Odontophoridae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA777908 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Natural history museum specimens of historical honeybees have been successfully used to explore the genomic past of the honeybee, indicating fast and rapid changes between historical and modern specimens, possibly as a response to current challenges. In our study we explore a potential untapped archive from natural history collections - specimens of beeswax. We examine an Apis mellifera mellifera queen cell specimen from the 19th century. The intact and closed cell was analysed by X-ray Computed Tomography (CT) to reveal a perfectly preserved queen bee inside her cell. Subsequently, a micro-destructive approach was used to evaluate the possibility of protein extraction from the cell. Our results show that studies on specimens such as these provide valuable information about the past rearing of queens, their diet and development, which is relevant for understanding current honeybee behaviour. In addition we evaluate the feasibility of using historical beeswax as a biomolecular archive for ancient proteins to study honeybees.
2024-09-05 | PXD034106 | Pride
Project description:The genetic structure of some native Bolivians has been substantially influenced by admixture from Europeans, which we estimate to have occurred approximately 360 – 384 years ago. Consistent with historical accounts of male admixture, Y-chromosome haplogroups typical of Europeans were found in 39% of our Bolivian samples. No evidence of African admixture was found in native Bolivians. The Mesoamerican Totonacs have little evidence of European or African admixture. Our analysis indicates that some admixed Bolivians have Native American mtDNA and Y-chromosomes but harbor up to 30% European autosomal ancestry, demonstrating the need for autosomal markers to assess ancestry in admixed populations. From a dense genome-wide panel of 815,377 markers, we developed a set of 324 AIMs, specific for Native American ancestry. As few a 40-50 of these markers successfully predict New World ancestry in the ascertainment panel of Bolivians and Totonacs. The markers easily distinguish New World from Old World ancestry, even for populations more closely related to the Americas such as central and eastern Asians, and were effective for New World vs. Old World comparisons in five other geographically and culturally distinct populations of the Americas. SNPs demonstrating very high divergence between the two Native American populations and major Old World populations are found on haplotypes that are shared and occur at similar frequencies in other indigenous low-admixture American populations examined here (i.e. Pima, Maya, Colombian, Karitiana, and Surui). After excluding the possibility of recent relatedness, our results indicate that native Bolivians and Totonacs share ancestry with other American populations through a substantial contribution from a common founding population, population bottlenecks, and possible natural selection on functional variation.
2011-06-09 | GSE29851 | GEO
Project description:Sequence capture phylogenomics of historical ethanol-preserved museum specimens: unlocking the rest of the vault
| PRJNA553236 | ENA
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-15 | GSE261169 | GEO
Project description:Mitogenomics of historical type specimens of Australasian turtles
| PRJEB31010 | ENA
Project description:Newcastle disease (ND) affects a few hundred avian species including chicken, and the clinical outcome of Newcastle disease virus (NDV) infection ranges from mild to severe fatal disease depending on the NDV pathotype and the host species involved. Japanese quails serve as natural reservoirs of NDV and play important role in NDV epidemiology. While infection of chicken with velogenic NDV results in severe often fatal illness, the same infection in Japanese quails is results in in apparent infection. The molecular basis of this contrasting clinical outcomes of NDV infection is not yet known. We compared global gene expression in spleens of chicken and Japanese quails infected with a lentogenic or velogenic NDVs. We found contrasting regulation of key genes associated with NF-κB pathway and T-cell activation between chicken and Japanese quails. Our data suggests association of NDV resistance in Japanese quails to activation of NF-κB pathway and T cell proliferation.
2018-12-31 | GSE98296 | GEO
Project description:<p>The living and dried specimens in botanical collections play an important role in society for scientific and recreational purposes, offering the opportunity to obtain both macroscopic and molecular information for individual plants, ecosystems, and environmental studies. Untargeted metabolomics is an analytical approach that permits the simultaneous study of multiple small molecules present in an organism, which allows us to statistically compare different conditions of interest. Metabolomic approaches have been used on living specimens in botanical collections, but, until now, not on historical dried material. Using the Nicotiana genus herbaceous plant (tobacco) as a case study, we propose an untargeted metabolomic study to evaluate the potential of dried historical specimens as a source of metabolomic information on the past. The metabolomic profile from polar and less-polar/apolar aqueous extracts of four modern handmade tobacco cigars (split into wrapper, binder, and filler leaves), and a set of eight late-19th to early-20th century tobacco specimens (seven tobacco leaves and one snuff powder) from the collection of the Royal Botanical Gardens at Kew (London, UK) were analysed by liquid chromatography coupled to high resolution mass spectrometry. Results showed a wide range of polar and less-polar/apolar molecules which are preserved in dried botanical material, providing information optimal for metabolomic studies. The metabolomic profiles of historical dried samples were distinct enough to classify as Nicotiana tabacum or Nicotiana rustica, and showed differences based on geographic provenance or product transformation/processing. Statistical models based on the molecular data from the historical material permitted us to validate the labelling of the historical collection, which identified one possible mislabelled specimen and offered some clues as to the species of one unknown Nicotiana sample. Finally, metabolomic differences in profiles between Nicotiana tabacum and modern cigars showed that both share a large proportion of their metabolomic profile, where molecular differences could be possibly associated with both location of growth and anthropogenic transformation suffered by the plant in the last two centuries. This study demonstrates that dry botanical collections are a feasible source of information, and, if applied to a large set of individuals, conclusions may be drawn about the possible evolution and anthropogenic modification over time in plant material. The results are significant for disciplines interested in the history of plants, such as botany, history and archaeology.</p>
2024-03-06 | MTBLS4564 | MetaboLights
Project description:We sought to identify genes and gene signatures which correlate with progression by sampling human melanomas from nevi, primary, and metastatic tumors. The large number of samples also permits analysis within groups. Human melanoma samples were isolated from historical frozen patient specimens. RNA was extracted and run on the human Affymetrix U133A microarray chip.
2013-05-01 | E-GEOD-46517 | biostudies-arrayexpress
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-01 | GSE256158 | GEO