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https://www.readbyqxmd.com/read/28241413/a-cross-species-gene-expression-marker-based-genetic-map-and-qtl-analysis-in-bambara-groundnut
#1
Hui Hui Chai, Wai Kuan Ho, Neil Graham, Sean May, Festo Massawe, Sean Mayes
Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip...
February 22, 2017: Genes
https://www.readbyqxmd.com/read/28240813/fabrication-and-characterization-of-conductive-conjugated-polymer-coated-antheraea-mylitta-silk-fibroin-fibers-for-biomedical-applications
#2
Darshan Gh, Dexu Kong, Julien Gautrot, Shyam Kumar Vootla
Conductive polymers are interesting materials for a number of biological and medical applications requiring electrical stimulation of cells or tissues. Highly conductive polymers (polypyrrole and polyaniline)/Antheraea mylitta silk fibroin coated fibers are fabricated successfully by in situ polymerization without any modification of the native silk fibroin. Coated fibers characterized by scanning electron microscopy confirm the silk fiber surface is covered by conductive polymers. Thermogravimetric analysis reveals preserved thermal stability of silk fiber after coating process...
February 27, 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/28239975/preparing-to-read-the-ubiquitin-code-top-down-analysis-of-unanchored-ubiquitin-tetramers
#3
Amanda E Lee, Lucia Geis-Asteggiante, Emma K Dixon, Meredith Miller, Yan Wang, David Fushman, Catherine Fenselau
The characterization of polyubiquitin chains has been an analytical challenge for several decades. It has been shown that anchored and unanchored polyubiquitin chains with different isopeptide linkages and lengths exhibit a wide range of profoundly different cellular functions. However, structure function studies have been hindered by the difficulty of characterizing these complex chain structures. This report presents a broadly applicable workflow to characterize ubiquitin tetramers without the need for genetic mutations or reiterative immunoprecipitations...
August 2016: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28239226/temperature-and-moisture-dependent-studies-on-alunogen-and-the-crystal-structure-of-meta-alunogen-determined-from-laboratory-powder-diffraction-data
#4
Volker Kahlenberg, Doris E Braun, Hannes Krüger, Daniela Schmidmair, Maria Orlova
Starting from a synthetic sample with composition Al2(SO4)3·16.6H2O, the high-temperature- and moisture-dependent behavior of alunogen has been unraveled by TGA measurements, in situ powder X-ray diffraction as well as by gravimetric moisture sorption/desorption studies. Heating experiments using the different techniques show that alunogen undergoes a first dehydration process already starting at temperatures slightly above 40 °C. The crystalline product of the temperature-induced dehydration corresponds to the synthetic equivalent of meta-alunogen and has the following chemical composition: Al2(SO4)3·13...
2017: Physics and Chemistry of Minerals
https://www.readbyqxmd.com/read/28238960/inter-and-intra-subtype-variation-of-blastocystis-subtypes-isolated-from-diarrheic-and-non-diarrheic-patients-in-iran
#5
Atefe Alinaghizade, Hamed Mirjalali, Mehdi Mohebali, Christen Rune Stensvold, Mostafa Rezaeian
Blastocystis is a common intestinal parasitic protist infecting birds and mammals. Blastocystis comprises at least 17 subtypes (ST), of which ST1-ST9 have been detected in humans. Significant correlation between certain subtypes and pathogenicity remains to be established. Nevertheless, some studies suggest a potential linkage between subtypes (inter- and intra-subtype variation) and clinical manifestations. The aim of this study was to identify intra-subtype genetic variation of subtypes of Blastocystis in stools samples submitted by diarrheic and non-diarrheic patients...
February 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28236820/developing-an-integrated-modeling-tool-for-river-water-quality-index-assessment
#6
Y C Lai, C C Chien, Z H Yang, Rao Y Surampalli, C M Kao
  The goal of this study was to establish a modeling tool for river water quality with a direct linkage to the water quality index (WQI5) calculation and the river water quality model, the Water Quality Analysis Simulation Program (WASP), for pollutant transport modeling. The integrated WASP and WQI5 tool was field-tested to assess pollutant loadings and their impacts on river environment. Suspended solid (SS) and electric conductivity (EC) correlation equations and the WQI5 calculation tool were included in the water quality model and direct WQI5 calculation...
March 1, 2017: Water Environment Research: a Research Publication of the Water Environment Federation
https://www.readbyqxmd.com/read/28235871/metatranscriptomic-profiling-reveals-linkages-between-the-active-rumen-microbiome-and-feed-efficiency-in-beef-cattle
#7
Fuyong Li, Le Luo Guan
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n=10; inefficient, n=10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic datasets...
