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80 results for “genetic improvement”
Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts
<p>Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (<i>Populus angustifolia</i>) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) <i>P. angustifolia</i> is differentiated into six genetic groups across its range from México to Canada, and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically-informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change, and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, <i>P. fremontii</i>. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.</p>
Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens - Data table and code for data analysis
<p>We provide data and code needed to re-do the analyses and figures presented in our preprint <em>Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent </em>Trichogramma evanescens (DOI : 10.1101/2020.08.21.257881 ):</p> <p>- data table : <em>data_repetition01.xls</em>, with informations about each column in the file <em>data_repetition_info.pdf</em></p> <p>- data table : <em>data_individual01.xls</em>, with informations about each column in the file <em>data_indivdual_info.pdf</em></p> <p><em>- </em>The R code used to do the analyses : <em>Rscript-Consistent variations in personality traits and their potential for genetic improvement in the biocontrol agent Trichogramma evanescens.R</em></p> <p><br> </p> <p> </p> <p> </p> <p> </p>
Genetic barcoding of museum eggshell improves data integrity of avian biological collections
<p>Natural history collections are often plagued by missing or inaccurate metadata for collection items, particularly for specimens that are difficult to verify or rare. Avian eggshell in particular can be challenging to identify due to extensive morphological ambiguity among taxa. Species identifications can be improved using DNA extracted from museum eggshell; however, the suitability of current methods for use on small museum eggshell specimens has not been rigorously tested, hindering uptake. In this study, we compare three sampling methodologies to genetically identify 45 data-poor eggshell specimens, including a putatively extinct bird's egg. Using an optimised drilling technique to retrieve eggshell powder, we demonstrate that sufficient DNA for molecular identification can be obtained from even the tiniest eggshells without significant alteration to the specimen's appearance or integrity. This method proved superior to swabbing the external surface or sampling the interior; however, we also show that these methods can be viable alternatives. We then applied our drilling method to confirm that a purported clutch of Paradise Parrot eggs collected 40 years after the species' accepted extinction date were falsely identified, laying to rest a 53-year-old ornithological controversy. Thus, even the smallest museum eggshells can offer new insights into old questions.</p>
Data related to the manuscript "Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor"
<p>These are the data that are related to the manuscript "Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor" by </p> <p>Eike K. Mahlandt<sup>1,*</sup>, Janine J. G. Arts<sup>1,2</sup>,Werner J. van der Meer<sup>1</sup>, Franka H. van der Linden<sup>1</sup>, Simon Tol<sup>2</sup>, Jaap D. van Buul<sup>1,2</sup>, Theodorus W. J. Gadella Jr.<sup>1</sup>, Joachim Goedhart<sup>1,*</sup></p> <p><sup>1</sup> Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands</p> <p><sup>2</sup> Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands</p>
Geomagnetic datasets of BJI station reconstructed through Artificial Neural Network improved by Genetic Algorithm in 2021
<p>Beijing station established in 1954 is one of the oldest geomagnetic observatories in China, which plays an important role in data exchange, and further provide data or standardization for satellite observation and geomagnetic model construction. With the development of urbanization, the observed data are greatly disturbed by subways, and data disturbed are almost unavailable. The dataset was reconstructed through Artificial Neural Network improved by Genetic Algorithm, including minutely data of three components (<em>D</em>, <em>H</em> and <em>Z</em>) in 2021. This reconstruction method has been proved to be effective.</p>
Evaluation of the Diagnostic Contribution of High-throughput Exome Sequencing for Patients With Convulsive Encephalopathy of Unknown Etiology: Pilot Study to Improve Genetic Counselling
ClinicalTrials.gov study NCT03652246. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Is Family Screening Improved by Genetic Testing of Familial Hypercholesterolemia
ClinicalTrials.gov study NCT04526457. IPD Sharing: NO. Countries: 0. Publications: 15.
The Genetics and Vascular Health Check Study (GENVASC) Aims to Help Determine Whether Gathering Genetic Information Can Improve the Prediction of Risk of Coronary Artery Disease (CAD)
ClinicalTrials.gov study NCT04417387. IPD Sharing: YES. Countries: 1. Publications: 1.
Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts
Open the record for dataset details and reuse information.
Data for: Improving population size estimation at Western Capercaillie leks: lek counts vs. genetic methods
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Data from: Sequencing improves our ability to study threatened migratory species: genetic population assignment in California's Central Valley Chinook salmon
Open the record for dataset details and reuse information.
Genetic barcoding of museum eggshell improves data integrity of avian biological collections
Open the record for dataset details and reuse information.
Ms3 dominant genetic male sterility for wheat improvement with molecular breeding
<p>Genetic dominant male sterility (DMS) has not been widely used as a breeding tool in wheat (<i>Triticum aestivum</i> L.), although DMS-facilitated backcross, mass selection, half-sib selection, and S<sub>1</sub> family recurrent selection strategies have been described, and <i>Ms2-</i>facilitated recurrent selection has been used in China. Our objective was to revisit these strategies using the tools of molecular breeding. Development of a mechanism for seedling identification of sterile progeny was a key component of designing practical DMS-facilitated molecular breeding systems. The DMS gene <i>Ms3</i> was previously localized to the centromeric region of chromosome 5A. The centromeric location is an advantage because recombination rates are very low. Once identified, a broadly informative marker would reliably predict the male-sterile phenotype. A set of 429 hybrids incorporating <i>Ms3</i> were constructed, both within US hard winter wheats, and between these winter wheats and Asian spring wheats. Association of the male-sterile phenotype with those polymorphic DNA sequence tags that localized to chromosome 5A was tested using case-control association analysis. Two highly significant (logarithm of odds [LOD] > 30) single nucleotide polymorphism (SNP)–trait associations were obtained. One SNP was developed into a highly sensitive, reliable molecular marker for the <i>Ms3</i>-associated male-sterile. Previously described breeding strategies using DMS were updated for trait-targeted marker-assisted backcrossing and gene pyramiding, S<sub>1</sub> recurrent selection, and early-generation genomic selection. Application of DMS to association mapping, with the particular use case of the multiparent advanced generation intercross population, is also described.</p>
STR data from: Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population
<p><span>Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (<i>Salmo trutta</i>) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna. </span></p>
Data from: A field-based analysis of genetic improvement for grain yield in winter wheat cultivars developed in the us central plains from 1992 to 2014
[No abstract entered]
Figure 3 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 3. Double staining with CMA/DAPI in accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Red arrows indicate CMA+ bands in the overlaid chromosome (B). White arrows indicate gaps formed by condensation (D). Dots indicate distended nucleolar organiser regions (NORs) (f). Bar = 10 µm. Figure 2. Double staining with CMA/DAPI in accessions "Cateto Roxo 99" (E), "Roxo de Minas" (F) and "Sergipe" (G). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Dots indicate distended nucleolar organiser regions (NORs) (F). Bar = 10 µm.
IMPROVING JUICE QUALITY OF SWEET ORANGES IN FLORIDA BY EXPLOITING GENETIC VARIATION FOUND IN OLL SOMACLONE-DERIVED NUCELLAR SEEDLINGS UNDER HLB ENDEMIC CONDITIONS
<p>Excel file with the whole data of measurements of the study</p>
Improving Juice Quality Of Sweet Oranges in Florida By Exploiting Genetic Variation Found inOLL Somaclone-derived Nucellar Seedlings Under HLB Endemic Conditions
<p>Appendix- Completed data set </p>
Improving Uptake of Genetic Cancer Risk Assessment in African American Women- Video
ClinicalTrials.gov study NCT04476654. IPD Sharing: NO. Countries: 1. Publications: 0.
Use of Personalized Recommendations, Through Genetic and Lifestyle Data, to Improve Healthcare Staff Wellbeing
ClinicalTrials.gov study NCT06042452. IPD Sharing: NO. Countries: 0. Publications: 4.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.