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703 results for “repetitions”
Detectability and impact of repetitive surveys on threatened West African crocodylians: Data M1
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Data from: Repetitive desiccation events weaken a salt marsh mutualism
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Evolution of repetitive genomic content and gene families over geo-climatic gradients in Brassicaceae
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Microglial cytokines mediate plasticity induced by 10 Hz repetitive magnetic stimulation
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Data from: Repetitive somatosensory stimulation shrinks the body image
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Estimates of mixed lyer gross primary productivity and photophysiology based on underway Lagrangian measurements of the dissolved chlorophyll fluorescence of phytoplankton usung Fast Repetition Rate Fluorometry (FRRF)
GPP was estimated on the P1706 cruise based on the photo-physiology of the mixed-layer phytoplankton community measured by FRRF. Shipboard measurements were made using a bench-top FastAct 2+ Fast TRAKA instrument (Chelsea, UK) plumbed into the ship’s running seawater system. Photosynthesis versus irradiance (P vs. E) curves were run continuously on a ~45 min sampling interval.
Data from: Repetitive flanking sequences challenge SSR marker development: a case study in the lepidopteran Melanargia galathea
Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages RepARK and RepeatMasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Ephydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra, and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabeled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labeled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development.
Microsaccades inhibition triggered by a repetitive visual distractor is not subject to habituation: implications for the programming of reflexive saccades
<p>Dataset relative to the manuscript entitled "<strong>Microsaccades inhibition triggered by a repetitive visual distractor is not subject to habituation: implications for the programming of reflexive saccades</strong>"</p>
Raw results of the experiments performed to evaluate irregular repetition slotted ALOHA with multiuser detection
<p>This zip file contains the data files needed to generate the figures of the numerical results presented in [1].</p> <p> </p> <p>[1] M. Fernández-Veiga, M.E. Sousa-Vieira, A. Fernández-Vilas, R.P. Díaz-Redondo. "Irregular repetition slotted ALOHA with multiuser detection: A density evolution analysis". Computer Networks, 234, 109921, 2023.</p>
Figure 5 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 5. Evolutionary trends and patterns of repeat distribution in the karyotype of Anguis and Pseudopus. The summary presents: the distribution pattern of interstitial telomeric repeats (ITRs) in macrochromosomes (red arrowheads), the presence of constitutive heterochromatin in the centromeric region of chromosome No. 2 (black arrowheads), and the number and topology of 18S rDNA sites (green signals). Phylogenetic relationships follow Gvoždík et al. (2023). Although all six species share 2n = 44 and macrochromosome morphology differs only subtly, several species-specific repeat accumulation patterns have been observed. A, The common ancestor of Anguis and Pseudopus had 10 macro- and 12 microchromosome pairs, and its metacentric chromosome No. 1 likely possessed ITRs in the centromeric region. B, Accumulation of ITRs on chromosomes Nos 2, 4, and 7, and heterochromatin on chromosome No. 2; translocation and accumulation of rDNA sites on microchromosomes in the Anguis ancestor. C, Accumulation (in A. cephallonica) or elimination (in the A. fragilis species complex ancestor) of ITRs on pair Nos 5 and 9 and of rDNA sites on one of the microchromosome pairs. An asterisk indicates two possible directions of chromosomal changes. D, Elimination of ITRs on pair No. 1 in the A. fragilis species complex ancestor. E, Elimination of ITRs on chromosomes Nos 2 and 7; elimination of heterochromatin on chromosome No. 2 in the common ancestor of A. colchica and A. graeca. F, Accumulation of ITRs on chromosome No. 3 in the ancestor of A. fragilis and A. veronensis. Anguis veronensis represents a composite ITR pattern of A. cephallonica and A. fragilis, providing support for the hypothesis of past contact between Italian and Peloponnese slow worms (Gvoždík et al. 2023), with remnants of these interactions likely persisting. An alternative hypothesis proposes a shared repeat pattern among all Anguis species, wherein the detection of ITRs depends on the repeat abundance and reveals accumulations only above the detection limit.
Figure 2 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 2. Distribution of constitutive heterochromatin (first column from the less side), GC/AT-positive regions (second column), telomeres and ITRs (third column), and 18S rDNA gene clusters (fourth column) in Anguis and Pseudopus (males, UN for unknown sex). First column (A, E, I, M, Q, U): presence (full arrowhead) and absence (empty arrowhead) of centromeric heterochromatin in chromosome pair No. 2. Second column (B, F, J, N, R, V): diffused GC+ pattern in distal part of pair No. 2 (empty arrowhead) or strong signal (full arrowhead) in the telomeric region of pair No. 1. Third column (C, G, K, O, S, W): ITRs (full arrowhead). Fourth column (D, H, L, P, T, X): hybridization of 18S rDNA on three pairs of microchromosomes (full arrowheads) and additional weak signal on another microchromosome pair (empty arrowheads). Where available, females do not differ from males and are shown in Supporting Information (Fig. S3).
Figure 4 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 4. Chromosome painting with Varanus komodoensis (VKO) macrochromosome probes on Anguis fragilis (AFR) and Pseudopus apodus (PAP) chromosomes. The probe identity is indicated (number and letter correspond to VKO chromosome and flow-sorted peak, respectively). Arrowheads mark the hybridization signal on the AFR (A–E) and PAP (F) homeologous chromosomes. Note that each of the probes VKO 1, 2, and 3 marks two different pairs of chromosomes, whereas the probes VKO 6 + 7 and 8 + 7 mark different arms of the same chromosome pair. The hybridization signal of the probes VKO 6 + 7 and 8 + 7 does not clearly overlap in Anguis, but it marks chromosome pair No. 7 in Pseudopus.
