Spatio-temporal mRNA tracking in the early zebrafish embryo.
Ontology highlight
ABSTRACT:
SUBMITTER: Holler K
PROVIDER: S-EPMC8184788 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We performed spatially resolved transcriptomics with sub-single-cell resolution in zebrafish embryos at the one-cell stage, which allowed us to identify a class of mRNAs that is specifically localized at an extraembryonic position in the yolk sac, the vegetal pole. The 3’ UTRs of these localized genes are enriched in specific sequence motifs. Comparison to two frog species revealed relatively low conservation of localized genes, but high conservation of sequence motifs. In vivo RNA labeling followed by scRNA-seq revealed that a large number of the localized transcripts are specifically transported to the primordial germ cells.
2020-12-07 | GSE158849 | GEO
Project description:Spatio-temporal mRNA tracking in the early zebrafish embryo
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Project description:Background:Spatio-temporal patterns of movement can characterize relationships between organisms and their surroundings, and address gaps in our understanding of species ecology, activity budgets, bioenergetics, and habitat resource management. Highly mobile waterfowl, which can exploit resources over large spatial extents, are excellent models to understand relationships between movements and resource usage, landscape interactions and specific habitat needs. Methods:We tracked 3 species of dabbling ducks with GPS-GSM transmitters in 2015-17 to examine fine-scale movement patterns over 24?h periods (30?min interval), dividing movement pathways into temporally continuous segments and spatially contiguous patches. We quantified distances moved, area used and time allocated across the day, using linear and generalized linear mixed models. We investigated behavior through relationships between these variables. Results:Movements and space-use were small, and varied by species, sex and season. Gadwall (Mareca strepera) generally moved least (FFDs: 0.5-0.7?km), but their larger foraging patches resulted from longer within-area movements. Pintails (Anas acuta) moved most, were more likely to conduct flights >?300?m, had FFDs of 0.8-1.1?km, used more segments and patches per day that they revisited more frequently, resulting in the longest daily total movements. Females and males differed only during the post-hunt season when females moved more. 23.6% of track segments were short duration (1-2 locations), approximately 1/3 more than would be expected if they occurred randomly, and were more dispersed in the landscape than longer segments. Distance moved in 30?min shortened as segment duration increased, likely reflecting phases of non-movement captured within segments. Conclusions:Pacific Flyway ducks spend the majority of time using smaller foraging and resting areas than expected or previously reported, implying that foraging areas may be highly localized, and nutrients obtainable from smaller areas. Additionally, movement reductions over time demonstrates behavioral adjustments that represent divergent energetic demands, the detection of which is a key advantage of higher frequency data. Ducks likely use less energy for movement than currently predicted and management, including distribution and configuration of essential habitat, may require reconsideration. Our study illustrates how fine-scale movement data from tracking help understand and inform various other fields of research.
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Project description:Embryogenesis in rice shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle, which differs from most dicotyledonous plants. To reveal the transcriptional features associated with developmental events during early embryogenesis in rice, we obtained transcriptome data, including the spatial and temporal data sets, using microarray experiments combined with a laser microdissection. We could predict the spatial expression foci of each expressed gene in the globular embryo, which revealed that the expression bias along the apical-basal and dorsal-ventral axes was correlated with temporal changes in expression levels during early embryogenesis. The spatial expression patterns of transcripts was suggestive of a potential contribution of phytohormone-related genes to early embryogenesis and was a characteristic feature of transcription factor genes. We also analyzed the relationship between expression sites of the genes in the globular embryo and those in embryonic organs at later stages. Based on in silico prediction of gene expression sites, we developed potential marker genes expressed in specific domains of the early embryo. The results and database will provide a framework for spatio-temporal gene expression in rice embryogenesis and increase our understanding of developmental diversity of plant embryogenesis.
2014-11-08 | GSE63110 | GEO
Project description:We develop So-Smart-seq to interrogate a comprehensive transcriptome inclusive of coding, noncoding, and repetitive element transcription. We reveal that, surprisingly, de novo silencing pertains only to a subset of paternal X (Xp) genes. In contrast, a set of evolutionarily older genes and LINEs demonstrate constitutive Xp silencing, adopt epigenetically distinct signatures, and do not require Xist to initiate silencing. On maternal X (Xm), however, these elements are hyperactivated. Thus, a significant subset of Xp elements appears to be inherited in a “pre-inactive” state. We also find that Xm-hyperactivation is timed to Xp silencing on an individual gene basis, giving rise to heterogeneity in the parallel track of dosage compensation as well. These conclusions have significant implications for the mechanism and evolution of imprinting in early mammals.
2024-03-15 | GSE168455 | GEO
Project description:The dengue virus has a single-stranded positive-sense RNA genome of approximately 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E) and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins. It possesses four antigenically distinct serotypes (DENV 1-4). Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA) were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1), closely related to the remaining 22 isolates (lineage 2). We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0) = 1.53 and values for lineage 2 of R(0) = 1.13. Under the exponential model, TMRCA of lineage 1 dated 1 year and lineage 2 dated 3.4 years before the last sampling. The possibility of inferring the spatio-temporal dynamics from genetic data has been generally little explored, and it may shed light on DENV circulation. The use of both geographic and temporally structured phylogenetic data provided a detailed view on the spread of at least two dengue viral strains in a populated urban area.
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