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ShareScore release 0.9.0
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222 results for “baits”
Whole-genome capture and sequencing of Mycobacterium tuberculosis directly from clinical samples - Design of RNA oligonucleotide baits for Agilent Technologies' SureSelect target enrichment
<p>This dataset comprises the sequence of <strong>44 278 RNA oligonucleotide "baits" (120 bp each) </strong>designed to perform <strong>whole-genome capture and sequencing of <em>Mycobacterium tuberculosis</em> directly from clinical samples</strong> (DNA) using Agilent Technologies’ SureSelect target enrichment system following the Illumina paired-end multiplexed sequencing library protocol. </p> <p>RNA oligonucleotide “baits” were designed to span the ∼4.5 Mb of the <em>M. tuberculosis</em> genome. In brief, the reference genome sequence of the MTBC H37Rv strain (Genbank #AL123456) was <em>in silico</em> fragmented into 120 bp sequences twice, to ensure an overlap of 60 bp between sequences. Due to their rich GC content, which could interfere with DNA capture, all MTBC genes of the PE, PPE and PE-PGRS family were also independently fragmented into 120 bp sequences, in order to increase capture sensitivity. All resulting sequences were BLASTn searched against the Human Genomic + Transcript database to excluded homologous sequences to the human genome. Overall, a total of 42,278 RNA probes were generated and this custom bait library was then uploaded to the SureDesign software (https://earray.chem.agilent.com/suredesign) and synthesized by Agilent Technologies. During synthesis, the 2198 sequences complementary to the PE, PPE and PE-PGRS family were unbalanced 8:1 to potentiate capture.</p> <p>More details can be found in the following publication:</p> <p>- Macedo, R., Isidro, J., Ferreira, R., Pinto, M., Borges, V., Duarte, S., Vieira, L., & Gomes, J. P. (2023). Molecular Capture of <em>Mycobacterium tuberculosis</em> Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. <em>International journal of molecular sciences</em>, <em>24</em>(3), 2912. https://doi.org/10.3390/ijms24032912</p>
Termite foraging data from bait mass loss at eleven locations at the Jornada Basin LTER site, 1988-2000
This data package contains data on yearly mass loss of termite baits at the Jornada Basin LTER site in southern New Mexico, USA. Termites are important to litter decomposition and nutrient cycling in desert grasslands. This study measured annual feeding activity on paper baits by subterranean termites in desert shrubland and black-grama (Bouteloua eriopoda) grassland ecosystems over twelve years. Eleven sites, known as the "consumer plots" were included in the study. Toilet paper roll termite baits were placed on grids on each consumer plot. Data include initial bait weights before deployment, and bait weights after they were retrieved from the field each year. Mass loss of the baits was calculated as a measure of termite foraging activity. This study is complete.
Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera
1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of "legacy" phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.
Fig. 1 in Yearly and seasonal changes in species composition of hornets (Hymenoptera: Vespidae) caught with bait traps on the Sea of Japan coast
Fig. 1. Yearly changes in the species composition of hornets in Sakata Park (A) and campus of Niigata University (B).
Figure 2 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)
Figure 2. Captures of Mediterranean fruit flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 5 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).
Figure 1 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)
Figure 1. Captures of oriental fruit flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 8 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).
Figure 3 in Weathering of Torula Yeast Borax Food Bait and Capture of Oriental, Mediterranean, and Melon Fruit Flies in Hawaii (Diptera: Tephritidae)
Figure 3. Captures of melon flies (males and females combined) in Multilure traps baited with torula yeast borax weathered 3, 6, 9, or 12 d. Traps operated for 2 d at weekly intervals over 4 consecutive weeks. Symbols represent means + 1 SE (N = 10 traps/treatment/sampling period).
Figure 2 in Field Capture of Male Melon Flies, Bactrocera cucurbitae (Coquillett), in Jackson Traps Baited with Cue-Lure Versus Raspberry Ketone Formate in Hawaii
Figure 2. Number of B. cucurbitae males captured in Jackson traps baited with cue-lure (CL) liquid (●) versus raspberry ketone formate (RKF) liquid (○) at four study sites on Oahu, Hawaii. At each site, 15 traps of each treatment were operated 1 day per week over 6 consecutive weeks. Symbols represent means (+ 1 SE, n = 15).
