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https://www.readbyqxmd.com/read/29330432/developing-genome-wide-snps-and-constructing-an-ultrahigh-density-linkage-map-in-oil-palm
#1
Bin Bai, Le Wang, Ying Jun Zhang, May Lee, Rahmadsyah Rahmadsyah, Yuzer Alfiko, Bao Qing Ye, Sigit Purwantomo, Antonius Suwanto, Nam-Hai Chua, Gen Hua Yue
Oil palm (Elaeis guineensis Jacq.) is the leading oil-producing crops and the most important edible oil resource worldwide. DNA markers and genetic linkage maps are essential resources for marker-assisted selection to accelerate genetic improvement. We conducted RAD-seq on an Illumina NextSeq500 to discover genome-wide SNPs, and used the SNPs to construct a linkage map for an oil palm (Tenera) population derived from a cross between a Deli Dura and an AVROS Pisifera. The RAD-seq produced 1,076 million single-end reads across the breeding population containing 155 trees...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29328157/talbot-lau-x-ray-deflectometry-phase-retrieval-methods-for-electron-density-diagnostics-in-high-energy-density-experiments
#2
Maria Pia Valdivia, Dan Stutman, Christian Stoeckl, Chad Mileham, Ildar A Begishev, Jake Bromage, Sean P Regan
Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment...
January 10, 2018: Applied Optics
https://www.readbyqxmd.com/read/29328079/high-resolution-coherent-x-ray-diffraction-imaging-of-metal-coated-polymer-microspheres
#3
Eirik T B Skjønsfjell, David Kleiven, Nilesh Patil, Yuriy Chushkin, Federico Zontone, Alain Gibaud, Dag W Breiby
Coherent x-ray diffraction imaging (CXDI) is becoming an important 3D quantitative microscopy technique, allowing structural investigation of a wide range of delicate mesoscale samples that cannot be imaged by other techniques like electron microscopy. Here we report high-resolution 3D CXDI performed on spherical microcomposites consisting of a polymer core coated with a triple layer of nickel-gold-silica. These composites are of high interest to the microelectronics industry, where they are applied in conducting adhesives as fine-pitch electrical contacts-which requires an exceptional degree of uniformity and reproducibility...
January 1, 2018: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29327365/millimeter-spatial-resolution-in-vivo-sodium-mri-of-the-human-eye-at-7-t-using-a-dedicated-radiofrequency-transceiver-array
#4
Daniel Wenz, Andre Kuehne, Till Huelnhagen, Armin M Nagel, Helmar Waiczies, Oliver Weinberger, Celal Oezerdem, Oliver Stachs, Soenke Langner, Erdmann Seeliger, Bert Flemming, Russell Hodge, Thoralf Niendorf
PURPOSE: The aim of this study was to achieve millimeter spatial resolution sodium in vivo MRI of the human eye at 7 T using a dedicated six-channel transceiver array. We present a detailed description of the radiofrequency coil design, along with electromagnetic field and specific absorption ratio simulations, data validation, and in vivo application. METHODS: Electromagnetic field and specific absorption ratio simulations were performed. Transmit field uniformity was optimized by using a multi-objective genetic algorithm...
January 12, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/29325965/genome-wide-association-mapping-for-seed-protein-and-oil-contents-using-a-large-panel-of-soybean-accessions
#5
Dongmei Li, Xue Zhao, Yingpeng Han, Wenbin Li, Futi Xie
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0...
January 8, 2018: Genomics
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#6
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29323885/unraveling-hidden-mg-mn-h-phase-relations-at-high-pressures-and-temperatures-by-in-situ-synchrotron-diffraction
#7
Kristina Spektor, Wilson A Crichton, Sumit Konar, Stanislav Filippov, Johan Klarbring, Sergei I Simak, Ulrich Häussermann
The Mg-Mn-H system was investigated by in situ high pressure studies of reaction mixtures MgH2-Mn-H2. The formation conditions of two complex hydrides with composition Mg3MnH7 were established. Previously known hexagonal Mg3MnH7 (h-Mg3MnH7) formed at pressures 1.5-2 GPa and temperatures between 480 and 500 °C, whereas an orthorhombic form (o-Mg3MnH7) was obtained at pressures above 5 GPa and temperatures above 600 °C. The crystal structures of the polymorphs feature octahedral [Mn(I)H6]5- complexes and interstitial H-...
