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Zhanfeng Si, Hui Liu, Jiankun Zhu, Jiedan Chen, Qiong Wang, Lei Fang, Fengkai Gao, Yue Tian, Yali Chen, Lijing Chang, Bingliang Liu, Zegang Han, Baoliang Zhou, Yan Hu, Xianzhong Huang, Tianzhen Zhang
In cotton, the formation of fruiting branches affects both plant architecture and fiber yield. Here, we report map-based cloning of the Gossypium barbadense axillary flowering (GbAF) mutation gene, which causes bolls to be borne directly on the main plant stem, and of the G. hirsutum clustered boll (cl1) mutation gene. Both mutant alleles were found to represent point mutations at the Cl1 locus of the corresponding species, and therefore we propose that the GbAF mutation be referred to as cl1b. These Cl1 loci correspond to homologs of tomato SELF-PRUNING (SP), i...
March 14, 2018: Journal of Experimental Botany
Xu Chen, Stefan Gustafsson, Thomas Whitington, Yan Borné, Erik Lorentzen, Jitong Sun, Peter Almgren, Jun Su, Robert Karlsson, Jie Song, Yi Lu, Yiqiang Zhan, Sara Hägg, Per Svensson, Karin E Smedby, Susan L Slager, Erik Ingelsson, Cecilia M Lindgren, Andrew P Morris, Olle Melander, Thomas Karlsson, Ulf de Faire, Kenneth Caidahl, Gunnar Engström, Lars Lind, Mikael C I Karlsson, Nancy L Pedersen, Johan Frostegård, Patrik K E Magnusson
Phosphorylcholine (PC) is an epitope on oxidized low-density lipoprotein (oxLDL), apoptotic cells and several pathogens like Streptococcus pneumoniae. Immunoglobulin M against PC (IgM anti-PC) has the ability to inhibit uptake of oxLDL by macrophages and increase clearance of apoptotic cells. From our genome-wide association studies (GWAS) in four European-ancestry cohorts, six SNPs in 11q24.1 were discovered (in 3002 individuals) and replicated (in 646 individuals) to be associated with serum level of IgM anti-PC (the leading SNP rs35923643-G, combined beta=0...
March 14, 2018: Human Molecular Genetics
Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Malgorzata A Gazda, Pedro Andrade, Sandra Afonso, Jolita Dilyte, John P Archer, Ricardo J Lopes, Rui Faria, Miguel Carneiro
Racing pigeons have been selectively bred to find their way home quickly over what are often extremely long distances. This breed is of substantial commercial value and is also an excellent avian model to gain empirical insights into the evolution of traits associated with flying performance and spatial orientation. Here, we investigate the molecular basis of the superior athletic and navigational capabilities of racing pigeons using whole-genome and RNA sequencing data. We inferred multiple signatures of positive selection distributed across the genome of racing pigeons...
March 13, 2018: Molecular Biology and Evolution
Pascal Fleurkens, Agnes van Minnen, Eni S Becker, Iris van Oostrom, Anne Speckens, Mike Rinck, Janna N Vrijsen
Depression risk genes in combination with childhood events have been associated with biased processing as an intermediate phenotype for depression. The aim of the present conceptual replication study was to investigate the role of biased automatic approach-avoidance tendencies as a candidate intermediate phenotype for depression, in the context of genes (5-HTTLPR polymorphism) and childhood trauma. A naturalistic remitted depressed patients sample (N = 209) performed an Approach-Avoidance Task (AAT) with facial expressions (angry, sad, happy and neutral)...
2018: PloS One
Davina Gale, Andrew R J Lawson, Karen Howarth, Mikidache Madi, Bradley Durham, Sarah Smalley, John Calaway, Shannon Blais, Greg Jones, James Clark, Peter Dimitrov, Michelle Pugh, Samuel Woodhouse, Michael Epstein, Ana Fernandez-Gonzalez, Alexandra S Whale, Jim F Huggett, Carole A Foy, Gerwyn M Jones, Hadas Raveh-Amit, Karin Schmitt, Alison Devonshire, Emma Green, Tim Forshew, Vincent Plagnol, Nitzan Rosenfeld
INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes...
2018: PloS One
Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tomoya Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
BACKGROUND: Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs...
2018: PloS One
Yuval B Simons, Kevin Bullaughey, Richard R Hudson, Guy Sella
Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes-notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space...
March 16, 2018: PLoS Biology
Hideaki Kagaya, Takenori Niioka, Mitsuru Saito, Takamitsu Inoue, Kazuyuki Numakura, Ryohei Yamamoto, Yumiko Akamine, Tomonori Habuchi, Shigeru Satoh, Masatomo Miura
While tacrolimus and everolimus have common metabolic pathways through CYP3A4/5, tacrolimus is metabolized solely by CYP3A4 in recipients with the CYP3A5*3 / *3 . The purpose of this study was to evaluate how the area under the blood concentration-time curves (AUC) of tacrolimus could be predicted based on CYP3A5 genotype and the AUC of everolimus in renal transplant patients taking both drugs. The dose-adjusted AUC (AUC/D) of tacrolimus and everolimus were calculated at one month and one year after transplantation...
March 16, 2018: International Journal of Molecular Sciences
Michael Baer, Bradley Klemetson, Diana Scott, Andrew S Murtishaw, James W Navalta, Jefferson W Kinney, Merrill R Landers
BACKGROUND AND PURPOSE: Because falls can have deleterious consequences, it is important to understand the influence of fatigue and medications on balance in persons with Parkinson disease (PD). Thus, the purpose of this study was to investigate the effects of fatigue on balance in individuals with PD. Because brain-derived neurotrophic factor (BDNF) has been shown to be related to motor performance, we also explored its role. METHODS: A total of 27 individuals (age = 65...
April 2018: Journal of Neurologic Physical Therapy: JNPT
Ivana Glavina Jelaš, Ivan Dević, Dalibor Karlović
BACKGROUND: the objective of this study was to examine the associations between Cloninger temperament and character dimensions with the DAT1 VNTR and COMT Val158Met polymorphisms. SUBJECTS AND METHODS: The study was conducted on 101 subjects, consisting of students of the Police College in Zagreb and staff of the Sestre Milosrdnice University Hospital in Zagreb. The Cloninger Temperament and Character Inventory (TCI) was used to test personality traits. RESULTS: A main effect of the DAT1 VNTR polymorphism was found on the subscale self-directedness - SD2 (F=5...
March 2018: Psychiatria Danubina
Marco Guarene, Carla Badulli, Anna L Cremaschi, Ilaria Sbarsi, Rosalia Cacciatore, Carmine Tinelli, Annamaria Pasi, Paola Bergamaschi, Cesare G Perotti
INTRODUCTION: Allele-level donor-recipient match at HLA-A, HLA-B, HLA-C and HLA-DRB1 loci impacts the outcome after cord blood transplantation for hematologic malignancies and modifies the strategy of donor selection. High definition of both class I and II HLA loci at time of listing is a way to improve the attractiveness of cord blood bank inventories, reducing the time for donor search and procurement and simplifying donor choice, in particular, for patients of non-European heritage...
March 1, 2018: International Journal of Artificial Organs
D Liao, H Yu, L Han, C Zhong, X Ran, D Wang, L Mo
PURPOSE: Evidences showed that paraoxonase 1 (PON1) gene polymorphism has an impact on women's susceptibility to polycystic ovarian syndrome (PCOS) by influencing the expression and activity of PON1. However, the effects of three PON1 polymorphisms (- 108 C>T, L55M and Q192R) on the incidence of PCOS have generated inconsistent results. Here, we conducted a meta-analysis to investigate the association between PON1 polymorphisms and PCOS risk. METHODS: All eligible trials were identified via systematic searches of multiple literature databases...
March 15, 2018: Journal of Endocrinological Investigation
Shiguang Wang, Bingtian Ma, Qiang Gao, Guojing Jiang, Lei Zhou, Bin Tu, Peng Qin, Xueqin Tan, Peixiong Liu, Yunhai Kang, Yuping Wang, Weilan Chen, Chengzhi Liang, Shigui Li
Shuhui498 (R498) is an elite parent of heavy panicle hybrid rice by pyramiding the rare gn1a and null gs3 alleles. This finding reveals the genetic basis and great potential application in future breeding of R498. The heavy panicle trait, defined as 5 g or more of grain weight per panicle, is one of the target traits in super-high-yield rice breeding programs. The use of heavy panicle-type hybrid rice has been shown to be a successful strategy for super-high-yield breeding programs, particularly under the environmental conditions of high humidity and deficient solar radiation in southwestern China...
March 15, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Carolina Ribeiro, Rosa Quinta, Ana Raposo, Ana Valentim, José Albuquerque, Manuela Grazina
Objective: Prospective observational study to analyze CYP2D6 pharmacogenetics in 55 Portuguese adult parturients undergoing elective cesarean section and to investigate the association between CYP2D6 alleles and pain score. Methods: DNA was extracted from peripheral blood by standard methods. Genetic analysis included allelic discrimination (CYP2D6*1, *2, *3, *4, *5, *6, *10, *17, and *41) and copy number determination with TaqMan probes by real-time polymerase chain reaction (PCR)...
March 12, 2018: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
Peng Wang, San-Pin Wu, Kelsey E Brooks, Andrew M Kelleher, Jessica Milano-Foster, Francesco J DeMayo, Thomas E Spencer
Forkhead box A2 (FOXA2) is a pioneer transcription factor involved in organ development, function and cancer. In the uterus, FOXA2 is essential for pregnancy and expressed specifically in the glands of the endometrium loss of FOXA2 function occurs during development of endometrial cancer in humans. The present study describes the development of a mouse model for conditional expression of mouse FOXA2. Using a system consisting of a minigene located at the Rosa26 locus, a CAG-S-mFOXA2 allele was generated in embryonic stem cells and subsequently in mice; before activation, the minigene is silent due to a floxed stop cassette inserted between the promoter and the transgene...
March 13, 2018: Endocrinology
Cyndya A Shibao, Jorge E Celedonio, Robyn Tamboli, Reem Sidani, Latisha Love-Gregory, Terri Pietka, Yanhua Xiong, Yan Wei, Naji N Abumrad, Nada A Abumrad, Charles Robb Flynn
Context: Abnormal fatty acid (FA) metabolism contributes to diabetes and cardiovascular disease. The FA receptor CD36 has been linked to risk of metabolic syndrome. In rodents CD36 regulates various aspects of fat metabolism but whether it has similar actions in humans is unknown. We examined impact of a coding single-nucleotide polymorphism in CD36 on post-prandial hormone and bile acid (BA) responses. Objective: To examine if the minor allele (G) of coding CD36 variant rs3211938 (G/T) which reduces CD36 level by approximately 50% influences hormonal responses to a high-fat meal (HFM)...
March 12, 2018: Journal of Clinical Endocrinology and Metabolism
Chonlaphat Sukasem, Chonlawat Chaichan, Thapanat Nakkrut, Patompong Satapornpong, Kanoot Jaruthamsophon, Thawinee Jantararoungtong, Napatrupron Koomdee, Suthida Sririttha, Sadeep Medhasi, Sarawut Oo-Puthinan, Ticha Rerkpattanapipat, Jettanong Klaewsongkram, Pawinee Rerknimitr, Papapit Tuchinda, Leena Chularojanamontri, Napatra Tovanabutra, Apichaya Puangpetch, Wichai Aekplakorn
The HLA-B ∗ 15:02 allele has been reported to have a strong association with carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) in Thai patients. The HLA-B alleles associated with carbamazepine-induced maculopapular exanthema (MPE) and the drug reaction with eosinophilia and systemic symptoms (DRESS) among the Thai population have never been reported. The aim of the present study was to carry out an analysis of the involvement of HLA-B alleles in carbamazepine-induced cutaneous adverse drug reactions (cADRs) in the Thai population...
2018: Journal of Immunology Research
Christine Ludwin Wanjala, Eliningaya J Kweka
Background: Malaria vector control efforts have taken malaria related cases down to appreciable number per annum after large scale of intervention tools. Insecticides-based tools remain the major control option for malaria vectors in Kenya and, therefore, the potential of such programs to be compromised by the reported insecticide resistance is of major concern. The objective of this study was to evaluate the status of insecticide resistance in malaria vectors in different agro ecosystems from western Kenya...
2018: Frontiers in Public Health
Xianhua Wang, Aiguo Ma, Xiuxia Han, Aishan Litifu, Feng Xue
Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that included 780 Xinjiang Muslim subjects (400 TB patients and 380 controls). Multiplex PCR and direct sequencing were used to detect ASAP1 gene polymorphisms...
April 2018: Experimental and Therapeutic Medicine
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