Figure 1 in Field Capture of Male Melon Flies, Bactrocera cucurbitae (Coquillett), in Jackson Traps Baited with Cue-Lure Versus Raspberry Ketone Formate in Hawaii
Figure 1. Number of B. cucurbitae males captured in Jackson traps baited with cue-lure (CL) liquid (●) versus raspberry ketone formate (RKF) plugs (○) at four study sites on Oahu, Hawaii. At each site, 15 traps of each treatment were operated 1 day per week over 6 consecutive weeks. Symbols represent means (+ 1 SE, n = 15).
Figure 4 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 4. Average percent survival (± SE) of G. dibranchiata (A) and Perinereis sp. (B) after exposed to southern California thermal conditions for five days. Gray bars indicate significant difference. No difference in survival was observed among the three temperature treatments for G. dibranchiata (F2,8 = 2.67, p = 0.130). There was a significant difference in survival of Perinereis sp. among the treatments (F2,8 = 11.08, p = 0.005).
Figure 1 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 1. Distribution by county of bait shops selling marine live bait in California according to survey responses. Live marine bait was sold in all counties shaded in grey. Numbers inside black circles indicate species sold in that county. Bait shops in shaded counties without black circles reported marine live bait sales but did not provide information on which species they sold.
Figure 3 in The marine live bait trade as a pathway for the introduction of non-indigenous species into California: patterns of importation and thermal tolerances of imported specimens
Figure 3. For each species of marine live bait, (A) the percentage of respondents who reported importing that species who answered that either seaweed (sometimes in combination with newspaper) or seawater were used as packing materials, and (B) the percentage of respondents who reported importing that species who observed hitchhikers in shipments of that species. Note that for (A), some respondents indicated that both seaweed and seawater were used as packing materials for a given species, so that the total percentage may add up to greater than 100 (e.g., for pileworms).
Fig. 2 in Effect of the height and distribution pattern of pheromone-baited traps on the capture of Scyphophorus acupunctatus (Coleoptera: Dryophthoridae) on blue agave (Asparagales: Asparagaceae)
Fig. 2. Mean (+ SE) numbers and sex ratios of Scyphophorus acupunctatus weevils captured per trap with various distribution pattern of traps in the field. Treatments with similar letters are not significantly different (Tukey's test, a = 0.05).
Fig. 1 in Effect of the height and distribution pattern of pheromone-baited traps on the capture of Scyphophorus acupunctatus (Coleoptera: Dryophthoridae) on blue agave (Asparagales: Asparagaceae)
Fig. 1. Distribution and arrangement of traps in the experiment of distribution pattern of traps, using 4 treatments: 1) traps placed in a triangle pattern with an inter-trap distance of 100 m; 2) traps placed a square with an inter-trap distance of 100 m; 3) traps placed in a triangle with an inter-trap distance of 200 m; and 4) traps placed in a square with an inter-trap distance of 200 m.
Fig. 2 in Fishing bait worm supplies in Japan in relation to their physiological traits
Fig. 2. Schematic representation of inhabitable salinity range of imported worms. The inhabitable range of salinity was evaluated from the 100 % survival of individuals after 5 days.
Fig. 2 in Diversity of forensically-important dipteran species in different environments in northeastern Brazil, with notes on the attractiveness of animal baits
Fig. 2. Similarity analysis (Cluster's dendrogram) of the diversity of necrophagous Diptera species in 4 types of environment in northeastern Brazil.
Fig. 1 in Toxicities and residual effects of toxic baits containing spinosad or malathion to control the adult Anastrepha fraterculus (Diptera: Tephritidae)
Fig. 1. The mortality of Anastrepha fraterculus adult afer 1, 3, 5 and 7 days of exposure to toxic baits. (Vertical bars indicate the standard error of the mean). Mortality was calculated by the formula of Schneider-Orelli (1947).
Fig. 4 in Palatability of baits containing (S)-methoprene to Wasmannia auropunctata (Hymenoptera: Formicidae)
Fig. 4. Effects of addition of 0.25% (S)-methoprene and increase in attractiveness of (S)-methoprene baits by the addition of an adjuvant as a masking agent. Treatments with different letters are significantly different (Pp <0.05).
Fig. 1 in Palatability of baits containing (S)-methoprene to Wasmannia auropunctata (Hymenoptera: Formicidae)
Fig. 1. Non-linear regression curve showing the relationship between ant recruitment and proportion of (S)-methoprene in the Hawaii Ant Lab's novel gel bait.
Fig. 2 in Palatability of baits containing (S)-methoprene to Wasmannia auropunctata (Hymenoptera: Formicidae)
Fig. 2. Mean recruitment of ants to baits containing different concentrations of (S)-methoprene. Treatments with different letters are significantly different (P <0.05).
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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)
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DANDI Archive for NWB datasets
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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.