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886 results for “genetic analysis”
Figure 2. Delta K in Analysis of the genetic diversity of Dragon fruit based on ISSR markers in Colombia
Figure 2. Delta K values obtained from Harvester Structure, calculated as the mean of the probability of K divided by the standard deviation of the probability of K.
Figure 1. Dendrogram showing relationships among 70 in Analysis of the genetic diversity of Dragon fruit based on ISSR markers in Colombia
Figure 1. Dendrogram showing relationships among 70 genotypes of Selenicereus megalanthus, according to the UPGMA analysis using eight ISSR markers.
Fig. 2 in Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis
Fig. 2. Structure analyses for putative genetic clusters of N. falcata. A: Graphs of ΔK values to determine the ideal number of groups present in the accessions of N. falcata. B: Estimated genetic structure of the 3 populations of brinjal based on STRUCTURE analysis K = 2 and K = 3.
Microsat Data for 'Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers'
<p>Microsattelite data from 94 samples (<em>Stunus vulgaris</em>) from 3 populations and including 29 loci. Used in the paper 'Simulated Disperser Analysis: determining the number of loci required to genetically identify dispersers'. </p>
Data for: A systematic review and meta-analysis of Drosophila short-term-memory genetics: robust reproducibility, but little independent replication
<p>All the data, code, analyses, and figures used in the study entitled: "A systematic review and meta-analysis of Drosophila short-term-memory genetics: robust reproducibility, but little independent replication" <em>(doi: https://doi.org/<a href="http://bb2sz3ek3z.search.serialssolutions.com/?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&__char_set=utf8&rft_id=info:doi/10.1101/247650&rfr_id=info:sid/libx&rft.genre=article">10.1101/247650</a>)</em></p> <p><strong>Abstract</strong></p> <p>Geneticists have long used olfactory conditioning techniques in <em>Drosophila</em> to identify the neurons and genes that mediate learning. While this method has characterized an abundance of memory-related genes, little is known about how these genes induce short-term memory (STM) via signaling pathways; characterizing these networks will be essential to developing mechanistic models of memory formation. Here, we investigated why elucidating the STM pathways has been relatively slow. One possibility is that the STM evidence base is weak due to publication of poorly reproducible results, as has been observed in other fields. We examined this hypothesis by performing a systematic review and subsequent meta-analysis of the STM genetics field. Using several metrics to quantify the variation between discovery articles and follow-up studies, we found that seven genes were highly replicated, showed no publication bias, and had generally high reproducibility. However, the remaining ~80% memory genes have not been replicated since their initial discovery. Although we observed only a few studies that investigated gene interactions, the reviewed genes could together account for >1000% memory. This large summed effect size indicates either that some of the gene findings are not reproducible, that many memory genes participate in shared pathways, or that current protocols lack the specificity needed to identify core plasticity memory genes. Mechanistic theories of memory and cognition will require the convergence of evidence from system, circuit, cellular, molecular, and genetic experiments. As this study demonstrates, systematic data synthesis is an essential tool for this integrated brain science.</p>
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp). in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 4. Electrophoresis after amplification: Electrophoretical analysis of mitochondrial DNA. mtDNA sequences were amplified by primers F15.412 and R16.169 (450 bp), R16.269 (550 bp), R16.519 (800 bp). Lane 1 are primers F15.412 + R16.169, lane 2 primers F15.412 + R16.269, lane 3 primers F15.412 + R16.519, NC – negative control – water, L – 100 bp DNA ladder (band size from 100 bp to 1500 bp).
Text-fig. 1. Bottom view of the spoke bone of the excavated greyhound-like dog (above) and the spoke bone of a dog of the same size category (below). The gracility of the spoke bone of the greyhound-like dog is clearly visible. Photo by D. Nývlt. in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 1. Bottom view of the spoke bone of the excavated greyhound-like dog (above) and the spoke bone of a dog of the same size category (below). The gracility of the spoke bone of the greyhound-like dog is clearly visible. Photo by D. Nývlt.
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114. in Genetic Analysis Of Possibly The Oldest Greyhound Remains Within The Territory Of The Czech Republic As Proof Of A Local Elite Presence At Chotěbuz-Podobora Hillfort In The 8 -9 Century Ad
Text-fig. 5. Multiple sequence alignment of mtDNA from ancient bone and recent greyhound, (Gundry et al. 2007) primer pair A – F15.719 and R16.114.
Figure 2 in High genetic distinctiveness of wild and farm fox (Vulpes vulpes L.) populations in Poland: evidence from mitochondrial DNA analysis
Figure 2. Neighbor-joining haplotype network based on frequencies showing relationships between concatenated MT-CO1 and MTATP6 sequences of fur farm and wild red foxes.
Figure 1 in High genetic distinctiveness of wild and farm fox (Vulpes vulpes L.) populations in Poland: evidence from mitochondrial DNA analysis
Figure 1. Distribution of sampling sites of wild and fur-farm red foxes in Poland: light gray areas represent the provinces from which samples of wild foxes were taken; the darker gray area indicated with a black circle shows the location of investigated fox farms; the numbers represent fox fur-farms in particular voivodeships.
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732). in A study of genetic diversity among different population of Orthochirus sp. based on cytochrome C oxidase subunit I and 16srRNA sequencing
Figure. Phylogram showing phylogenetic relationships estimated using maximum likelihood analysis of 16S rRNA and COXI gene revealed the grouping of Orthochirus iranus, O. farzanpay, O. stockwelli, O. zagrosensis, O. innesi (JQ514244.1 Morocco), and O. bicolor (KT716038.1 India), with the outgroup species Androctonus crassicauda (FJ217732).
Genetic analysis of mycobacteria isolated from suspect bovine tuberculosis lesions in Wolaita, Ethiopia - code and datasets.
<p>Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to assess the prevalence and causative agents of bTB in cattle from four abattoirs in the Wolaita region of Ethiopia. </p>
Phenotype, genotype and fitness data related to genetic analysis of praziquantel response in schistosome parasites.
<p>These data are related to the study of the Genetic analysis of praziquantel response in schistosome parasites implicates a Transient Receptor Potential channel.</p> <p>Mass treatment with praziquantel (PZQ) monotherapy is the mainstay for schistosomiasis treatment. This drug shows imperfect cure rates in the field and parasites showing reduced PZQ response can be selected in the laboratory, but the extent of resistance in <em>Schistosoma mansoni</em> populations is unknown. We examined the genetic basis of variation in PZQ response in a <em>S. mansoni</em> population (SmLE-PZQ-R) selected with PZQ in the laboratory: 35% of these worms survive high dose (73 µg/mL) PZQ treatment. We used genome wide association to map loci underlying PZQ response. The major chr. 3 peak contains a transient receptor potential (Sm.TRPM_PZQ) channel (Smp_246790), activated by nanomolar concentrations of PZQ. PZQ response shows recessive inheritance and marker-assisted selection of parasites at a single Sm.TRPM_PZQ SNP enriched populations of PZQ-resistant (PZQ-ER) and sensitive (PZQ-ES) parasites showing >377 fold difference in PZQ response. The PZQ-ER parasites survived treatment in rodents better than PZQ-ES. Resistant parasites show 2.25-fold lower expression of Sm.TRPM_PZQ than sensitive parasites. Specific chemical blockers of Sm.TRPM_PZQ enhanced PZQ resistance, while Sm.TRPM_PZQ activators increased sensitivity. A single SNP in Sm.TRPM_PZQ differentiated PZQ-ER and PZQ-ES lines, but mutagenesis showed this was not involved in PZQ response, suggesting linked regulatory changes. We surveyed Sm.TRPM_PZQ sequence variation in 259 parasites from the New and Old World revealing one nonsense mutation that results in a truncated protein with no PZQ-binding site. Our results demonstrate that Sm.TRPM_PZQ underlies variation in PZQ response in <em>S. mansoni</em> and provides an approach for monitoring emerging PZQ-resistance alleles in schistosome elimination programs.</p> <p>This dataset is divided in 3 folders. Each folder has a readme detailing its content.</p> <p><strong>1-Phenotyping_data</strong></p> <p>This folder includes the data tables related to the phenotyping of the worms performed during this study. The phenotype measured was the viability of worms following PZQ treatment (i.e., PZQ response). This viability was assessed microscopically or using worm lactate production released in culture media.</p> <p>The data correspond to the following experiments:</p> <ul> <li>PZQ response of single adult male worms from SmLE and SmLE-PZQ-R populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>Lactate production from single SmLE-PZQ-R adult male worms and correlation with visual observation. This was a proof-of-principle that lactate production can be used to efficiently and unbiasedly phenotype schistosome adult male worms in response to PZQ drug.</li> <li>PZQ response of single SmLE-PZQ-R adult male worms. These worms were then divided in low and high producer in response to PZQ and used to perform a genome-wide association study.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations in presence of Sm.TRPM_PZQ blocker (MB2) and activator (MV1) with and without PZQ drug.</li> <li>In vivo PZQ response of schistosome worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations.</li> </ul> <p><strong>2-Genotyping_data</strong></p> <p>This folder includes the data tables related to the genotyping of the worms performed during this study. Worms were genotyping using PCR-RFLP (genotyping of single nucleotide polymorphisms (SNPs) on chr2 and chr3 QTLs) or using qPCR (genotyping of a copy number variation (CNV) on chr3 QTL).</p> <p>The data correspond to the following experiment:</p> <ul> <li>Association between PZQ response of single adult male worms from SmLE-PZQ-R population and their respective genotype on chromosome 2 (SNP) and chromosome 3 (SNP and CNV) loci.</li> </ul> <p><strong>3-Fitness_data</strong></p> <p>This folder includes the data tables related to the fitness of the parasite populations. We collected data regarding:</p> <ul> <li>The number of surviving and infected snails after exposure to SmLE-PZQ-ER or SmLE-PZQ-ES miracidia.</li> <li>The number of adult worms recovered from golden Syrian female hamsters exposed to SmLE-PZQ-ER or SmLE-PZQ-ES cercariae.</li> </ul> <p>All the data were collected during 12 generations of parasites and are used to evaluate a potential impact of PZQ resistance on the parasite fitness.</p>
Fig. 2. Principal Component Analysis plot showing the 42 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. 2. Principal Component Analysis plot showing the 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Fig. S1. Principal Component Analysis plot showing 28 in Evidence of genetic connectivity between fragmented pig populations in a tropical urban city-state
Fig. S1. Principal Component Analysis plot showing 28 out of 42 individuals from the Central Catchment Nature Reserve (CCNR) and the Northeast with kinship values <0.2. Individuals are differentiated by sex and age class. Individuals exhibiting genetic admixture are labelled. Percentage variation accounted for by each principal component is indicated in brackets.
Figure S1 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland
Figure S1. Bayesian consensus tree of the Mesobuthus caucasicus complex reconstructed from mitochondrial DNA sequences.
Figure 9 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland
Figure 9. Phylogeny the Mesobuthus caucasicus complex reconstructed using mitochondrial DNA sequences. The Przewalski's scorpion (M. przewalskii) is deeply diverged from other species and the Chinese scorpion (M. martensii) belongs to the species complex. Node supports are shown by bootstrapping probabilities from 1000 replicates and Bayesian posterior probabilities.
Figures 1–8 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland
Figures 1–8. Mesobuthus przewalskii stat. nov., from Qiemo, Xinjiang. 1. Male, dorsal view. 2. Male, ventral view. 3. Female, dorsal view. 4. Female, ventral view. 5. Male, dentition of pedipalp chela movable finger. 6. Male, dentition of pedipalp chela fixed finger. 7. Male, ventral aspect of genital operculum and pectines. 8. Female, ventral aspect of genital operculum and pectines. Scale bars: 1–4 = 5.0 mm; 5–8 = 2.0 mm.
Figure 11 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland
Figure 11. Ecological niche models of Mesobuthus scorpions. Potential distribution areas for the Przewalski's scorpion M. przewalsii (purple) is shown together with the Chinese scorpion M. martensii (green) and other species of the M. caucasicus complex (yellow). The entire Tarim Basin and adjacent Gobi region are suitable for survival of M. przewalskii. No area to the west of the Tianshan Mountains and the Pamir Plateau is suitable for M. przewalskii, and similarly no area to the east of the Tianshan Mountains and the Pamir Plateau is suitable for other species of the M. caucasicus complex. There are overlaps in predicted suitable distribution areas between M. przewalskii and M. martensii along the northeast edge of the Qinghai-Tibet Plateau. The suitable areas in the Junggar Basin and to the north of the Tianshan Mountains are likely due to over prediction of the model, because M. przewalskii does not occur in these regions. Ecological niche model for M. martensii was adopted from Shi et al. 2007.
Figure 10 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland
Figure 10. Phylogenetic network for the Mesobuthus caucasicus species complex. Although the interrelationships between species is poorly resolved, no reticulations have occurred in the most recent common ancestors for each species. The Przewalski's scorpion M. przewalskii is clearly diverged from other member of the species complex and warrants a species rank. The divergence of the Chinese scorpion M. martensii is comparable to the divergences among the members of the species complex.
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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.