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 MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.
Project description:Human anatomical specimen museums are commonly used by medical, nursing, and paramedical students. Through dissection and prosection, the specimens housed in these museums allow students to appreciate the complex relationships of organs and structures in more detail than textbooks could provide. However, it may be difficult for students, particularly novices, to identify the various parts of these anatomical structures without additional explanations from a docent or supplemental illustrations. Recently, augmented reality (AR) has been used in many museum exhibits to display virtual objects in videos captured from the real world. This technology can significantly enhance the learning experience. In this study, three AR-based support systems for tours in medical specimen museums were developed, and their usability and effectiveness for learning were examined. The first system was constructed using an AR marker. This system could display virtual label information for specimens by capturing AR markers using a tablet camera. Individual AR markers were required for all specimens, but their presence in and on the prosected specimens could also be obtrusive. The second system was developed to set the specimen image itself as an image marker, as most specimens were displayed in cross section. Visitors could then obtain the label information presented by AR without any markers intruding on the display or anatomical specimens. The third system was comprised of a head-mounted display combined with a natural click interface. The system could provide visitors with an environment for the natural manipulation of virtual objects with future scalability.
Project description:Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
Project description:To explore the heterogeneity of stromal compartment of bladder cancer, we performed scRNAseq on two muscle-invasive bladder cancer specimens
Project description:Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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.
Project description:We assembled and annotated the first complete mitochondrial genome of a species from the subfamily Microweiseinae, Coccidophilus cariba Gordon, a predator of scale insect pest. The circular mitogenome consists of 15,343?bp in length, including 13 PCGs, 22 tRNA, and 2 rRNA genes, and exhibits the typical ladybird mitogenome structure. A phylogenetic analysis with the published mitogenomes of other 12 ladybirds is presented, which confirms the position of Microweiseinae as a sister group of Coccinellinae. The C. cariba mitogenome could be a useful source to future studies in the relationships inside the subfamily and the genus.
Project description:Cuora yunnanensis is an extinct turtle known from 12 specimens collected from Yunnan, China, before 1908. We used ancient DNA methods to sequence 1723 base pairs of mitochondrial DNA from a museum specimen of C. yunnanensis. Unlike some rare 'species' recently described from the pet trade, C. yunnanensis represents a lineage that is distinct from other known turtles. Besides C. yunnanensis, two other valid species (C. mccordi, C. zhoui) are unknown in the wild but are supposedly from Yunnan. Intensive field surveys for surviving wild populations of these critically endangered species are urgently needed.