Biology subjects

Thaler, D. S.

Publications and source records attributed to Thaler, D. S..

3 recordsLinked to original sources

bioRxiv2026

Biological signatures of history: Examination of composite biomes and Y chromosome analysis from da Vinci-associated cultural artifacts

Cultural heritage objects can accumulate DNA from materials, environments, and repeated human contact, but biomolecular profiling of such items is constrained by nondestructive sampling requirements, ultra-low biomass, and high contamination risk. Here we present a minimally invasive workflow that integrates gentle swab collection, low- input whole-metagenome sequencing, taxonomic profiling, and Y-chromosome analyses to recover "biological signatures of history" from Renaissance-era artwork and archival correspondence associated with ancestors of Leonardo da Vinci. Across artifacts, we recovered heterogeneous mixtures of microbial and eukaryotic DNA (including bacteria, fungi, plants, and viruses) consistent with composite "biomes" that reflect differences in substrate, storage, conservation treatments, and handling. Multivariate comparisons show reproducible sample-to-sample separations. In parallel, we assessed human Y-chromosome signal using a panel of [~]90,000 phylogenetically informative markers and partial Y-STR profiling where feasible. Across multiple independent swabs from Leonardo da Vinci-associated items, the obtained Y chromosome marker data suggested assignments withing the broader E1b1/E1b1b clade. However, the control samples also indicate mixed contributions consistent with modern handling and other sources. Together, these data demonstrate the feasibility as well as limitations of combining metagenomics and human DNA marker analysis for cultural heritage science, providing a baseline workflow for future conservation science studies and hypothesis-driven investigations of provenance, authentication and handling history.

genomics↗

bioRxiv2021

Systematic exploration of Escherichia coli phage-host interactions with the BASEL phage collection

Bacteriophages, the viruses infecting bacteria, hold great potential for the treatment of multidrug-resistant bacterial infections and other applications due to their unparalleled diversity and recent breakthroughs in their genetic engineering. However, fundamental knowledge of molecular mechanisms underlying phage-host interactions is mostly confined to a few traditional model systems and did not keep pace with the recent massive expansion of the field. The true potential of molecular biology encoded by these viruses has therefore remained largely untapped, and phages for therapy or other applications are often still selected empirically. We therefore sought to promote a systematic exploration of phage-host interactions by composing a well-assorted library of 66 newly isolated phages infecting the model organism Escherichia coli that we share with the community as the BASEL collection (BActeriophage SElection for your Laboratory). This collection is largely representative of natural E. coli phage diversity and was intensively characterized phenotypically and genomically alongside ten well-studied traditional model phages. We experimentally determined essential host receptors of all phages, quantified their sensitivity to eleven defense systems across different layers of bacterial immunity, and matched these results to the phages host range across a panel of pathogenic enterobacterial strains. Our results reveal clear patterns in the distribution of phage phenotypes and genomic features that highlight systematic differences in the potency of different immunity systems and point towards the molecular basis of receptor specificity in several phage groups. Strong trade-offs were detected between fitness traits like broad host recognition and resistance to bacterial immunity that might drive the divergent adaptation of different phage groups to specific niches. We envision that the BASEL collection will inspire future work exploring the biology of bacteriophages and their hosts by facilitating the discovery of underlying molecular mechanisms as the basis for an effective translation into biotechnology or therapeutic applications.

microbiology↗

bioRxiv2018

Why Should Mitochondria Define Species?

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes--drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

evolutionary biology↗