February 24, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28230170/modeling-continuous-admixture-using-admixture-induced-linkage-disequilibrium
#8
Ying Zhou, Hongxiang Qiu, Shuhua Xu
Recent migrations and inter-ethnic mating of long isolated populations have resulted in genetically admixed populations. To understand the complex population admixture process, which is critical to both evolutionary and medical studies, here we used admixture induced linkage disequilibrium (LD) to infer continuous admixture events, which is common for most existing admixed populations. Unlike previous studies, we expanded the typical continuous admixture model to a more general scenario with isolation after a certain duration of continuous gene flow...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28230092/rtfc-4931414p19rik-regulates-in-vitro-thyroid-differentiation-and-in-vivo-thyroid-function
#9
Yang Yu, Chang Liu, Junxia Zhang, Mimi Zhang, Wei Wen, Xianhui Ruan, Dapeng Li, Shuang Zhang, Ming Gao, Lingyi Chen
Thyroid is a one of the most important endocrine organs. Understanding the molecular mechanism underlying thyroid development and function, as well as thyroid diseases, is beneficial for the clinical treatment of thyroid diseases and tumors. Through genetic linkage analysis and exome sequencing, we previously identified an uncharacterized gene C14orf93 (RTFC, mouse homolog: 4931414P19Rik) as a novel susceptibility gene for familial non-medullary thyroid carcinoma, and demonstrated its function in promoting thyroid tumor...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229454/analysis-of-a-fully-penetrant-spinocerebellar-ataxia-type-8-brazilian-family
#10
V P Cintra, C M Lourenço, M M V Rocha, P J Tomaselli, W Marques
Spinocerebellar ataxia type 8 (SCA8) is a progressive neurological disorder caused by the expanded repeat CTA/CTG of two overlapping genes, ATXN8OS and ATXN8, expressed bidirectionally. Normal alleles have 15-50 repeats, and pathogenic alleles range from 71 to 1300 repeats. The disorder is relatively rare, accounting for about 2%-5% of the autosomal dominant forms of hereditary ataxia worldwide. However, the prevalence of disease-causing ATXN8OS/ATXN8 expansions is higher than the disease because of the reduced penetrance of the expanded allele...
February 22, 2017: Acta Neurologica Scandinavica
https://www.readbyqxmd.com/read/28224024/topological-and-functional-analysis-of-nonalcoholic-steatohepatitis-through-protein-interaction-mapping
#11
Hamid Asadzadeh-Aghdaee, Vahid Mansouri, Ali Asghar Peyvandi, Fathollah Moztarzadeh, Farshad Okhovatian, Farhad Lahmi, Reza Vafaee, Mohammad Reza Zali
AIM: The corresponding proteins are important for network mapping since the interaction analysis can provide a new interpretation about disease underlying mechanisms as the aim of this study. BACKGROUD: Nonalcoholic steatohepatitis (NASH) is one of the main causes of liver disease in the world. It has been known with many susceptible proteins that play essential role in its pathogenesis. METHODS: In this paper, protein-protein interaction (PPI) network analysis of fatty liver disease retrieved from STRING db by the application of Cytoscape Software...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28222770/what-do-patients-with-diabetes-and-providers-think-of-an-innovative-australian-model-of-remote-diabetic-retinopathy-screening-a-qualitative-study
#12
Nicola M Glasson, Sarah L Larkins, Lisa J Crossland
BACKGROUND: Diabetic retinopathy (DR) is the commonest cause of preventable blindness in working age populations, but up to 98% of visual loss secondary to DR can be prevented with early detection and treatment. In 2012, an innovative outreach DR screening model was implemented in remote communities in a state of Australia. The aim of this study was to explore the acceptability of this unique DR screening model to patients, health professionals and other key stakeholders. METHODS: This descriptive qualitative study used semi-structured interviews with patients opportunistically recruited whilst attending DR screening, and purposefully selected health care professionals either working within or impacted by the programme...
February 22, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28222735/advancing-gender-equality-through-the-athena-swan-charter-for-women-in-science-an-exploratory-study-of-women-s-and-men-s-perceptions
#13
Pavel V Ovseiko, Alison Chapple, Laurel D Edmunds, Sue Ziebland
BACKGROUND: While in the United Kingdom, Ireland, and Australia, higher education and research institutions are widely engaged with the Athena SWAN Charter for Women in Science to advance gender equality, empirical research on this process and its impact is rare. This study combined two data sets (free- text comments from a survey and qualitative interviews) to explore the range of experiences and perceptions of participation in Athena SWAN in medical science departments of a research-intensive university in Oxford, United Kingdom...
