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2,281 results for “laboratories”
Linked collectors and determiners for: Harold W. Manter Laboratory of Parasitology Collection (HWML) Parasite Collection (Arctos).
Natural history specimen data linked to collectors and determiners held within, "Harold W. Manter Laboratory of Parasitology Collection (HWML) Parasite Collection (Arctos)". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d">https://bionomia.net/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d">https://gbif.org/dataset/c43384a9-8d9d-40c0-8cda-40ad47d2d69d</a>. Formatted as a Frictionless Data package.
Data from: Wild and laboratory exposure to cues of predation risk increases relative brain mass in male guppies
There is considerable diversity in brain size within and among species, and substantial dispute over the causes, consequences and importance of this variation. Comparative and developmental studies are essential in addressing this controversy. Predation pressure has been proposed as a major force shaping brain, behaviour and life history. The Trinidadian guppy, Poecilia reticulata, shows dramatic variation in predation pressure across populations. We compared the brain mass of guppies from high and low predation populations collected in the wild. Male but not female guppies exposed to high predation possessed heavier brains for their body size compared to fish from low predation populations. The brain is a plastic organ, so it is possible that the population differences we observed were partly due to developmental responses rather than evolved differences. In a follow‐up study, we raised guppies under cues of predation risk or in a control condition. Male guppies exposed to predator cues early in life had heavier brains relative to their body size than control males, while females showed no significant effect of treatment. Collectively our results suggest that male guppies exposed to predation invest more in neural tissue, and that these differences are at least partly driven by plastic responses.
Data from: Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution.
Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.
Novel laboratory index, based on fasting blood parameters, accurately reflects insulin sensitivity
<p>Simple and reliable measurement of insulin sensitivity may be important for the prevention of insulin-resistance related diseases. Surrogate indices of insulin sensitivity are of limited utility in population without signs of metabolic syndrome. The aim of our study was to provide simple and accurate index of insulin sensitivity. The study group comprised 150 young healthy participants. Hyperinsulinemic-euglycemic clamp was performed. Regression models with different laboratory parameters were constructed. Validation cohort 1 comprised independent group of 110 subjects, including individuals with prediabetes and newly diagnosed type 2 diabetes. Validation cohort 2 comprised 38 obese subjects before and after diet-induced weight loss. Validation cohort 3 comprised 60 nondiabetic subjects from an independent center. The supervised principal component model established optimal set of variables correlated with insulin sensitivity. This model (Fasting Laboratory Assessment of Insulin Sensitivity, FLAIS) used red blood cell count, alanine aminotransferase activity, serum C-peptide, SHBG, IGF-binding protein 1 and adiponectin concentrations. FLAIS exhibited strong correlation with clamp-derived insulin sensitivity. The sensitivity of the model was 90% and the specificity was 68%. In the validation cohort 1, differences in FLAIS among the groups paralleled those observed with the clamp, with the lowest values in prediabetes and diabetes. In the validation cohort 2, FLAIS reflected the change in insulin sensitivity after weight loss. The main findings were confirmed in the validation cohort 3. We provide simple and accurate method of assessing insulin sensitivity, which allows to identify insulin resistance even in the population without overt metabolic disturbances.</p>
Figure 7 in Juvenile development and growth patterns in the mud crab Eurytium limosum (Say, 1818) (Decapoda, Brachyura, Xanthidae) under laboratory conditions
Figure 7. Eurytium limosum. (a) Abdome of first juvenile stage; (b) female abdome of C7; (c) male abdome of C7.
Figure 17. Pilumnus spinifer H. Milne Edwards, 1834 in The complete larval development of the crab Pilumnus spinifer (Brachyura: Xanthoidea: Pilumnidae) reared in the laboratory
Figure 17. Pilumnus spinifer H. Milne Edwards, 1834. Megalopa: (A) pleopod 1; (B) pleopod 4; (C) uropod. Scale bars: 0.1 mm.
Figure 5. Pilumnus spinifer H. Milne Edwards, 1834 in The complete larval development of the crab Pilumnus spinifer (Brachyura: Xanthoidea: Pilumnidae) reared in the laboratory
Figure 5. Pilumnus spinifer H. Milne Edwards, 1834. Mandible: (A) zoea IV; (B) megalopa. Scale bars: 0.1 mm.
Figure 4 in Comparative analysis of the karyotype sensitivities of Apodemus flavicollis and laboratory mice to DNA-damaging agents
Figure 4. Pericentric inversions in bone marrow cell of A. flavicollis after Mitomycin C treatment.
Figure 2 in Comparative analysis of the karyotype sensitivities of Apodemus flavicollis and laboratory mice to DNA-damaging agents
Figure 2. Breaks and fragments in bone marrow cell of A. flavicollis after Mitomycin C treatment.
