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In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.
A novel method was developed for the extraction of DNA from environmental material. Soil or sediment samples were encapsulated in agarose blocks and, following treatment with lysis reagents, the DNA was extracted by electroelution.
The electrostatic potential of B-DNA is calculated on its surface envelope for two homopolymeric base pair sequences using models representing the effects of both counterion binding and of aqueous solution. The influence of these two factors on the resulting potentials is established and the significance of calculations which omit such effects is discussed.
IgG antibodies to DNA, influenza virus haemagglutinin (HA), adenovirus hexon (HX) and mannan from Candida albicans (MN) have been determined in supernatants from 2-day unstimulated cultures of peripheral blood mononuclear cells from SLE patients and controls. Mean values were much higher in the SLE group, with from 20% (MN) to 85% (DNA) of patients giving values above the normal range. Although a significant correlation was observed between anti-DNA and anti-HA production, anti-HX and anti-MN showed no such correlations. The specificity of the ELISA assays was demonstrated by inhibition tests. It is concluded that a selective form of polyclonal activation in SLE results in the production of antibodies to foreign as well as to self antigens.
Jakobids are a group of free-living heterotrophic flagellates that hold a key phylogenetic position for understanding early eukaryote evolution and are particularly notable for their gene-rich, bacteria-like mitochondrial genomes. Although the number of formally described species is small, jakobids are frequently detected in anoxic marine habitats. However, their edaphic diversity remains unexplored, with the few documented isolations from soil over the past two decades, each yielding a new genus. Here, we describe a novel jakobid, Celatomonas quasimodo gen. et sp. nov., isolated from commercial potting soil used for cultivating indoor plants. The organism was characterised by light and scanning electron microscopy, and its phylogenetic position was inferred using 18S rRNA gene phylogenetic analysis. While exhibiting typical jakobid features, the cells adopt a highly unusual curved-triangular morphology during division, which has not been reported for any other jakobid. Phylogenetic analysis placed C. quasimodo as the firmly supported sister lineage of Moramonas marocensis within the family Moramonadidae (suborder Histionina). Despite this close affinity, the two taxa present a level of 18S rRNA gene divergence comparable to that between already recognised genera of Moramonadidae. Together, these data support the recognition of Celatomonas quasimodo as a new genus and species within Moramonadidae. Furthermore, screening of soil environmental DNA datasets revealed the presence of multiple novel jakobid lineages, alongside a novel jakobid clade (JENV-1) of uncertain phylogenetic position from equatorial environments. This newly described jakobid genus provides a valuable model for future comparative studies of cellular ultrastructure and the evolution of jakobid mitochondrial genomes. Combined with the environmental DNA screening results, our findings underscore the importance of soil habitats as reservoirs of unexplored eukaryotic diversity and provide new insights into jakobid systematics.
Crown-of-thorns starfish (COTS) outbreaks seriously threaten coral reef ecosystems, while conventional monitoring approaches are time-consuming and often lack sufficient sensitivity for early warning. Existing electrochemical DNA sensors usually require complex electrode-surface immobilization procedures, which can lead to uneven probe distribution, significant steric hindrance, and poor stability. Meanwhile, the low concentration of environmental DNA (eDNA) in marine environments further complicates detection. To overcome these challenges, this study developed a homogeneous electrochemical DNA sensor assisted by recombinase polymerase amplification (RPA) for COTS eDNA detection. Target DNA was first amplified by RPA, and the amplification products were then hybridized in solution with capture probe (CP)-modified magnetic beads (MB) and biotin-labeled signal probe (SP) to form sandwich-structured MB complexes. These complexes were subsequently magnetically enriched and immobilized on the electrode surface for electrochemical signal readout. Under optimized conditions, the sensor displayed a linear response to COTS genomic DNA from 3.77 fg/μL to 1 ng/μL, with an LOD of 2.02 fg/μL and an LOQ of 3.77 fg/μL. The sensor was applied to Xisha Islands samples, and the results agreed with droplet digital PCR (ddPCR) (P > 0.05), demonstrating its potential for sensitive and reliable on-site COTS eDNA detection.
Ancient DNA (aDNA) enables the reconstruction of chronologically sampled genomes from ancient humans, animals, plants, pathogens, and microorganisms, as well as environmental DNA, providing a record of biological changes through time. Improvements in short and degraded DNA extraction methods and low-cost sequencing now enable the generation of broad, cross-regional datasets that expand evolutionary analyses from past population demography to biological mechanisms. By tracking temporal shifts of allele frequencies, integrating functional genomics resources (e.g., gene expression, chromatin structure variation), modeling population demography to separate selection from genetic drift, and aligning genetic changes with archaeological, cultural, and climatic data, aDNA has the potential to link sequence variation to physiological function within their temporal and environmental contexts. In this review, we summarize illustrative case studies from aDNA research spanning complex traits, dietary adaptations, and responses to pathogens and other environmental changes, showing how human biology has evolved under multiple selective pressures through time. These dated signals help triage experimental work and expose mechanisms that are rare or absent in living cohorts. Although some challenges remain, such as geographic and temporal sampling disparities, limitations in data resolution and variant detection, and genotype-phenotype uncertainties, rapid methodological progress and stronger ethical frameworks are expanding what can be inferred, making aDNA a promising tool for refining physiological pathways, their timing, and their drivers.
Cells spontaneously secreting IgG or IgM antibodies to DNA or to common environmental antigens--influenza virus haemagglutinin, adenovirus hexon and mannan from Candida albicans--have been enumerated by ELISA spot in blood from patients with systemic lupus erythematosus (SLE) and normal donors. Mean values were raised for all antigens in the disease, with those for DNA being no greater than for the other antigens. In normal donors, levels of IgM-secreting cells were similar for DNA and the environmental antigens whereas virtually no IgG anti-DNA secreting cells were found. When results were expressed relative to total numbers of IgG or IgM-secreting cells, the differences between the groups disappeared or were greatly reduced in all systems except IgG anti-DNA. These findings are consistent with a requirement for both polyclonal activation and a self-antigen response in the production of IgG autoantibodies in SLE.
Bacterial pathogens undergo profound physiological changes when they infect their hosts, requiring coordinated regulation of gene expression in response to the stresses encountered during infection. A number of environmental stresses (such as osmotic shock and anaerobiosis) have been shown to induce changes in DNA supercoiling that can directly affect the transcription of a specific subset of bacterial genes, at least some of which (the outer-membrane porins and type 1 fimbriae) play a part in bacterial virulence. Here, we demonstrate that the virR gene of S. flexneri, implicated in the temperature regulation of plasmid-encoded virulence genes, is equivalent to the osmZ gene of Escherichia coli, which has previously been shown to mediate its regulatory effects through changes in DNA supercoiling. Our results imply that environmentally induced changes in DNA supercoiling are important in the coordinated control of virulence gene expression in S. flexneri and have general implications for the control of bacterial virulence.
In metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets. However, public molecular databases (i.e., SILVA, EUKARYOME, BOLD) for most microbial metazoan phyla (nematodes, tardigrades, kinorhynchs, etc.) are sparsely populated, negatively impacting our ability to assign ecologically meaningful taxonomy to these understudied groups. Additionally, the choice of bioinformatics parameters and computational algorithms can further impact the accuracy of eDNA taxonomy assignments. Here, we use two in-silico datasets to show that taxonomy assignments using the 18S rRNA gene can be dramatically improved by curating Linnaean taxonomy strings associated with each reference sequence and closing phylogenetic gaps by improving taxon sampling. Using free-living nematodes as a case study, we applied two commonly used taxonomy assignment algorithms (BLAST+ and the QIIME2 Naïve Bayes classifier) across six iterations of the SILVA 138 reference database to evaluate the precision and accuracy of taxonomy assignments. The BLAST+ top hit with a 90% sequence similarity cutoff often returned the highest percentage of correctly assigned taxonomy at the genus level, and the QIIME2 Naïve Bayes classifier performed similarly well when paired with a reference database containing corrected taxonomy strings. Our results highlight the urgent need for phylogenetically-informed expansions of public reference databases (encompassing both genomes and common gene markers), focused on poorly sampled lineages which are now robustly recovered via eDNA metabarcoding approaches. Additional taxonomy curation efforts should be applied to popular reference databases such as SILVA, and taxon sampling could be rapidly improved by more frequent incorporation of newly published GenBank sequences linked to genus and/or species level identifications.