February 21, 2017: Health Research Policy and Systems
https://www.readbyqxmd.com/read/28222201/linkage-and-mapping-of-quantitative-trait-loci-associated-with-angular-leaf-spot-and-powdery-mildew-resistance-in-common-beans
#14
Denis Bassi, Boris Briñez, Juliana Santa Rosa, Paula Rodrigues Oblessuc, Caléo Panhoca de Almeida, Stella Maris Nucci, Larissa Chariel Domingos da Silva, Alisson Fernando Chiorato, Rosana Pereira Vianello, Luis Eduardo Aranha Camargo, Matthew Wohlgemuth Blair, Luciana Lasry Benchimol-Reis
Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis...
February 20, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28221991/detecting-clinically-meaningful-shape-clusters-in-medical-image-data-metrics-analysis-for-hierarchical-clustering-applied-to-healthy-and-pathological-aortic-arches
#15
Jan L Bruse, Maria A Zuluaga, Abbas Khushnood, Kristin McLeod, Hopewell N Ntsinjana, Tain-Yen Hsia, Maxime Sermesant, Xavier Pennec, Andrew M Taylor, Silvia Schievano
OBJECTIVE: Today's growing medical image databases call for novel processing tools to structure the bulk of data and extract clinically relevant information. Unsupervised hierarchical clustering may reveal clusters within anatomical shape data of patient populations as required for modern Precision Medicine strategies. Few studies have applied hierarchical clustering techniques to three-dimensional patient shape data and results depend heavily on the chosen clustering distance metrics and linkage functions...
February 16, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28220352/purification-characterization-and-overexpression-of-an-endo-1-4-%C3%AE-mannanase-from-thermotolerant-bacillus-sp-swu60
#16
Weeranuch Seesom, Polphet Thongket, Tomohiro Yamamoto, Shigeo Takenaka, Tatsuji Sakamoto, Wasana Sukhumsirichart
Endo-β-1,4-mannanases are important catalytic agents in several industries. The enzymes randomly cleave the β-1,4-linkage in the mannan backbone and release short β-1,4-mannooligosaccharides and mannose. In the present study, mannanase (ManS2) from thermotolerant Bacillus sp. SWU60 was purified, characterized, and its gene was cloned and overexpressed in Escherichia coli. ManS2 was purified from culture filtrate (300 ml) by using hydrophobic, ion-exchange, and size-exclusive liquid chromatography. The apparent molecular mass was 38 kDa...
March 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28220206/a-user-guide-to-the-brassica-60k-illumina-infinium%C3%A2-snp-genotyping-array
#17
REVIEW
Annaliese S Mason, Erin E Higgins, Rod J Snowdon, Jacqueline Batley, Anna Stein, Christian Werner, Isobel A P Parkin
The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies...
February 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28220151/prioritizing-zoonotic-diseases-in-ethiopia-using-a-one-health-approach
#18
Emily G Pieracci, Aron J Hall, Radhika Gharpure, Abraham Haile, Elias Walelign, Asefa Deressa, Getahun Bahiru, Meron Kibebe, Henry Walke, Ermias Belay
BACKGROUND: Ethiopia has the second largest human population in Africa and the largest livestock population on the continent. About 80% of Ethiopians are dependent on agriculture and have direct contact with livestock or other domestic animals. As a result, the country is vulnerable to the spread of zoonotic diseases. As the first step of the country's engagement in the Global Health Security Agenda, a zoonotic disease prioritization workshop was held to identify significant zoonotic diseases of mutual concern for animal and human health agencies...
December 2016: One Health
https://www.readbyqxmd.com/read/28220139/genome-wide-single-nucleotide-polymorphism-discovery-and-the-construction-of-a-high-density-genetic-map-for-melon-cucumis-melo-l-using-genotyping-by-sequencing
#19
Che-Wei Chang, Yu-Hua Wang, Chih-Wei Tung
Although genotyping-by-sequencing (GBS) enables the efficient and low-cost generation of large numbers of markers, the utility of resultant genotypes are limited, because they are enormously error-prone and contain high proportions of missing data. In this study, we generated single nucleotide polymorphism (SNP) markers for 109 recombinant inbred lines of melon (Cucumis melo L.) using the GBS approach and ordered them according to their physical position on the draft double haploid line DHL92 genome. Next, by investigating associations between these SNPs, we discovered that some segments on the physical map conflict with linkage relationships...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28220132/identification-of-marker-trait-associations-for-lint-traits-in-cotton
#20
Muhammad A Iqbal, Mehboob-Ur- Rahman
Harvesting high quality lint, a long-awaited breeding goal-accomplished partly, can be achieved by identifying DNA markers which could be used for diagnosing cotton plants containing the desired traits. In the present studies, a total of 185 cotton genotypes exhibiting diversity for lint traits were selected from a set of 546 genotypes evaluated for fiber traits in 2009. These genotypes were extensively studied for three consecutive years (2011-2013) at three different locations. Significant genetic variations were found for average boll weight, ginning out turn (GOT), micronaire value, staple length, fiber bundle strength, and uniformity index...
2017: Frontiers in Plant Science
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