Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 1; peer review: 1 approved, 1 approved with reservations]

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.Bioarchaeolog

Antibacterial activity of ethanolic extract of Sweet Basil (Ocimumbasilicum L.) leaves against Escherichia coli in experimentally infected Rats

The present study was carried out to investigate the antibacterial activity of Ocimumbasilicum (OB)ethanolic extract in-vivo by inducing diarrhea in rats which was caused by oral administration of pathogenic Escherichea coli. The experiment that performed in this present study included study in-vivo antibacterial activity of the extract after inducing infectious diarrhea with oral pathogenic E. coli in five rats groups (eight rats of each). Two doses of O.B extract 100, 200 mg/kg. BW was used to treat this infection for fourteen days orally which compared with group E that treated with Trimethoprim/sulfa at dose 6.85mg/kg BW. The yielding percentage of Ocimumbasilicum 95% ethyl alcohol leaves extract was 13%. Phytochemicals analysis indicated the presence of alkaloids, phenols, tannins, saponins, flavonoids, steroids and terpenoids, while glycosides were absent, but Alkaloid, phenols, saponins and tannins were seemed to be found in high levels in the crude extract. Biochemical analysis of serum albumin showed different results; Albumin values returned to normal values during treatment with Ocimumbasilicum leaves extract dose of 200 mg/kg BW and Trimethoprim/sulfa at dose 6.85mg/kg BW also these two kinds of therapy returned intestinal secretory nearly to normal levels after treatment for seven days in comparison with other groups, while a dose of 100 mg/kg BW of OB extract showed a little decrease in albumin concentrations after 7 days of treatment. From the results obtained, it could be concluded that ethanolic extract of O.B leaves at dose 200 mg/kg BW was more effective and safe in comparison with antibacterial agent and other O.B dose, this antidiarrheal activity of O.Bethanolic extract may be due to its constituents of secondary metabolites that are responsible for the antibacterial activity with different mechanisms of action

Study the internal cracks effect on vibration of laminated composite square plates

Purpose: The study of cracks behaviour in a composite plate is of significant importance in the dynamics of the Mechanical parts in order to avoid design failures due to resonance or high amplitude vibrations. Design/methodology/approach: In this paper, a square glass-epoxy composite plate is adopted. The plate has four layers with symmetric and asymmetric lamination. Assuming the cracks are profound as defects. The results were obtained by using a numerical solution of mechanical APDL from ANSYS. Findings: It has been found for different boundary conditions that the rank of natural frequencies is decreased by increasing the crack ratio due to the reduction of the plate’s stiffness, whereas the crack direction has no mentioned effect for a small angle of rotation. Research limitations/implications: The accuracy of results is verified by comparing a single case of the current work with other previous investigations. value: Evaluate the influence of the crack length ratio, angle of the crack rotation, boundary conditions and lamination angles on the natural frequencies of the square composite plate with glass-epoxy materials

A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.

In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case. Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations. The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly