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Find video protocols related to scientific articles indexed in Pubmed.
A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat.
BMC Plant Biol.
PUBLISHED: 07-10-2014
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Crown rust, caused by Puccinia coronata f. sp. avenae, is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations.
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Investigating the Molecular Structural Features of Hulless Barley (Hordeum vulgare L.) in Relation to Metabolic Characteristics Using Synchrotron-Based Fourier Transform Infrared Microspectroscopy.
J. Agric. Food Chem.
PUBLISHED: 11-18-2013
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The synchrotron-based Fourier transform infrared microspectroscopy (SR-FTIRM) technique was used to quantify molecular structural features of the four hulless barley lines with altered carbohydrate traits [amylose, 1-40% of dry matter (DM); ?-glucan, 5-10% of DM] in relation to rumen degradation kinetics, intestinal nutrient digestion, and predicted protein supply. Spectral features of ?-glucan (both area and heights) in hulless barley lines showed a negative correlation with protein availability in the small intestine, including truly digested protein in the small intestine (DVE) (r = -0.76, P < 0.01; r = -0.84, P < 0.01) and total metabolizable protein (MP) (r = -0.71, P < 0.05; r = -0.84, P < 0.01). Variation in absorption intensities of total carbohydrate (CHO) was observed with negative effects on protein degradation, digestion, and potential protein supply (P < 0.05). Molecular structural features of CHO in hulless barley have negative effects on the supply of true protein to ruminants. The results clearly indicated the impact of the carbohydrate-protein structure and matrix.
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SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.
PLoS ONE
PUBLISHED: 01-30-2013
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A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n?=?6x?=?42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
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Finite element analysis of heel pad with insoles.
J Biomech
PUBLISHED: 02-24-2011
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To design optimal insoles for reduction of pedal tissue trauma, experimental measurements and computational analyses were performed. To characterize the mechanical properties of the tissues, indentation tests were performed. Pedal tissue geometry and morphology were obtained from magnetic resonance scan of the subjects foot. Axisymmetrical finite element models of the heel of the foot were created with 1/4 of body weight load applied. The stress, strain and strain energy density (SED) fields produced in the pedal tissues were computed. The effects of various insole designs and materials on the resulting stress, strain, and SED in the soft pedal tissues were analyzed. The results showed: (a) Flat insoles made of soft material provide some reductions in the maximum stress, strain and SED produced in the pedal tissues. These maximum values were computed near the calcaneus. (b) Flat insoles, with conical/cylindrical reliefs, provided more reductions in these maximum values than without reliefs. (c) Custom insoles, contoured to match the pedal geometry provide most reductions in the maximum stress, strain and SED. Also note, the maximum stress, strain and SED computed near the calcaneus were found to be about 10 times the corresponding peak values computed on the skin surface. Based on the FEA analysis, it can be concluded that changing insole design and using different material can significantly redistribute the stress/strain inside the heel pad as well as on the skin surface.
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Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology.
BMC Genomics
PUBLISHED: 01-27-2011
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Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat.
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Comparison of male and female foot shape.
J Am Podiatr Med Assoc
PUBLISHED: 09-22-2009
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Morphological and geometric differences between male and female feet can be the decisive factor of whether well-fitting, functional, and comfortable footwear is available for both men and women.
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An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials.
Genome
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The first doubled haploid oat linkage map constructed at MTT Agrifood Research Finland was supplemented with additional microsatellites and Diversity Array Technology (DArT) markers to produce a map containing 1058 DNA markers and 34 linkage groups. The map was used to locate quantitative trait loci (QTLs) for 11 important breeding traits analyzed from Finnish and Canadian field trials. The new markers enabled most of the linkage groups to be anchored to the Kanota × Ogle oat ( Avena sativa L.) reference map and allowed comparison of the QTLs located in this study with those found previously. Two to 12 QTLs for each trait were discovered, of which several were expressed consistently across several environments.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.