January 11, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29321632/genome-wide-association-study-in-asia-adapted-tropical-maize-reveals-novel-and-explored-genomic-regions-for-sorghum-downy-mildew-resistance
#8
Zerka Rashid, Pradeep Kumar Singh, Hindu Vemuri, Pervez Haider Zaidi, Boddupalli Maruthi Prasanna, Sudha Krishnan Nair
Globally, downy mildews are among the important foliar diseases of maize that cause significant yield losses. We conducted a genome-wide association study for sorghum downy mildew (SDM; Peronosclerospora sorghi) resistance in a panel of 368 inbred lines adapted to the Asian tropics. High density SNPs from Genotyping-by-sequencing were used in GWAS after controlling for population structure and kinship in the panel using a single locus mixed model. The study identified a set of 26 SNPs that were significantly associated with SDM resistance, with Bonferroni corrected P values ≤ 0...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320477/a-global-map-of-travel-time-to-cities-to-assess-inequalities-in-accessibility-in-2015
#9
D J Weiss, A Nelson, H S Gibson, W Temperley, S Peedell, A Lieber, M Hancher, E Poyart, S Belchior, N Fullman, B Mappin, U Dalrymple, J Rozier, T C D Lucas, R E Howes, L S Tusting, S Y Kang, E Cameron, D Bisanzio, K E Battle, S Bhatt, P W Gething
The economic and man-made resources that sustain human wellbeing are not distributed evenly across the world, but are instead heavily concentrated in cities. Poor access to opportunities and services offered by urban centres (a function of distance, transport infrastructure, and the spatial distribution of cities) is a major barrier to improved livelihoods and overall development. Advancing accessibility worldwide underpins the equity agenda of 'leaving no one behind' established by the Sustainable Development Goals of the United Nations...
January 10, 2018: Nature
https://www.readbyqxmd.com/read/29318634/high-density-contact-and-non-invasive-mapping-of-focal-atrial-tachycardia-evidence-of-dual-endocardial-exits-from-an-epicardial-focus
#10
Seigo Yamashita, Darren A Hooks, Ghassen Cheniti, Pierre Jais
We report a case of recurrent focal atrial tachycardia (AT) which mechanisms could be resolved by using non-invasive electrocardiographic imaging (ECGI) reconstructing epicardial potentials and rapid high-density endocardial contact mapping (Rhythmia™). ECGI demonstrated focal activity from the anterior of the left superior pulmonary vein antrum, although Rhythmia™ showed focal activity from the high anterior left atrium with the 2nd focus originating from the site where identical to the focus on the ECGI map with slightly delay (by 8 ms)...
January 10, 2018: Pacing and Clinical Electrophysiology: PACE
https://www.readbyqxmd.com/read/29317972/high-density-mapping-in-ventricular-tachycardia-ablation-a-pentaray%C3%A2-study
#11
Petra Maagh, Arnd Christoph, Henning Dopp, Markus Sebastian Mueller, Gunnar Plehn, Axel Meissner
Background: High-density mapping of ventricular tachycardia (VT) with PentaRay® (Biosense-Webster) provides high resolution with discrimination of local abnormal electrograms and slow conducting channels. We evaluate the feasibility of PentaRay® to characterize the anatomical substrate and assume an influence of the outcome despite limitations. Methods: Over a 24-month period, 26 endocardial and four epicardial maps were obtained of 26 VT patients (18 ischemic cardiomyopathy (ICM, 69...
December 2017: Cardiology Research
https://www.readbyqxmd.com/read/29315991/efficacy-of-catheter-ablation-of-focal-sources-in-persistent-atrial-fibrillation
#12
Yoshihide Takahashi, Syu Yamashita, Masahito Suzuki, Kento Yabe, Kenzo Hirao
INTRODUCTION: Recent studies suggest that atrial fibrillation (AF) is maintained by electrical activity arising from focal sources. We sought to test whether catheter ablation that targets focal sources can improve on current ablation protocols for persistent AF. METHODS AND RESULTS: In patients with persistent AF whose AF did not terminate with pulmonary vein isolation, the left atrium was mapped with a 20-pole high-density mapping catheter using CARTO®3 navigation...
January 9, 2018: Journal of Cardiovascular Electrophysiology
https://www.readbyqxmd.com/read/29312815/satellite-tagging-highlights-the-importance-of-productive-mozambican-coastal-waters-to-the-ecology-and-conservation-of-whale-sharks
#13
Christoph A Rohner, Anthony J Richardson, Fabrice R A Jaine, Michael B Bennett, Scarla J Weeks, Geremy Cliff, David P Robinson, Katie E Reeve-Arnold, Simon J Pierce
The whale shark Rhincodon typus is an endangered, highly migratory species with a wide, albeit patchy, distribution through tropical oceans. Ten aerial survey flights along the southern Mozambican coast, conducted between 2004-2008, documented a relatively high density of whale sharks along a 200 km stretch of the Inhambane Province, with a pronounced hotspot adjacent to Praia do Tofo. To examine the residency and movement of whale sharks in coastal areas around Praia do Tofo, where they may be more susceptible to gill net entanglement, we tagged 15 juveniles with SPOT5 satellite tags and tracked them for 2-88 days (mean = 27 days) as they dispersed from this area...
