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846 results for “Homologization”
Deep cis-regulatory homology of the butterfly wing pattern groundplan
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Data from: Cellular morphology of leg musculature in the water bear Hypsibius exemplaris (Tardigrada) unravels serial homologies
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Efficient targeted integration directed by short homology in zebrafish and mammalian cells
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Data from: Serial homology and correlated characters in morphological phylogenetics: modeling the evolution of dental crests in placentals
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Data from: Divergent color signals from homologous unfeathered ornaments in two congeneric grouse
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Systemic paralogy and function of retinal determination network homologs in arachnids
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FIG. 7. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 7. — Monchenkocyclops mehmetadami n. sp., allotype ♂: A, urosome, ventral view; B, urosome, dorsal view; C, P6, lateral view. Roman numerals indicating terminology proposed by Huys et al. (1996). Scale bars: A, B, 50 µm; C, 25 µm.
FIG. 9. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 9. — Monchenkocyclops mehmetadami n. sp., allotype ♂: A, antennule, dorsal view; B, antennule, anterior view; C, antennule, distal segments, ventral view. Roman numerals indicating segment homologies as proposed by Huys & Boxshall (1991). Scale bar: 50 µm.
FIG. 5. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 5. — Monchenkocyclops mehmetadami n. sp., holotype ♀, swimming legs: A, P1, anterior view, arrow indicating inner basal seta; B, P2, posterior view; C, P3, anterior view; D, P4, anterior view; E, P4, praecoxa, coxa and intercoxal sclerite posterior view. Scale bar: 50 µm.
FIG. 2 in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 2. — Scanning electron micrographs of Monchenkocyclops mehmetadami n. sp.: A, paratype ♀, habitus, ventral view; B, inset showing hyaline frills on the third abdominal somite; C, details of caudal ramus, ventral view; D, inset showing seta I; E, F, rostrum, arrow indicating a sensilla; G, paratype ♂, habitus, ventral view; H, paratype ♂, rostrum, anterior view. Scale bars: A, G, 20 µm; B, 2 µm; C, E, H, 4 µm; D, F, 1 µm.
FIG. 3. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 3. — Monchenkocyclops mehmetadami n. sp., holotype ♀: A, antennule, ventral view, roman numerals indicating segment homologies as proposed by Huys & Boxshall (1991); B, antenna, caudal view; C, labrum, anterior view; D, mandible, ventral view; E, mandible, anterior view; F, maxillule, posterior view; G, maxilla, anterior view; H, maxilliped, posterior view; I, maxillulary palp, anterior view; J, P5, ventral view. Scale bars: A-H, 50 µm; I-J, 25 µm.
FIG. 8 in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 8. — Scanning electron micrographs of Monchenkocyclops mehmetadami n. sp., paratype ♂: A, inset of caudal rami, detail of seta I; B, urosome,ventral view; C, plates of P6, arrow indicating setal elements of P6; D, details of P6 showing setal elements; E, P5 ventral view. Scale bars: A, D; 1 µm, B, 10 µm; C, 5 µm; D, 1 µm; E, 4 µm.
FIG. 4 in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 4. — Scanning electron micrographs of Monchenkocyclops mehmetadami n. sp., paratype ♀: A, mouth region, ventral view; B, mandible, exopod, ventral view; C, anterior end of maxilliped, ventral view. Scale bars: A, 5 µm; B, 1 µm; C, 3 µm.
Fig. 6 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 6. Neophyllobius tescalicola sp. nov., ♀, holotype. A. Palp. B. Subcapitulum. C. Dorsal idiosoma. D. Ventral idiosoma. E. Trochanter–tibia of leg I. F. Tarsus I.
