, we show that cancer cells can subvert macrophages yielding cells that have gained pro-tumor functions. When macrophages isolated from mice or humans are co-cultured with dead cancer cell line cells, induced to undergo apoptosis to mimic chemotherapy, up-regulation of pro-tumor gene expression was identified. Phagocytosis of apoptotic cancer cells by macrophages resulted in their transformation into tumor stem (initiating)-like cells, as indicated by the expression of epithelial markers (e...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137253/g-t-haplotype-established-by-rs3785889-rs16941382-in-gosr2-gene-is-associated-with-coronary-artery-disease-in-chinese-han-population
#13
Shuo Pan, Gong-Chang Guan, Ying Lv, Zhong-Wei Liu, Fu-Qiang Liu, Yong Zhang, Shun-Ming Zhu, Rong-Huai Zhang, Na Zhao, Shuang Shi, Tomohiro Nakayama, Jun-Kui Wang
Objectives: The aim of the present study is to assess the association between the human GOSR2 gene and coronary artery disease using a haplotype-based case-control study in Chinese Han population. Methods: A total of 283 coronary artery disease patients and 280 controls were genotyped for the human GOSR2 gene (rs197932, rs3785889, rs197922, rs17608766, and rs16941382). Data were analyzed for three separate groups: the total subjects, men, and women. Results: For the total subjects, the frequency of the G-T haplotype established by rs3785889-rs16941382 was significantly higher in the coronary artery disease patients as compared to the control subjects (P=0...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137252/a-novel-mutation-r190h-in-the-at-hook-1-domain-of-mecp2-identified-in-an-atypical-rett-syndrome
#14
Xiao Zhou, Yuangao Liao, Miaojing Xu, Zhong Ji, Yunqi Xu, Liang Zhou, Xiaoming Wei, Peiqian Hu, Peng Han, Fanghan Yang, Suyue Pan, Yafang Hu
Background: Mutations in Methyl-CpG binding protein 2 (MECP2) have been identified as the disease-causing mutations in Rett Syndrome (RTT). However, no mutation in the AT-hook 1 domain of MECP2 has been reported in RTT yet. The function of AT-hook 1 domain of MECP2 has not been described either. Methods: The clinical and radiological features of a girl with progressive hyperactivity and loss of acquired linguistic and motor functions were presented. Next generation sequencing was used to screen the causative gene...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29137034/uniparental-disomy-and-prenatal-phenotype-two-case-reports-and-review
#15
Xiaofei Li, Yan Liu, Song Yue, Li Wang, Tiejuan Zhang, Cuixia Guo, Wenjie Hu, Karl-Oliver Kagan, Qingqing Wu
RATIONALE: Uniparental disomy (UPD) gives a description of the inheritance of both homologues of a chromosome pair from the same parent. The consequences of UPD depend on the specific chromosome/segment involved and its parental origin. PATIENT CONCERNS: We report prenatal phenotypes of 2 rare cases of UPD. DIAGNOSES: The prenatal phenotype of case 1 included sonographic markers such as enlarged nuchal translucency (NT), absent nasal bone, short femur and humerus length, and several structural malformations involving Dandy-Walker malformation and congenital heart defects...
November 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29136686/-clinicopathologic-and-molecular-characteristics-of-malignant-gastrointestinal-neuroectodermal-tumors
#16
M Zhao, T W Zhao, J Ma, C Y Wu, L Chen, G Q Ru, X L He
Objective: To investigate the clinicopathologic and molecular characteristics, diagnostic, differential diagnostic and prognostic features of malignant gastrointestinal neuroectodermal tumor. Methods: Two cases of malignant gastrointestinal neuroectodermal tumor were retrieved; the clinical and radiologic features, histomorphology, immunophenotype, molecular genetics and prognosis were analyzed and the relevant literature reviewed. Results: Case 1 was a 57-year-old male, presented with recurrent abdominal pain and melena...
November 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29136656/genetic-diversity-linkage-disequilibrium-and-association-mapping-analyses-of-gossypium-barbadense-l-germplasm
#17
Alisher A Abdullaev, Ilkhom B Salakhutdinov, Sharof S Egamberdiev, Ernest E Khurshut, Sofiya M Rizaeva, Mauricio Ulloa, Ibrokhim Y Abdurakhmonov
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers...
2017: PloS One
https://www.readbyqxmd.com/read/29136404/galectin-3-expression-is-prognostic-in-diffuse-type-gastric-adenocarcinoma-confers-aggressive-phenotype-and-can-be-targeted-by-yap1-bet-inhibitors
#18
Jaffer A Ajani, Jeannelyn S Estrella, Qiongrong Chen, Arlene M Correa, Lang Ma, Ailing W Scott, Jiankang Jin, Bin Liu, Min Xie, Kazuki Sudo, Hironori Shiozaki, Brian Badgwell, Brian Weston, Jeffrey H Lee, Manoop S Bhutani, Hisashi Onodera, Koyu Suzuki, Akihiro Suzuki, Sheng Ding, Wayne L Hofstetter, Randy L Johnson, Robert S Bresalier, Shumei Song
BACKGROUND: Overexpression of Galectin-3 (Gal-3), a β-galactoside binding protein, has been noted in many tumour types but its functional significance and clinical utility in gastric adenocarcinoma (GAC) are not well known. METHODS: We studied 184 GAC patients characterised by histologic grade, sub-phenotypes (diffuse vs intestinal), and ethnicity (Asians vs North Americans). Immunohistochemistry was performed to assess the expression of Gal-3 in human GACs and we correlated it to the clinical outcomes...
November 14, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29136139/rad-seq-reveals-patterns-of-additive-polygenic-variation-caused-by-spatially-varying-selection-in-the-american-eel-anguilla-rostrata
#19
Charles Babin, Pierre-Alexandre Gagnaire, Scott A Pavey, Louis Bernatchez
The American Eel (Anguilla rostrata) has an exceptional life cycle characterised by panmictic reproduction at the species scale, random dispersal and selection in a highly heterogeneous habitat extending from subtropical to subarctic latitudes. The genetic consequences of spatially-varying selection in this species have been investigated for decades, revealing subtle clines in allele frequency at a few loci that contrast with complete panmixia on the vast majority of the genome. Because reproduction homogenizes allele frequencies every generation, sampling size and genomic coverage are critical to reach sufficient power to detect selected loci in this context...
November 10, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29135311/atm-bcl2-and-tgf%C3%AE-gene-polymorphisms-as-radiotherapy-outcome-biomarkers-in-head-and-neck-squamous-cell-carcinoma-patients
#20
Lidiane P Agostini, Elaine Stur, Fernanda M Garcia, Diego P Ventorim, Raquel S Dos Reis, Raquel S Dettogni, Eldamária V W Dos Santos, Gabriela T Peterle, Lucas L Maia, Suzanny O Mendes, Marcos B de Carvalho, Eloiza H Tajara, Flavia de Paula, Marcelo Dos Santos, Adriana M A da Silva, Iúri Drumond Louro
AIMS: Polymorphisms in cell cycle genes are considered prognostic and radiosensitivity markers in patients with head and neck squamous cell carcinoma. Therefore, we have aimed to investigate the relationship of ATM 5557G>A, ATM IVS62 + 60G>A, TP53 215G>C, BCL2-938C>A, TGFβ-509C>T, and TGFβ 29C>T with radiotherapy response. MATERIALS AND METHODS: Genotyping was performed by polymerase chain reaction followed by restriction fragment length polymorphism in 210 patients with oral cavity/oropharynx carcinoma and 101 patients with larynx tumors...
November 14, 2017: Genetic Testing and Molecular Biomarkers
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