SilicoDArT marker data of a Aegilops biuncialis collection
Ontology highlight
ABSTRACT:
ORGANISM(S): Aegilops biuncialis
SUBMITTER: Istv?n Monostori
PROVIDER: S-BSST277 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Aegilops caudata is an important gene source for wheat breeding. Intensive evaluation of its utilization value is an essential first step prior to its application in breeding. In this research, the agronomical and quality traits of Triticum aestivum-Ae. caudata additions B-G (homoeologous groups not identified) were analyzed and evaluated. Disease resistance tests showed that chromosome D of Ae. caudata might possess leaf rust resistance, and chromosome E might carry stem rust and powdery mildew resistance genes. Investigations into agronomical traits suggested that the introduction of the Ae. caudata chromosome in addition line F could reduce plant height. Grain quality tests showed that the introduction of chromosomes E or F into wheat could increase its protein and wet gluten content. Therefore, wheat-Ae. caudata additions D-F are all potentially useful candidates for chromosome engineering activities to create useful wheat-alien chromosome introgressions. A total of 55 EST-based molecular markers were developed and then used to identify the chromosome homoeologous group of each of the Ae. caudata B-G chromosomes. Marker analysis indicated that the Ae. caudata chromosomes in addition lines B to G were structurally altered, therefore, a large population combined with intensive screening pressure should be taken into consideration when inducing and screening for wheat-Ae. caudata compensating translocations. Marker data also indicated that the Ae. caudata chromosomes in addition lines C-F were 5C, 6C, 7C, and 3C, respectively, while the homoeologous group of chromosomes B and G of Ae. caudata are as yet undetermined and need further research.
| S-EPMC5644244 | biostudies-literature
Project description: Not available
| S-BSST1163 | biostudies-other
Project description:The cryoEM method Microcrystal Electron Diffraction (MicroED) involves transmission electron microscope (TEM) and electron detector working in synchrony to collect electron diffraction data by continuous rotation. We previously reported several protein, peptide, and small molecule structures by MicroED using manual control of the microscope and detector to collect data. Here we present a procedure to automate this process using a script developed for the popular open-source software package SerialEM. With this approach, SerialEM coordinates stage rotation, microscope operation, and camera functions for automated continuous-rotation MicroED data collection. Depending on crystal and substrate geometry, more than 300 datasets can be collected overnight in this way, facilitating high-throughput MicroED data collection for large-scale data analyses.
| S-EPMC6752703 | biostudies-literature
Project description:MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.
| S-EPMC4487423 | biostudies-literature
Project description:Collection of data for ESGLI WGS typing design group
| PRJEB13587 | ENA
Project description:Collection of data for ESGLI WGS typing design
| PRJEB13666 | ENA
Project description:Despite of the ongoing interest in the fusion of multi-band images for surveillance applications and a steady stream of publications in this area, there is only a very small number of static registered multi-band test images (and a total lack of dynamic image sequences) publicly available for the development and evaluation of image fusion algorithms. To fill this gap, the TNO Multiband Image Collection provides intensified visual (390-700 nm), near-infrared (700-1000 nm), and longwave infrared (8-12 µm) nighttime imagery of different military and surveillance scenarios, showing different objects and targets (e.g., people, vehicles) in a range of different (e.g., rural, urban) backgrounds. The dataset will be useful for the development of static and dynamic image fusion algorithms, color fusion algorithms, multispectral target detection and recognition algorithms, and dim target detection algorithms.
| S-EPMC5635205 | biostudies-literature
Project description:Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions.
| S-EPMC4896361 | biostudies-literature
Project description:Survival after colorectal cancer (CRC) diagnosis strongly depends on local tumor extent, lymph node involvement and the presence of distant metastases. However, there remains great inter-patient variability regarding treatment outcome. A combination of biochemical factors, histopathological features, genomic profile, environmental factors and other clinical factors are likely to influence prognosis and treatment effect, independent from tumor stage, but it is still unclear which, how, and to what extent these factors can influence tumor recurrence and mortality in both early stage (I-III) and late stage (IV) CRC.
Although the results from prospective clinical trials will remain the backbone of evidence based medicine, this concerns a highly selected patient population since the large majority (85%-95%) of cancer patients do not participate in clinical trials for various reasons. It is unlikely that trial participation will significantly improve in the near future. This fact has the following implications: 1) It is highly desirable to validate the results from trials in the general patient population. However, this is complicated by the fact that the documentation of patients treated in general practice (i.e. outside the scope of clinical trials) is largely insufficient to provide comparable patient cohorts in terms of prognostic characteristics and treatment parameters. 2) There is an increased availability of novel technologies that provide molecular markers with potential prognostic and/or predictive value. To test the clinical value of these markers large numbers of patients are required which greatly exceeds the number of patients who consent to participate in prospective clinical trials. 3) as a result of rapid technical developments, a range of new minimally invasive treatment options for CRC are entering the market. These interventions have the potential to be of great benefit for patients in terms of improved local control, higher probability of complete tumor removal, less damage to surrounding tissue, faster recovery and less short and long term side effects. Still, the interventions will have to prove their effectiveness, safety and superiority (or non-inferiority) to standard cancer treatments on a patient level. A prospective observational cohort study has the great opportunity to fill this gap.
| 2161372 | ecrin-mdr-crc
Project description:A multi-dataset (MDS) data-collection strategy is proposed and analyzed for macromolecular crystal diffraction data acquisition. The theoretical analysis indicated that the MDS strategy can reduce the standard deviation (background noise) of diffraction data compared with the commonly used single-dataset strategy for a fixed X-ray dose. In order to validate the hypothesis experimentally, a data-quality evaluation process, termed a readiness test of the X-ray data-collection system, was developed. The anomalous signals of sulfur atoms in zinc-free insulin crystals were used as the probe to differentiate the quality of data collected using different data-collection strategies. The data-collection results using home-laboratory-based rotating-anode X-ray and synchrotron X-ray systems indicate that the diffraction data collected with the MDS strategy contain more accurate anomalous signals from sulfur atoms than the data collected with a regular data-collection strategy. In addition, the MDS strategy offered more advantages with respect to radiation-damage-sensitive crystals and better usage of rotating-anode as well as synchrotron X-rays.
| S-EPMC3211246 | biostudies-literature