Health risks to man associated with the use of chemicals include carcinogenesis, mutagenesis, and systems damage. Adverse effects from chemical exposures are determined by the nature and amount of the chemical, the type and length of exposure, and individual susceptibility to the chemical. A series of short- or long-term tests have been devised to predict human risk from suspect chemicals. These tests have provided enough information to establish guidelines for human safety, but they are not capable of providing sufficient information for unequivocal, scientifically valid standards for exposure limits. New methods now under development promise to provide more detailed information on early effects and cumulative damage to individuals. Developing countries should use existing data and regulatory experiences to the greatest possible extent to establish exposure limits according to local needs. When more ideal methods for the detection of chemical damage to man are available, these approaches and the data derived from their use can be incorporated into the programs in developing countries.
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The exploration of metagenomes from extremophiles has emerged as a promising approach for discovering novel glycoside hydrolases (GHs) with potential industrial applications. Extremophiles, which thrive in harsh conditions such as high salinity, extreme temperatures, and acidic or alkaline environments, produce enzymes naturally adapted to function under these conditions. This unique adaptability makes them highly desirable for industrial processes requiring robust and efficient biocatalysts. These biocatalysts reduce reliance on harsh chemicals and energy-intensive processes, contributing to greener industrial operations. This review underscores the power of metagenomics in bypassing the need to culture large libraries of extremophiles in the lab. High-throughput sequencing and bioinformatics enable the identification of novel GH-encoding genes directly from environmental DNA. While metagenomic mining has yielded promising results, challenges such as the expression of extremophile-derived genes in mesophilic hosts, low activity yields, and scalability remain. Advances in synthetic biology and protein engineering could address these bottlenecks, enabling more efficient utilization of GHs. Additionally, integrating machine learning for predictive functional annotation may accelerate the identification of high-value candidates.
Crayfish plague, caused by Aphanomyces astaci (Aa), is an infectious disease invasive in Europe, where its rapid spread has resulted in sharp declines of native crayfish species. Monitoring currently relies on a highly sensitive, but costly and time-consuming qPCR approach. Here, we designed a simplified, rapid and cost-efficient molecular assay for on-site detection of Aa. The novel rapid assay employs a combination of isothermal recombinase polymerase amplification and CRISPR-Cas12a-based detection that can be coupled with fluorescence or lateral flow visualisation. We demonstrate that the novel assay can detect A. astaci from tissue and environmental DNA with higher sensitivity than the available qPCR assay and readily distinguishes Aa from its non-pathogenic sister taxon A. fennicus. We tested two genomic marker sites for Aa that discriminate closely related oomycetes and incorporate field-deployable lateral flow and fluorescence readouts. Our work will make crayfish plague monitoring broadly accessible to practitioners and non-academic stakeholders as a tool to curb further Aa-driven loss of Europe's imperilled freshwater crustaceans and strengthen preparedness against future incursions of the pathogen in other regions.
Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.
The effect of environmental pollution on DNA adducts in humans was analysed in a highly industrialized area of Poland. Coded samples of white blood cell DNA were analysed by 32P-postlabelling and immunoassay from three populations: coke workers, exposed occupationally to high levels of polycyclic aromatic hydrocarbons (PAHs); residents of the towns around cokeries (local controls); and residents from rural Poland (countryside controls). Local controls exhibited adduct levels and patterns similar to those of coke workers, while the levels in rural controls were 2-3 times lower. The results, based on coded samples and two different assays, suggest that environmental pollution is likely to contribute to the adduct levels in local controls. Furthermore, the results show that the levels of aromatic adducts in white blood cell DNA do not linearily relate to ambient air levels of PAHs but other sources such as food may be important contributors.
The chromosome number and DNA content in Euglena gracilis cell have been shown by the number of investigators to vary essentially under the influence of some environmental factors (low phosphate and acetate concentrations, density of culture, temperature, light/dark regime, streptomycin treatment). Variability in the nuclear DNA quantity is supposed to be an important peculiarity of the structure and functional activity of the genome of Euglena gracilis.