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population genetic

Jianhui Wu, Shuo Huang, Qingdong Zeng, Shengjie Liu, Qilin Wang, Jingmei Mu, Shizhou Yu, Dejun Han, Zhensheng Kang
A major stripe rust resistance QTL on chromosome 4BL was localized to a 4.5-Mb interval using comparative QTL mapping methods and validated in 276 wheat genotypes by haplotype analysis. CYMMIT-derived wheat line P10103 was previously identified to have adult plant resistance (APR) to stripe rust in the greenhouse and field. The conventional approach for QTL mapping in common wheat is laborious. Here, we performed QTL detection of APR using a combination of genome-wide scanning and extreme pool-genotyping. SNP-based genetic maps were constructed using the Wheat55 K SNP array to genotype a recombinant inbred line (RIL) population derived from the cross Mingxian 169 × P10103...
June 16, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Zhi-Ming Dai, Jian-Rui Lv, Kang Liu, Xiao-Ming Lei, Wei Li, Gang Wu, Xing-Han Liu, Yu-Xiao Zhu, Qian Hao, Zhi-Jun Dai
The role of rs4919510 polymorphism in microRNA-608 (miR-608) and cancer susceptibility and prognosis remain controversial and debatable. We conducted a meta-analysis of twenty-four eligible publications on the association of rs4919510 polymorphism with cancer risk and/or prognosis. Odds ratios, hazard ratios, and 95% confidence interval were used to investigate the association between this polymorphism and susceptibility, overall survival, and recurrence-free survival of cancer. Overall, eighteen case-control studies and nine cohort studies evaluated the susceptibility and prognostic value of rs4919510 polymorphism in cancer, respectively...
June 16, 2018: Aging
D Gareth Evans, Naomi L Bowers, Simon Tobi, Claire Hartley, Andrew J Wallace, Andrew T King, Simon K W Lloyd, Scott A Rutherford, Charlotte Hammerbeck-Ward, Omar N Pathmanaban, Simon R Freeman, John Ealing, Mark Kellett, Roger Laitt, Owen Thomas, Dorothy Halliday, Rosalie Ferner, Amy Taylor, Chris Duff, Elaine F Harkness, Miriam J Smith
OBJECTIVES: Schwannomatosis is a dominantly inherited condition predisposing to schwannomas of mainly spinal and peripheral nerves with some diagnostic overlap with neurofibromatosis-2 (NF2), but the underlying epidemiology is poorly understood. We present the birth incidence and prevalence allowing for overlap with NF2. METHODS: Schwannomatosis and NF2 cases were ascertained from the Manchester region of England (population=4.8 million) and from across the UK. Point prevalence and birth incidence were calculated from regional birth statistics...
June 16, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
Chris Carlsten
Paradoxically, the vast majority of research models intended to understand the relationship between exogenous exposures and lung disease are reduced to a single inhalant. This is understandable given the practical challenges of investigation, but is problematic in terms of translation to the real-world human condition. Furthermore, use of data from such models can lead to under-estimation of effect, which may adversely impact regulatory imperatives to protect public health based on the most robust information...
June 14, 2018: Chest
Pooja Jha, Molly T McDevitt, Rahul Gupta, Pedro M Quiros, Evan G Williams, Karim Gariani, Maroun B Sleiman, Leo Diserens, Adam Jochem, Arne Ulbrich, Joshua J Coon, Johan Auwerx, David J Pagliarini
The genetics of individual lipid species and their relevance in disease is largely unresolved. We profiled a subset of storage, signaling, membrane, and mitochondrial liver lipids across 385 mice from 47 strains of the BXD mouse population fed chow or high-fat diet and integrated these data with complementary multi-omics datasets. We identified several lipid species and lipid clusters with specific phenotypic and molecular signatures and, in particular, cardiolipin species with signatures of healthy and fatty liver...
June 7, 2018: Cell Systems
Pooja Jha, Molly T McDevitt, Emina Halilbasic, Evan G Williams, Pedro M Quiros, Karim Gariani, Maroun B Sleiman, Rahul Gupta, Arne Ulbrich, Adam Jochem, Joshua J Coon, Michael Trauner, David J Pagliarini, Johan Auwerx
The genetic regulation and physiological impact of most lipid species are unexplored. Here, we profiled 129 plasma lipid species across 49 strains of the BXD mouse genetic reference population fed either chow or a high-fat diet. By integrating these data with genomics and phenomics datasets, we elucidated genes by environment (diet) interactions that regulate systemic metabolism. We found quantitative trait loci (QTLs) for ∼94% of the lipids measured. Several QTLs harbored genes associated with blood lipid levels and abnormal lipid metabolism in human genome-wide association studies...
May 31, 2018: Cell Systems
Ilaria Panzeri, John Andrew Pospisilik
BACKGROUND: The alarming rise of obesity and its associated comorbidities represents a medical burden and a major global health and economic issue. Understanding etiological mechanisms underpinning susceptibility and therapeutic response is of primary importance. Obesity, diabetes, and metabolic diseases are complex trait disorders with only partial genetic heritability, indicating important roles for environmental programing and epigenetic effects. SCOPE OF THE REVIEW: We will highlight some of the reasons for the scarce predictability of metabolic diseases...
May 18, 2018: Molecular Metabolism
Matthew Pontifex, David Vauzour, Anne-Marie Minihane
An apolipoprotein E ε4 (APOE-ε4) genotype is the strongest common genetic determinant of Alzheimer's disease (AD). The pleiotropic nature of apolipoprotein E has made elucidation of the aetiological basis difficult to establish, which is further complicated by the fact that the penetrance of the APOE-ε4 allele is modulated by sex, age, and nutrition. A greater metabolic consequence of the APOE-ε4 allele is likely to contribute to the fact that two-thirds of AD patients are female. A higher tissue status of the marine n-3 fatty acid docosahexaenoic acid (DHA) is associated with a lower AD risk...
May 21, 2018: Neurobiology of Aging
Tian-Sin Fan, Ruey-Meei Wu, Han-I Lin, Chieh Cheng, Chin-Hsien Lin
Mutations in the phosphodiesterase 8B gene (PDE8B) were recently linked to autosomal-dominant striatal degeneration clinically presenting as slowly progressive parkinsonism. PDE8B degrades cyclic adenosine monophosphate (cAMP), a second messenger involved in dopamine signaling. Dopamine deficiency is the pathognomonic feature of Parkinson's disease (PD). Few studies have explored the role of PDE8B in PD. We aim to address the genetic contribution of PDE8B in early-onset and familial PD in a Taiwanese population...
May 26, 2018: Neurobiology of Aging
Angel A Criollo-Rayo, Mabel Bohórquez, Rodrigo Prieto, Kimberley Howarth, Cesar Culma, Angel Carracedo, Ian Tomlinson, Maria M Echeverry de Polnaco, Luis G Carvajal Carmona
Andean populations have variable degrees of Native American and European ancestry, representing an opportunity to study admixture dynamics in the populations from Latin America (also known as Hispanics). We characterized the genetic structure of two indigenous (Nasa and Pijao) and three admixed (Ibagué, Ortega and Planadas) groups from Tolima, in the Colombian Andes. DNA samples from 348 individuals were genotyped for six mitochondrial DNA (mtDNA), seven non-recombining Y-chromosome (NRY) region and 100 autosomal ancestry informative markers...
June 7, 2018: Forensic Science International. Genetics
Jazelyn M Salvador, Dame Loveliness T Apaga, Frederick C Delfin, Gayvelline C Calacal, Sheila Estacio Dennis, Maria Corazon A De Ungria
Demands for solving complex kinship scenarios where only distant relatives are available for testing have risen in the past years. In these instances, other genetic markers such as X-chromosome short tandem repeat (X-STR) markers are employed to supplement autosomal and Y-chromosomal STR DNA typing. However, prior to use, the degree of STR polymorphism in the population requires evaluation through generation of an allele or haplotype frequency population database. This population database is also used for statistical evaluation of DNA typing results...