FIG. 4 in Larval and early juvenile stages of Pirimela denticulata (Montagu, 1808) (Crustacea, Brachyura, Pirimelidae) reared in the laboratory
FIG. 4. Pirimela denticulata (Montagu): (a±d) maxilla of ®rst to fourth zoeas. Scale bar 5 0.1 mm.
FIG. 1 in Larval development of Maja crispata Risso 1827 (Crustacea, Decapoda, Majidae) reared in the laboratory
FIG. 1. Maja crispata: zoea I (A, C), zoea II (B, D); megalop (E, F, G). Scale bar in mm.
Fig. 5 in The Lecithotrophic Zoea Of Chirostylus Ortmanni Miyake & Baba, 1968 (Crustacea: Anomura: Galatheoidea: Chirostylidae) Described From Laboratory Hatched Material
Fig. 5. Chirostylus ortmanni Miyake & Baba, 1968: a, dorsal view of abdomen; b, lateral view of abdomen.
Supplemental table from: CLIA laboratory testing for Facioscapulohumeral Dystrophy (FSHD): a retrospective analysis
<p><span><span><span><span><span><span><span><span><span><span><span><b>Objective:</b> To summarize facioscapulohumeral muscular dystrophy (FSHD) diagnostic testing results from the University of Iowa Molecular Pathology Laboratory. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods:</b> All FSHD tests performed in the diagnostic laboratory January 2015-July 2019 were retrospectively reviewed. Testing was by restriction enzyme digestion and Southern blot analysis with sequencing of <i>SMCHD1,</i> if indicated. Cases were classified as FSHD1 (4q35 EcoRI size ≤40kb; 1-10 D4Z4 repeats), FSHD2 (permissive 4q35A allele, D4Z4 hypomethylation, and pathogenic <i>SMCHD1</i> variant), or non-FSHD1,2. We also noted cases with borderline EcoRI fragment size (41-43kb; 11 D4Z4 repeats), cases that meet criteria for both FSHD1 and FSHD2, somatic mosaicism, and cases with hybrid alleles that add complexity to test interpretation. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results:</b> Of the 1594 FSHD tests included in the analysis, 703 (44.1%) were diagnosed with FSHD. Among these positive tests, 664 (94.5%) met criteria for FSHD1 and 39 (5.5%) met criteria for FSHD2. Of all 1594 cases, 20 (1.3%) had a 4q35 allele of borderline size, 23 (1.5%) were somatic mosaics, and 328 (20.9%) had undergone translocation events. Considering only cases with at least one 4q35A allele, D4Z4 repeat number differed significantly among groups: FSHD1 cases median of 6.0 (IQR: 4-7) repeats, FSHD2 cases 15.0 (IQR: 12-22) repeats, and non-FSHD1,2 cases 28.0 (IQR: 19-40) repeats. </span></span></span></span></span></span></span></span></span></span></span></p> <p><strong>Conclusion: </strong>FSHD1 accounts for 94.5% of genetically confirmed cases of FSHD. The data show a continuum of D4Z4 repeat numbers with FSHD1 samples having the fewest, FSHD2 an intermediate number, and non-FSHD1,2 the most.</p>
Figure 1 from: David J, Geoffroy J (2011) Additional moults into 'elongatus' males in laboratory-reared Polydesmus angustus Latzel, 1884 (Diplopoda, Polydesmida, Polydesmidae) – implications for taxonomy. ZooKeys 156: 41-48. https://doi.org/10.3897/zookeys.156.2045
Figure 1 - Dorsal view of a Polydesmus angustus male of stadium IX after its death at the age of 19 months. The trunk consists of 19 podous rings – bearing 32 pairs of legs plus regressed gonopods (8th leg-pair) – and one apodous ring anterior to the telson.
Figure 2 from: Schutze MK, Dammalage T, Jessup A, Vreysen MJB, Wornoayporn V, Clarke AR (2015) Effects of laboratory colonization on Bactrocera dorsalis (Diptera, Tephritidae) mating behaviour: 'what a difference a year makes'. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 369-383. https://doi.org/10.3897/zookeys.540.9770
Figure 2 - Index of Sexual Isolation (ISI) and relative performance indices for males (MRPI) and females (FRPI) with associated 95% confidence intervals calculated for 2010 and 2011 mating compatibility comparisons between Bactrocera dorsalis from Saraburi and Nakhon Si Thammarat, Thailand. Dotted line (0.00) represents random mating (ISI) or equal participation by the sexes (MRPI and FRPI).