Fig. 3 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 3. Schematic leg setations of Neophyllobius cibyci sp. nov. A–D. ♀, holotype. A. Trochanter–tibia of leg I. B. Trochanter–tibia of leg II. C. Trochanter–tibia of leg III. D. Trochanter–tibia of leg IV. E–H. ♁, paratype (CNAC009238). E. Trochanter–tibia of leg I. F. Trochanter–tibia of leg II. G. Trochanter–tibia of leg III. H.Trochanter–tibia of leg IV. I–L. Protonymph, paratype (CNAC009241). I. Trochantertibia of leg I. J. Trochanter–tibia of leg II. K. Trochanter–tibia of leg III. L. Trochanter–tibia of leg IV. M–O. Larva, paratype (CNAC009242). M. Trochanter–tibia of leg I. N. Trochanter–tibia of leg II. O. Trochanter–tibia of leg III.
Data from: Snakeskin gourami (Trichopodus pectoralis) exhibits XX/XY sex determination and putative young Y chromosome shares sex chromosomal linkage homologies with those of amniotes
<p class="CxSpFirst"><span>Snakeskin gourami (<i>Trichopodus pectoralis</i>) is one of the most common air-breathing freshwater fish of the Indochina peninsula. It has a high meat yield and is one of the top five aquaculture freshwater fish in Thailand. However, it takes 2–3<b> </b>years for adults to reach sexual maturity. Snakeskin gourami is not externally sexually dimorphic and its sex determination remains unknown, complicating many aspects of broodstock management including sex manipulation. Understanding the sex determination system will contribute significantly towards full-scale commercialization. By characterizing the sex determination system in snakeskin gourami using cytogenetic approaches and Diversity Arrays Technology, we identified sex-specific loci in 16 phenotypic sex assignments of snakeskin gourami. Of the 39 loci present in all males, 4<b> </b>male-linked loci reached the criteria of moderately sex-linked loci (70:30; males:females and 80:20; males:females). By contrast, only one female-linked locus was detected from moderately sex-linked loci. This suggests that snakeskin gourami exhibits an XX/XY sex determination mode. No different chromosomal patterns were observed in karyotype, C-banding, and microsatellite repeat fluorescence <i>in situ</i> hybridization mapping between males and females, and no male-specific loci of 100:0 (males:females) were observed in snakeskin gourami. This suggests that the putative Y chromosome is young and the non-recombination region is very cryptic. A total of<b> </b>10.26% male-linked loci were involved with the sex developmental pathway in vertebrates and 5.13% showed partial homology with several amniote sex chromosomal linkages. Surprisingly, the hypothesis of an ancestral amniote super-sex chromosome with overlaps of partial sex chromosomal linkages was also found in teleosts. This approach provides a solid baseline to reveal the sex determination mechanism<b> </b>and identify potential sex determination regions in teleosts, allowing further investigation of genetic improvements in snakeskin gourami.</span></p>
Data from: Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences
Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here. Results: Phylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing the strong phylogenetic performance of random subsets of data also shown in this study. Phylogenetic results for both the 19-taxon and 44-taxon datasets corroborate previous hypotheses about the placement of Photobacterium and Aliivibrio within Vibrionaceae and also highlight problems with how Photobacterium is delimited and indicate that it likely should be dissolved into Vibrio to produce a phylogenetic taxonomy. The 19-taxon and 44-taxon trees based on the large chromosome are congruent for the majority of taxa that are present in both datasets. Analyses of the 44-taxon sampling based on the second, small chromosome are quite different from those based on the large chromosome, which is not surprising given the dramatically divergent nature of the small chromosome and the difficulty in postulating primary homologies. Conclusions: The phylogenetic analyses presented here represent the most comprehensive genome-level phylogenetic analyses in terms of taxa and data. Based on the availability of genome data for many bacterial species on GenBank, many other bacterial groups would also be amenable to similar genome-scale phylogenetic analyses even when present in multiple contigs. The result that collinear subsets of data are incongruent with the concatenated dataset and with each other while random data subsets show very little incongruence echoes the result of previous work on Shewanellaceae. The 44-taxon phylogenetic analysis presented here thus represents the future of phylogenomic analyses in scope and complexity.