June 8, 2018: Forensic Science International. Genetics
Nicole E Adams, Kentaro Inoue, Richard A Seidel, Brian K Lang, David J Berg
Vicariance and dispersal events affect current biodiversity patterns in desert springs. Whether major diversification events are due to environmental changes leading to radiation or due to isolation resulting in relict species is largely unknown. We seek to understand whether the Gammarus pecos species complex underwent major diversification events due to environmental changes in the area leading either to radiation into novel habitats, or formation of relicts due to isolation. Specifically, we tested the hypothesis that Gammarus in the northern Chihuahuan Desert of New Mexico and Texas, USA are descendants of an ancient marine lineage now containing multiple undescribed species...
June 14, 2018: Molecular Phylogenetics and Evolution
Satoshi Nakamura, Sachiko Tsunoda, Hiroshi Sakaida, Sawako Masuda, Ahamad Shah Said, Kazuhiko Takeuchi
BACKGROUND: Genetic and environmental factors are proposed to be involved in cedar pollen allergy sensitization and onset. The impact of these factors will provide key information for the prevention of cedar pollen sensitization and allergy onset, which we investigated in this cross-sectional study. METHODS: Subjects were 382 young adult volunteers who completed a self-administered questionnaire on self-reported subjective symptoms of pollinosis, physician-diagnosed pollinosis, and background factors...
June 13, 2018: Allergology International: Official Journal of the Japanese Society of Allergology
Karen D Weynberg
Viruses infect all kingdoms of marine life from bacteria to whales. Viruses in the world's oceans play important roles in the mortality of phytoplankton, and as drivers of evolution and biogeochemical cycling. They shape host population abundance and distribution and can lead to the termination of algal blooms. As discoveries about this huge reservoir of genetic and biological diversity grow, our understanding of the major influences viruses exert in the global marine environment continues to expand. This chapter discusses the key discoveries that have been made to date about marine viruses and the current direction of this field of research...
2018: Advances in Virus Research
Fionnuala Mone, Fionnuala M McAuliffe, Sally Ann Lynch
Irish Travellers are an endogamous nomadic ethnic minority population mostly resident on the island of Ireland with smaller populations living in Europe & USA. As they practice consanguinity, rare and ultra-rare autosomal recessive conditions are observed which are infrequently seen in the general population. Awareness of the rare genetic disorders within an antenatal setting that recur within this population should facilitate quicker cost-effective diagnosis. These include disorders leading to recurrent miscarriage and multiple congenital anomalies...
June 9, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Anat Milman, Jean-Baptiste Gourraud, Antoine Andorin, Pieter G Postema, Frederic Sacher, Philippe Mabo, Giulio Conte, Carla Giustetto, Georgia Sarquella-Brugada, Aviram Hochstadt, Sung-Hwan Kim, Jimmy Jm Juang, Shingo Maeda, Yoshihide Takahashi, Tsukasa Kamakura, Takeshi Aiba, Eran Leshem, Yoav Michowitz, Michael Rahkovich, Yuka Mizusawa, Elena Arbelo, Zhengrong Huang, Isabelle Denjoy, Yanushi D Wijeyeratne, Carlo Napolitano, Ramon Brugada, Ruben Casado-Arroyo, Jean Champagne, Leonardo Calo, Jacob Tfelt-Hansen, Silvia G Priori, Masahiko Takagi, Christian Veltmann, Pietro Delise, Domenico Corrado, Elijah R Behr, Fiorenzo Gaita, Gan-Xin Yan, Josep Brugada, Antoine Leenhardt, Arthur A M Wilde, Pedro Brugada, Kengo F Kusano, Kenzo Hirao, Gi-Byoung Nam, Vincent Probst, Bernard Belhassen
BACKGROUND: There is limited information on gender differences in patients with Brugada syndrome (BrS) who experienced arrhythmic events (AEs). OBJECTIVES: To compare clinical, electrocardiographic (ECG), electrophysiologic (EP) and genetic characteristics between males and females in BrS-patients with their first AE. METHODS: The multicenter Survey on AE in BrS (SABRUS) collected data on first AE in 678 BrS-patients including 619 (91.3%) males and 59 (8...
June 13, 2018: Heart Rhythm: the Official Journal of the Heart Rhythm Society
Juan M Galarza, Rodrigo Barquera, Ana M Tito Álvarez, Diana I Hernández Zaragoza, Gabriela Peralta Sevilla, Andrea Tamayo, Mariel Pérez, David Dávila, Lotty Birnberg, Víctor Acuña Alonzo, Johannes Krause, Marcelo Grijalva
We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in a total of 1101 Ecuadorian individuals from three regions of the country, the Coastal region, the Andean region, and the Amazonian region, to obtain information regarding allelic and haplotypic frequencies and their linkage disequilibrium. We find that the most frequent HLA haplotypes with significant linkage disequilibrium in those populations are HLA-A∗24∼B∗35∼DRB1∗04∼DQB1∗03:02, A∗02∼B∗35∼DRB1∗04∼DQB1∗03:02, A∗24∼B∗35∼DRB1∗14∼DQB1∗03:01, A∗02∼B∗35∼DRB1∗14∼DQB1∗03:01 and A∗02∼B∗40:02∼DRB1∗04∼DQB1∗03:02...
June 13, 2018: Human Immunology
D Goindin, A Cannet, C Delannay, C Ramdini, J Gustave, C Atyame, A Vega-Rúa
Guadeloupe islands are threatened by several mosquito-borne viruses such as Dengue, Chikungunya, Zika and West Nile virus. It appears essential to look for alternative mosquito control methods such as the incompatible insect technique (ITT) aiming at sterilizing wild females by inundative releases of incompatible males. Before considering the implementation of such a strategy, the characterization of genetic diversity of the endocellular bacterium Wolbachia regarding the local mosquito populations is a critical issue...
June 13, 2018: Acta Tropica
Rachel S Kelly, Bo L Chawes, Kevin Blighe, Yamini V Virkud, Damien C Croteau-Chonka, Michael J McGeachie, Clary B Clish, Kevin Bullock, Juan C Celedón, Scott T Weiss, Jessica A Lasky-Su
BACKGROUND: Single-omic analyses have provided some insight into the basis of lung function in asthmatic children, but the underlying biological pathways are still poorly understood. METHODS: Weighted gene co-expression network analysis (WGCNA) was used to identify modules of co-regulated gene transcripts and metabolites in blood, among 325 children with asthma from the 'Genetic Epidemiology of Asthma in Costa Rica' study. The biology of modules associated with lung function; as measured by FEV1 , FEV1 /FVC-ratio, bronchodilator response, and airway responsiveness to methacholine, was explored...
June 13, 2018: Chest
YongFeng Pei, HuiNi Huang, HengCong Li, JieRun Chen, GuoGuang Wu
The distribution of human leucocyte antigen (HLA) allele and haplotype varied among different ethnic populations. In this study, we investigated the allele and haplotype frequencies of HLA-A, HLA-B and HLA-DRB1 loci in the Nanning Han population who live in Guangxi province of China. We identified 26 HLA-A, 56 HLA-B and 31 HLA-DRB1 alleles in 562 Nanning individuals of Han ethnic group by sequence-based typing method. Of these, the three most common alleles in HLA-A, HLA-B and HLA-DRB1 loci, respectively, were A*11:01 (32...
June 15, 2018: International Journal of Immunogenetics
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