2018: PeerJ
https://www.readbyqxmd.com/read/29306332/world-wide-research-architecture-of-vitamin-d-research-density-equalizing-mapping-studies-and-socio-economic-analysis
#14
Dörthe Brüggmann, Annahita Alafi, Jenny Jaque, Doris Klingelhöfer, Michael H Bendels, Daniela Ohlendorf, David Quarcoo, Frank Louwen, Sue A Ingles, Eileen M Wanke, David A Groneberg
BACKGROUND: Despite the numerous associations of vitamin D with health and disease, vitamin D deficiency is still common from a global perspective. While basic research, clinical and preventive activities grow constantly in vitamin D research, there is no in-depth analysis of the related global scientific productivity available so far. METHODS: Density equalizing mapping procedures (DEMP) were combined with socioeconomic benchmarks using the NewQIS platform. RESULTS: A total of 25,992 vitamin D-related research articles were identified between 1900 to 2014 with a significant increase (r2 = ...
January 6, 2018: Nutrition Journal
https://www.readbyqxmd.com/read/29304028/high-density-single-nucleotide-polymorphism-snp-mapping-and-quantitative-trait-loci-qtl-analysis-in-a-biparental-spring-triticale-population-localized-major-and-minor-effect-fusarium-head-blight-resistance-and-associated-traits-qtl
#15
Raman Dhariwal, George Fedak, Yves Dion, Curtis Pozniak, André Laroche, François Eudes, Harpinder Singh Randhawa
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping...
January 5, 2018: Genes
https://www.readbyqxmd.com/read/29303782/associations-of-leptin-insulin-and-lipids-with-retinal-microvasculature-in-children-and-adolescents
#16
Carola J C van Aart, Nathalie Michels, Isabelle Sioen, Annelies De Decker, Tim S Nawrot, Stefaan De Henauw
BACKGROUND: We investigated whether cardiometabolic risk factors measured in serum (total cholesterol [TC], high-density lipoprotein [HDL], triglyceride, leptin, insulin, glucose and insulin resistance) are associated with the retinal microvasculature, a marker of cardiovascular aging, in healthy children and adolescents. Moreover, we tested whether these associations are due to direct biological effects or more indirectly due to adiposity-related side effects. METHODS: We recruited 168 healthy Flemish children (7-16 years old, 54...
January 5, 2018: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/29302127/census-independent-population-mapping-in-northern-nigeria
#17
Eric M Weber, Vincent Y Seaman, Robert N Stewart, Tomas J Bird, Andrew J Tatem, Jacob J McKee, Budhendra L Bhaduri, Jessica J Moehl, Andrew E Reith
Although remote sensing has long been used to aid in the estimation of population, it has usually been in the context of spatial disaggregation of national census data, with the census counts serving both as observational data for specifying models and as constraints on model outputs. Here we present a framework for estimating populations from the bottom up, entirely independently of national census data, a critical need in areas without recent and reliable census data. To make observations of population density, we replace national census data with a microcensus, in which we enumerate population for a sample of small areas within the states of Kano and Kaduna in northern Nigeria...
January 2018: Remote Sensing of Environment
https://www.readbyqxmd.com/read/29290830/constructing-a-chromonome-of-yellowtail-seriola-quinqueradiata-for-comparative-analysis-of-chromosomal-rearrangements
#18
Junya Kawase, Jun-Ya Aoki, Kazuo Araki
To investigate chromosome evolution in fish species, we newly mapped 181 markers that allowed us to construct a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map with 1,713 DNA markers, which was far denser than a previous map, and we anchored the de novo assembled sequences onto the RH physical map. Finally, we mapped a total of 13,977 expressed sequence tags (ESTs) on a genome sequence assembly aligned with the physical map. Using the high-density physical map and anchored genome sequences, we accurately compared the yellowtail genome structure with the genome structures of five model fishes to identify characteristics of the yellowtail genome...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29286391/development-of-new-methods-for-quantifying-fish-density-using-underwater-stereo-video-tools
#19
Christian Denney, Ryan Fields, Mary Gleason, Richard Starr
The use of video camera systems in ecological studies of fish continues to gain traction as a viable, non-extractive method of measuring fish lengths and estimating fish abundance. We developed and implemented a rotating stereo-video camera tool that covers a full 360 degrees of sampling, which maximizes sampling effort compared to stationary camera tools. A variety of studies have detailed the ability of static, stereo-camera systems to obtain highly accurate and precise measurements of fish; the focus here was on the development of methodological approaches to quantify fish density using rotating camera systems...
November 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29284405/highly-accurate-sequence-imputation-enables-precise-qtl-mapping-in-brown-swiss-cattle
#20
Mirjam Frischknecht, Hubert Pausch, Beat Bapst, Heidi Signer-Hasler, Christine Flury, Dorian Garrick, Christian Stricker, Ruedi Fries, Birgit Gredler-Grandl
BACKGROUND: Within the last few years a large amount of genomic information has become available in cattle. Densities of genomic information vary from a few thousand variants up to whole genome sequence information. In order to combine genomic information from different sources and infer genotypes for a common set of variants, genotype imputation is required. RESULTS: In this study we evaluated the accuracy of imputation from high density chips to whole genome sequence data in Brown Swiss cattle...
December 29, 2017: BMC Genomics
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