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linkage analysis

Chengguang Dong, Juan Wang, Quanjia Chen, Yu Yu, Baocheng Li
Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped...
July 2018: Genes & Genomics
Belize A Lane, Samuel Sandoval-Solis, Eric D Stein, Sarah M Yarnell, Gregory B Pasternack, Helen E Dahlke
Balancing ecological and human water needs often requires characterizing key aspects of the natural flow regime and then predicting ecological response to flow alterations. Flow metrics are generally relied upon to characterize long-term average statistical properties of the natural flow regime (hydrologic baseline conditions). However, some key aspects of hydrologic baseline conditions may be better understood through more complete consideration of continuous patterns of daily, seasonal, and inter-annual variability than through summary metrics...
June 22, 2018: Environmental Management
Daniel I McIsaac, Chelsey Saunders, Emily Hladkowicz, Gregory L Bryson, Alan J Forster, Sylvain Gagne, Allen Huang, Manoj Lalu, Luke T Lavallee, Husein Moloo, Julie Nantel, Barbara Power, Celena Scheede-Bergdahl, Monica Taljaard, Carl van Walraven, Colin J L McCartney
INTRODUCTION: Exercise prehabilitation may improve outcomes after surgery. Frailty is a key predictor of adverse postoperative outcomes in older people; the multidimensional nature of frailty makes this a population who may derive substantial benefit from exercise prehabilitation. The objective of this trial is to test the efficacy of exercise prehabilitation to improve postoperative functional outcomes for people living with frailty having cancer surgery with curative intent. METHODS AND ANALYSIS: We will conduct a single-centre, parallel-arm randomised controlled trial of home-based exercise prehabilitation versus standard care among consenting patients >60 years having elective cancer surgery (intra-abdominal and intrathoracic) and who are frail (Clinical Frailty Scale >4<u>)</u>...
June 22, 2018: BMJ Open
B Abrahams, N Sitas, K J Esler
Moving towards more integrative approaches within the invasion sciences has been recognized as a means of improving linkages between science, policy, and practice. Yet despite the recognition that biological invasions pose complex social-ecological challenges, the invasion literature poorly covers social-ecological or distinctly integrative research. Various initiatives and investments have been made towards building research capacity and conducting more integrative research aimed at improving the management of biological invasions...
June 19, 2018: Journal of Environmental Management
Cheng-Tao Li, Min Zhang, Yun-Xuan Weng, Jia-Xiang Qin
The difference of enzymatic degradation behavior between Poly (butylene succinate-co-diethylene glycol succinate) (PBS-co-DEGS) and Poly (butylene succinate-co-butylene diglycolic acid) (PBS-co-BDGA) was studied in a Tetrahydrofuran (THF)/toluene mixed system by Novozym 435 (N435, immobilized Candida Antarctica lipase supported on acrylic resin) catalysis for 30 h. These two copolymers (modified with alcoholic acid by ether linkage) were synthesized by melt polycondensation and characterized by 1 H NMR. The average molecular weight and thermal property before and after degradation were determined by gel permeation chromatography (GPC) and thermogravimetric analysis (TGA), respectively...
June 19, 2018: International Journal of Biological Macromolecules
Hila Behar, Sean W Graham, Harry Brumer
Carbohydrate-active enzymes (CAZymes) are central to the biosynthesis and modification of the plant cell wall. An ancient clade of bifunctional plant endo-glucanases (EG16 members) was recently revealed and proposed to represent a transitional group uniting plant xyloglucan endo-transglycosylase/hydrolase (XTH) gene products and bacterial mixed-linkage endo-glucanases in the phylogeny of Glycoside Hydrolase Family 16 (GH16). To gain broader insights into the distribution and frequency of EG16 and other GH16 members in plants, the Phytozome, Plaza, NCBI, and 1000 Plants databases were mined to build a comprehensive census among 1289 species spanning the broad phylogenetic diversity of multiple algae through recent plant lineages...
June 22, 2018: Plant Journal: for Cell and Molecular Biology
Kalpita R Karan, Parthasarthy Satishchandra, Sanjib Sinha, Anuranjan Anand
Hot water epilepsy (HWE) is a rare form of sensory epilepsy where seizures are precipitated by a stimulus of contact with hot water. While earlier studies have suggested causal role of genes for HWE, specific underpinnings are beginning to be explored only recently. We carried out a whole genome-based linkage analysis in a family where most of its members affected by HWE and found evidence of a previously unknown locus at chromosome 9p24.3-p23. Parametric two-point analysis suggested linkage with the greatest LOD score of 3...
June 2018: Journal of Genetics
Nilotpal Sanyal, Min-Tzu Lo, Karolina Kauppi, Srdjan Djurovic, Ole A Andreassen, Valen E Johnson, Chi-Hua Chen
Motivation: Multiple marker analysis of the genome-wide association study (GWAS) data has gained ample attention in recent years. However, because of the ultra high-dimensionality of GWAS data, such analysis is challenging. Frequently used penalized regression methods often lead to large number of false positives, whereas Bayesian methods are computationally very expensive. Motivated to ameliorate these issues simultaneously, we consider the novel approach of using nonlocal priors in an iterative variable selection framework...
June 19, 2018: Bioinformatics
Yu Zhu, Depeng Zhang, Zhanwen Zhang, Zhigang Wang
The widespread application of hydrocarbon polymer materials has spurred an increasing interest in the study of their dissociation mechanism, which is related to key issues such as environmental protection. In this work, the last-step dissociation characteristics of carbon chain polymers were investigated. By using density functional theory, we considered all possible structures, including three typical normal linkage polymers and four typical abnormal linkage ones. In these structures, it can be found that the energy barrier required for the complete degradation of chain-end saturated and unsaturated polymers are in the range of 3...
June 2018: ChemistryOpen
Yoshiji Yamada, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Tetsuo Fujimaki, Yoshiki Yasukochi, Ichiro Takeuchi, Jun Sakuma
Given that early-onset type 2 diabetes mellitus (T2DM), metabolic syndrome (MetS), and hyperuricemia have been shown to have strong genetic components, the statistical power of a genetic association study may be increased by focusing on early-onset subjects with these conditions. Although genome-wide association studies have identified various genes and loci significantly associated with T2DM, MetS, and hyperuricemia, genetic variants that contribute to predisposition to these conditions in Japanese subjects remain to be identified definitively...
July 2018: Biomedical Reports
Yoshiji Yamada, Kimihiko Kato, Mitsutoshi Oguri, Hideki Horibe, Tetsuo Fujimaki, Yoshiki Yasukochi, Ichiro Takeuchi, Jun Sakuma
Given that substantial genetic components have been shown in ischemic stroke, intracerebral hemorrhage (ICH), and subarachnoid hemorrhage (SAH), heritability may be higher in early-onset than late-onset individuals with these conditions. Although genome-wide association studies (GWASs) have identified various genes and loci significantly associated with ischemic stroke, ICH, or intracranial aneurysm mainly in European ancestry populations, genetic variants that contribute to susceptibility to these disorders remain to be identified definitively...
July 2018: Biomedical Reports
Zhen-Feng Fang, Tao Zhang, Xiao-Qin Cao, Lu Shi
A novel sesquilignan compound (1), possesing an unusual carbon skeleton of aryltetralin unit linked with a C6-C3 unit and a five-membered ring by a C-7″ and C-4 linkage pattern via an oxygen atom, and a new lignan glycoside (2) have been isolated from the twigs and leaves of Illicium majus. Their structures were determined by spectroscopic analysis and chemical methods. The absolute configurations of 1 and 2 are confirmed by observing the circular dichroism. At 10 μM, Compounds 1 and 2 showed in Vitro inhibitory activity against the release of β-glucuronidase in rat polymorphonuclear leukocytes induced by platelet-activating factor...
June 18, 2018: Fitoterapia
Ayyappa Kumar Sista Kameshwar, Wensheng Qin
Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2...
2018: Journal of Genomics
Isabela Maia Diniz, Augusto Afonso Guerra, Livia Lovato Pires de Lemos, Kathiaja M Souza, Brian Godman, Marion Bennie, Björn Wettermark, Francisco de Assis Acurcio, Juliana Alvares, Eli Iola Gurgel Andrade, Mariangela Leal Cherchiglia, Vânia Eloisa de Araújo
BACKGROUND: Multiple Sclerosis (MS) is a disease that appreciably impacts on the quality of life of patients and is associated with high expenditure. MS is a chronic multifactorial disease, characterized by inflammation, demyelination and axonal loss. The Brazilian public health system provides pharmacological treatment as well as hospital and outpatient care for patients with relapsing-remitting and secondary progressive multiple sclerosis. However, we are not aware of any previous publications assessing total direct medical costs in patients with a long follow-up within the Brazilian healthcare system...
2018: PloS One
Yujuan Zhang, Donghua Li, Yanyan Wang, Rong Zhou, Linhai Wang, Yanxin Zhang, Jingyin Yu, Huihui Gong, Jun You, Xiurong Zhang
The NAM, ATAF1/2, and CUC2 (NAC) family constitutes a large family of plant-specific transcription factors, involved in many aspects of physiological processes and a variety of abiotic stresses. There is little information concerning the NAC family in Sesamum indicum. In this study, 87 sesame NAC genes were identified and phylogenetically clustered into 12 groups with Arabidopsis NAC genes. A total of 83 SiNAC genes were distributed non-randomly on the 16 linkage groups in sesame. Four and 49 SiNACs were found to be tandemly and segmentally duplicated, respectively...
2018: PloS One
Qing Sung, Caiyun Liu, Guanyun Zhang, Jian Zhang, Chen-Ho Tung, Yifeng Wang
Novel 17-nuclear Zr-/Hf- oxide clusters ({Zr17} and {Hf17}) are isolated from aqueous systems. In the clusters, Zr/Hf ions are connected via μ3-O, μ3-OH and μ2-OH linkages into a pinwheel core which is wrapped with SO42-, HCOO- and aqua ligands. Octahedral hexanuclear Zr-/Hf- oxide clusters ({Zr6}oct and {Hf6}oct) are also isolated from the same hydrothermal system by decreasing the synthesis temperature. Structural analysis, synthetic conditions, vibrational spectra and ionic conductivity of the clusters are studied...
June 21, 2018: Chemistry: a European Journal
Mohammad A Al Sallakh, Sarah E Rodgers, Ronan A Lyons, Aziz Sheikh, Gwyneth A Davies
Asthma and chronic obstructive pulmonary disease (COPD) are two common different clinical diagnoses with overlapping clinical features. Both conditions have been increasingly studied using electronic health records (EHR). Asthma-COPD overlap syndrome (ACOS) is an emerging concept where clinical features from both conditions co-exist, and for which, however, there is no consensus definition. Nonetheless, we expect EHR data of people with ACOS to be systematically different from those with "asthma only" or "COPD only"...
June 20, 2018: NPJ Primary Care Respiratory Medicine
Halie M Rando, Marta Farré, Michael P Robson, Naomi B Won, Jennifer L Johnson, Ronak Buch, Estelle R Bastounes, Xueyan Xiang, Shaohong Feng, Shiping Liu, Zijun Xiong, Jaebum Kim, Guojie Zhang, Lyudmila N Trut, Denis M Larkin, Anna V Kukekova
The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model...
June 20, 2018: Genes
Saad M Al Shareef, Sulman Basit, Sha Li, Corinne Pfister, Sylvain Pradervand, Michel Lecendreux, Geert Mayer, Yves Dauvilliers, Vincenzo Salpietro, Henry Houlden, Ahmed S BaHammam, Mehdi Tafti
Kleine-Levin syndrome (KLS) is a rare periodic hypersomnia with associated behavioural abnormalities but with often favourable prognosis. There is excess risk of KLS in first-degree relatives, suggesting a strong genetic contribution. So far, no mutation is identified in KLS and comprehensive genetic analysis of affected individuals is lacking. Here we performed whole genome single-nucleotide polymorphism (SNP) genotyping and exome sequencing in a large family with seven affected members. The identified gene with a mutation was resequenced in 38 sporadic KLS patients and the expression of the gene product was mapped in the mouse brain...
June 19, 2018: Journal of Sleep Research
Adam J de Smith, Kyle M Walsh, Stephen S Francis, Chenan Zhang, Helen M Hansen, Ivan Smirnov, Libby Morimoto, Todd P Whitehead, Alice Kang, Xiaorong Shao, Lisa F Barcellos, Roberta McKean-Cowdin, Luoping Zhang, Cecilia Fu, Rong Wang, Herbert Yu, Josephine Hoh, Andrew T Dewan, Catherine Metayer, Xiaomei Ma, Joseph L Wiemels
Genome-wide association studies of childhood acute lymphoblastic leukemia (ALL) have identified regions of association at PIP4K2A and upstream of BMI1 at chromosome 10p12.31-12.2. The contribution of both loci to ALL risk and underlying functional variants remain to be elucidated. We carried out single nucleotide polymorphism (SNP) imputation across chromosome 10p12.31-12.2 in Latino and non-Latino white ALL cases and controls from two independent California childhood leukemia studies, and additional Genetic Epidemiology Research on Aging study controls...
June 19, 2018: International Journal of Cancer. Journal International du Cancer
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