Data from: An antagonistic pair of FT homologs mediates the control of flowering time in sugar beet
Cultivated beets (Beta vulgaris) are unable to form reproductive shoots during the first year of their life cycle. Flowering only occurs if plants get vernalized, i.e. pass through the winter, and are subsequently exposed to an increasing day length (photoperiod) in spring. Here we show that the regulation of flowering time in beet is controlled by the interplay of two paralogs of the FLOWERING LOCUS T (FT) gene in Arabidopsis that have evolved antagonistic functions. BvFT2 is functionally conserved with FT and essential for flowering. In contrast, BvFT1, which is down-regulated in response to vernalization, represses flowering and is crucial for the vernalization response in beet. These data suggest that beet utilizes a different strategy relative to Arabidopsis and cereals to regulate vernalization.
Data from: Multiple pairwise analysis of non-homologous centromere coupling reveals preferential chromosome size-dependent interactions and a role for bouquet formation in establishing the interaction pattern
During meiosis, chromosomes undergo a homology search in order to locate their homolog to form stable pairs and exchange genetic material. Early in prophase, chromosomes associate in mostly non-homologous pairs, tethered only at their centromeres. This phenomenon, conserved through higher eukaryotes, is termed centromere coupling in budding yeast. Both initiation of recombination and the presence of homologs are dispensable for centromere coupling (occurring in spo11 mutants and haploids induced to undergo meiosis) but the presence of the synaptonemal complex (SC) protein Zip1 is required. The nature and mechanism of coupling have yet to be elucidated. Here we present the first pairwise analysis of centromere coupling in an effort to uncover underlying rules that may exist within these non-homologous interactions. We designed a novel chromosome conformation capture (3C)-based assay to detect all possible interactions between non-homologous yeast centromeres during early meiosis. Using this variant of 3C-qPCR, we found a size-dependent interaction pattern, in which chromosomes assort preferentially with chromosomes of similar sizes, in haploid and diploid spo11 cells, but not in a coupling-defective mutant (spo11 zip1 haploid and diploid yeast). This pattern is also observed in wild-type diploids early in meiosis but disappears as meiosis progresses and homologous chromosomes pair. We found no evidence to support the notion that ancestral centromere homology plays a role in pattern establishment in S. cerevisiae post-genome duplication. Moreover, we found a role for the meiotic bouquet in establishing the size dependence of centromere coupling, as abolishing bouquet (using the bouquet-defective spo11 ndj1 mutant) reduces it. Coupling in spo11 ndj1 rather follows telomere clustering preferences. We propose that a chromosome size preference for centromere coupling helps establish efficient homolog recognition.
Data from: Testing for homologies in the axial skeleton of primitive echinoderms
The extraxial axial theory is used to investigate homology of ambulacral and oral plating because it predicts terminal branching and terminal addition of plates in the axial skeleton, although exceptions to the former may occur in some Paleozoic echinoderms. The variety of morphological designs and anomalous individuals also provide tests of plate homology. Homology of ambulacra is generally accepted, with the hydropore and/or single gonopore in Carpenter's CD interray. In the 2-1-2 ambulacral pattern the unbranched ambulacrum is always in Carpenter's A ray. All ambulacral morphology requires just three instructions: 'grow,' 'branch,' and 'stop.' The range of variation in echinoderms with fewer than five ambulacra implies that both the 'branch' and 'stop' instructions acted independently in all five rays. Numbers of ambulacra may or may not correlate with numbers of orals. Two basic patterns of 'cystoid' oral plating occur; with a single radial (circum-oral, CO) plate from each ambulacrum plus a sixth in the CD interray, and with all six interradial peri-oral (PO) plates, with two in the CD interambulacrum. Five 'orals' may involve loss of PO3 or PO6. Erect ambulacral structures are lost first in taphonomy and so poorly known. All ambulacral skeletal elements bear the same topological relationship to ambulacral soft tissues. Where branched ambulacra occur, the trunk or flooring plates are often modified first brachiolars or pinnulars. Both brachioles and pinnules may arise from facets developed on one or two flooring plates. Terminal addition of plates, spacing of brachioles/pinnules, and lack of musculature to open cover plates all suggest that 'cystoids' had extensions of the water vascular system in their ambulacra.
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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
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.