Figure 3 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 3. Male (A, C, E, G) and female (B, D, F, H) comparative genomic hybridization in four Anguis species. Male-specific DNA is labelled with fluorescein d-UTP (green), and female-specific DNA with Cy3 d-UTP (red). The yellow regions reflect regions of accumulated repetitive elements existing in equilibrium in the male and female genomes. Slightly reddish (E, F) or greenish (G, H) regions indicate certain enrichment of the repetitive fraction in the genome of one of the individuals.
Figure 1 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 1. Karyograms of Anguis and Pseudopus. Male karyograms are shown, the karyograms of A. veronensis and P. apodus are from a juvenile of unknown sex. All tested individuals including females share the karyotype of 2n = 44 consisting of 20 macrochromosomes and 24 microchromosomes. Where available, karyograms of both sexes are shown in Supporting Information Figure S1. Scale bar = 10 µm. Photos on the right, not to scale.
Figure 6 in Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes
Figure 6. Schematic illustration of the homeology of the Varanus and Anguis + Pseudopus macrochromosomes with respect to the putative toxicoferan ancestor. The simplified arrangement of the macrochromosomes of the toxicoferan ancestor follows the hypothesis of Deakin and Ezaz (2019). Based on the fission(s) leading to Varanus and Anguis, we can assume that both lizards exhibit a derived stage of macrochromosome organization rather than variants of the putative ancestral arrangement of their common anguiform ancestor. The homeology of VKO 5 and AFR 6 (red and white hatched) is tentative and requires further evidence. The colour code depicts the chromosome homeology.
Differential influence of the dorsal premotor and primary somatosensory cortex on corticospinal excitability during kinesthetic and visual motor imagery: a low-frequency repetitive transcranial magnetic stimulation study
<p>Consistent evidence suggests that motor imagery involves activation of several sensorimotor areas also involved during action execution, including the dorsal premotor (dPMC) and primary somatosensory cortex (S1). However, it is still unclear whether their involvement is specific for either kinesthetic or visual imagery or whether they contribute to motor activation for both modalities. Although sensorial experience during motor imagery is often multimodal, identifying the modality exerting greater facilitation of the motor system may allow to optimize the functional outcomes of rehabilitation interventions. In a sample of healthy adults, we combined 1-HZ repetitive transcranial magnetic stimulation (TMS) to suppress neural activity of the dPMC, S1, and primary motor cortex (M1) with single-pulse TMS over M1 for measuring cortico-spinal excitability (CSE) during kinesthetic and visual motor imagery of finger movements as compared to static imagery conditions. We found that rTMS over both dPMC and S1, but not over M1, modulated the muscle-specific facilitation of CSE during kinesthetic, but not during visual motor imagery. Furthermore, dPMC-rTMS suppressed the facilitation of CSE, whereas S1-rTMS boosted it. The results highlight the differential pattern of cortico-cortical connectivity within the sensorimotor system during the mental simulation of the kinesthetic and visual consequences of actions.</p>
Data for Pump–probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates
<p>Datasets and analysis scripts used in publication: Gerlinger et al., <em>Pump–probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates</em></p>
Data for: The role of repetitive DNA in re-patterning of major rDNA clusters in Lepidoptera
<p><span>Genes for major ribosomal RNAs (rDNA) are present in multiple copies organized in tandem arrays. Number and position of rDNA loci can change dynamically and their re-patterning is presumably driven by repetitive sequences. We explored a peculiar rDNA organization in several representatives of Lepidoptera with either extremely large or numerous rDNA clusters. We combined molecular cytogenetics with analyses of second and third generation sequencing data to show that rDNA spreads as a transcription unit and reveal association between rDNA and various repeats. Furthermore, we performed comparative long read analyses between the species with derived rDNA distribution and moths with a single rDNA locus, which is considered ancestral. Our results suggest that satellite arrays, rather than mobile elements, facilitate homology-mediated spread of rDNA via either integration of extrachromosomal rDNA circles or ectopic recombination. The latter arguably better explains preferential spread of rDNA into terminal regions of lepidopteran chromosomes as efficiency of ectopic recombination depends on proximity of homologous sequences to telomeres.</span></p>
Fig. 2 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps
Fig. 2. The essence of glucosinolate (GSL) biosynthesis as imagined for the presumably ancient 2-methylpropylGSL and a β-hydroxylated derivative, 2-hydroxy-2-methylpropylGSL. The three steps between the CYP83 product and thiohydroximic acid in general GSL biosynthesis involves glutathione, serving as the donor of sulfur. The illustrated hypothetic pathway is based on the known biosynthetic pathway of more recently evolved GSLs (Sønderby et al., 2010).
Fig. 8 in Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps
Fig. 8. Biochemical aspects of aliphatic side chain oxidation of glucosinolates (GSLs). A. Biosynthesis of three well-investigated GSLs, all involving enzymes of the class "2-oxoglutarate-dependent dioxygenases", although the case of BAR biosynthesis is still tentative (Byrne et al., 2017). B. Conserved metabolism of an OAT into the corresponding oxazolidine-2-one (OAO) in three Brassicales species (Barbarea vulgaris, Nasturtium officinale and Reseda luteola). MYR, myrosinase; GS-OH, glucosinolate hydroxylating enzyme; GRS, glucoraphasatin synthase.
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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.