Figure 1 from: Schutze MK, Dammalage T, Jessup A, Vreysen MJB, Wornoayporn V, Clarke AR (2015) Effects of laboratory colonization on Bactrocera dorsalis (Diptera, Tephritidae) mating behaviour: 'what a difference a year makes'. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 369-383. https://doi.org/10.3897/zookeys.540.9770
Figure 1 - Behavioural parameters of Bactrocera dorsalis flies from Saraburi (S) and Nakhon Si Thammarat (N) (Thailand) during mating compatibility trials in 2010 and 2011. A Relative percentages and total numbers of each possible couple formed. Numbers in bars are total numbers of each couple formed summed across replicates B Mating latency as average time since first couple observed for couples formed C Average percentage of respective couples collected from the tree for each of the six mating compatibility comparisons. For all graphs, columns surmounted by the same letter within a year are not significantly different at α = 0.05.
Data for "Evolution upon leather manufacturing: comparison of the two Halobacterium salinarum strains isolated in the early 20-th century with the twin laboratory strains NRC-1 and R1"
<p>This set of files contains data associated with the emerging manuscript<br> "Evolution upon leather manufacturing: comparison of the two<br> Halobacterium salinarum strains isolated in the early 20-th century<br> with the twin laboratory strains NRC-1 and R1."<br> by Friedhelm Pfeiffer and Mike Dyall-Smith.</p> <p>The manuscript provides a detailed comparison of the complete genome<br> sequences from four strains of Halobacterium salinarum:<br> 91-R6 (NRC 34002, the type strain of Halobacterium salinarum);<br> 63-R2 (NRC 34001, a strain originally reported as 'cutirubra');<br> NRC-1 and R1 (two laboratory strains).</p> <p>A detailed comparison of the complete genome sequences of three strains<br> (excluding 63-R2) has been previously reported:<br> Microbiologyopen (2020) 9: e974 (doi: 10.1002/mbo3.974; PMID:31797576).</p> <p>The 'seq_' series of files contains newly reported sequences of<br> episomal plasmids (pHcu190, pHcu229) and plasmid integrants into<br> the chromosome (contigDRAFT1, contigDRAFT2) from strain 63-R2.</p> <p>There are two versions for pHcu229, as this plasmid could only<br> be partially assembled (_asAssembled, 170458 bp) but could be<br> completed in silico (_inSilicoCompleted, 229124 bp).</p> <p>The 'tagMGE_' series of files contains the sequences of all<br> replicons (the main chromosome and all plasmids) with markup<br> of all mobile genetic elements (MGEs) for each of the<br> four strains of Halobacterium salinarum.</p> <p>The file dbHsAllStrainsTotal.fasta contains the complete sequences<br> of the chromosomes and plasmids in a single file.</p> <p>The dbHsAllStrainsCore.fasta contains the same set of sequences but<br> with strain-specific copies of mobile genetic elements removed. This<br> version was generated to facilitate inter-strain sequence comparison.<br> </p>
Supplementary material 1 from: Abram PK, Nelson TD, Marshall V, Gariepy TD, Haye T, Zhang J, Hueppelsheuser T, Acheampong S, Moffat CE (2023) Genetic relationships among laboratory lines of the egg parasitoid Trissolcus japonicus from native and adventive populations. NeoBiota 82: 145-161. https://doi.org/10.3897/neobiota.82.97881
Supplementary information
Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory
<p><span>What causes evolution to be repeatable is a fundamental question in evolutionary biology. Pleiotropy, i.e. the effect of an allele on multiple traits, is thought to enhance repeatability by constraining the number of available beneficial mutations. Additionally, pleiotropy may promote repeatability by allowing large fitness benefits of single mutations via adaptive combinations of phenotypic effects. Yet, this latter evolutionary potential may be reaped solely by specific types of mutations able to realize optimal combinations of phenotypic effects while avoiding the costs of pleiotropy. Here, we address the interaction of gene pleiotropy and mutation type on evolutionary repeatability in a meta-analysis of experimental evolution studies with <em>Escherichia coli</em>. We hypothesize that single-nucleotide polymorphisms are principally able to yield large fitness benefits by targeting highly pleiotropic genes, whereas indels and structural variants provide smaller benefits and are restricted to genes with lower pleiotropy. By using gene connectivity as proxy for pleiotropy, we show that nondisruptive single-nucleotide polymorphisms (SNPs) in highly pleiotropic genes yield the largest fitness benefits, since they contribute more to parallel evolution, especially in large populations, than inactivating SNPs, indels and structural variants. Our findings underscore the importance of considering genetic architecture together with mutation type for understanding evolutionary repeatability.</span></p>
Dataset of laboratory research of paper "Mutation Analysis and Characteristics of the 5T Allele in the Cystic Fibrosis Trans Membrane Gene"
<p>Dataset contains</p> <p>1. Blood Lymphocite</p> <p>2. Utensils and raw Materials</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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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.