Biology subjects

Gygax, D.

Publications and source records attributed to Gygax, D..

6 recordsLinked to original sources

bioRxiv2026

Monitoring terrestrial vertebrates with airborne DNA in the Luangwa Valley, Zambia

Vertebrates play vital roles in maintaining ecosystem processes and services and serve as valuable indicators of environmental health, making them an important target for monitoring and conservation efforts. Within the environmental DNA (eDNA) toolbox, airborne environmental DNA has recently emerged as a novel approach for vertebrate monitoring. In this study, we evaluated on-site airborne eDNA for terrestrial vertebrate monitoring in the Luangwa Valley savanna in Zambia, which represents a major biodiversity stronghold of largely intact wilderness and with high levels of vertebrate diversity and endemism. Six air samplers were deployed over four days alongside camera traps for validation, and samples were processed using a mobile molecular laboratory. In total, 120 terrestrial vertebrate taxa were detected with airborne eDNA, including 16 of the 17 taxa recorded by camera traps, demonstrating high sensitivity. Notably, 72.5% of taxa were detected on the first day, and a single sampler recovered 61.7% of all taxa; the taxonomic richness incrementally increased with extended sampling efforts, but the magnitude of these increases declined progressively. The detected taxa spanned the four terrestrial vertebrate classes and encompassed a wide range of ecological traits. These results show that airborne eDNA can quickly recover a substantial and representative fraction of local vertebrate diversity within a short sampling window, while extended sampling can improve detection of less common taxa. Despite existing limitations, our findings support the use of airborne eDNA as an efficient and scalable complementary tool for community-level biodiversity assessments in terrestrial ecosystems such as Zambezian savannas.

ecology↗

bioRxiv2025

Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems

Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens typically requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data, and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites, and used environmental DNA (eDNA) to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/674394v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1a006f2org.highwire.dtl.DTLVardef@12824c2org.highwire.dtl.DTLVardef@8554bdorg.highwire.dtl.DTLVardef@17e800e_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem resistance. We here evaluate the use of long-read nanopore sequencing to investigate carbapenem resistance dynamics and the role of plasmid transfers and environmental reservoirs in the hospital setting. Over 13 months, routine clinical diagnostics identified recurring isolates of carbapenem-resistant Citrobacter species carrying Klebsiella pneumoniae carbapenemases (KPC) and/or OXA-48-like carbapenemases from patient screening and hospital drain samples. While routine diagnostic approaches provided limited insights into the carbapenem resistance dynamics, we show that near-complete de novo assembly of chromosomes and plasmids by long-read nanopore sequencing allowed for high-resolution strain identification, plasmid profiling, and antibiotic resistance gene detection. Notably, genomically nearly indistinguishable Citrobacter freundii of the high-risk sequence type ST91 genomes were recovered from screening samples collected in the same hospital room one year apart. We further provide evidence of a KPC-2 encoding IncN plasmid that is likely to have spread across bacterial species and between patient and drain isolates, which emphasizes the role of contaminated drains in the persistence and dissemination of resistances within the hospital environment. Overall, this study demonstrates the value of long-read nanopore sequencing for uncovering the complex dynamics of carbapenem resistance spread and persistence in the hospital setting, and its potential implications for Infection Prevention and Control. Impact statementThis study demonstrates how long-read nanopore sequencing can resolve the complex dynamics of plasmid-mediated antimicrobial resistance in clinical and environmental samples within the hospital setting. By linking patient- and drain-derived isolates through near-complete de novo assemblies, we reveal hidden reservoirs and dynamics behind the persistence of cabapenem resistance over extended time periods. This work shows how long-read sequencing approaches can uncover resistance dynamics that are missed using standard diagnostic methods, with implications for infection control and surveillance. Data SummaryThe study sequences are available at the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA1297122. The raw sequence read data is available at NCBI sequence read archive (SRA (https://www.ncbi.nlm.nih.gov/sra)) under accession numbers SRR34727947-59. The chromosomal assemblies of all ST91 strains are available at NCBI GenBank under the Biosample accession numbers SAMN50449475-80. All other supporting data are provided in the article and supplementary data files.

microbiology↗

bioRxiv2025

Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries

Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers a cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection of rare, cryptic, and elusive species from environmental samples. However, limited access to genomic technologies restricts the application of eDNA metabarcoding in highly biodiverse remote regions and low- and middle-income countries (LMICs). Here, we directly compared the latest portable nanopore sequencing methods with established Illumina sequencing for vertebrate eDNA metabarcoding of Zambian water samples. Our results show that due to recent improvements in sequencing chemistry and optimized basecalling, nanopore sequencing data can recapitulate or even surpass established protocols, demonstrating the feasibility of in situ biodiversity assessments. eDNA- and camera trap-based species detections had minimal overlap in species detections, suggesting a complementary rather than substituting application of these biodiversity monitoring technologies. We finally demonstrate that our entire eDNA workflow can be successfully implemented in a mobile laboratory under remote field conditions by completing all steps--from sample collection to data analysis--within the Luambe National Park in Zambia. This approach has important implications for capacity building in LMICs and for overcoming limitations associated with sample export.

molecular biology↗

bioRxiv2024

Sex-biased migration and demographic history of the big European firefly Lampyris noctiluca

Differential dispersion between the sexes can impact population structure and connectivity between populations, which in turn, can have an effect on the evolvability capability of a species. Here we explored the demographic history of the big European firefly, Lampyris noctiluca, which exhibits female neoteny. L. noctiluca distribution extends throughout Europe, but nothing is known on how its colonization processes. To investigate this, we produced the first Lampyris genome (653Mb), including an IsoSeq annotation and the identification of the X chromosome. We collected 115 individuals from six populations of L. noctiluca (Finland to Italy) and generated whole genome re-sequencing for each individual. We inferred several population expansions and bottlenecks throughout the Pleistocene that correlate with glaciation events. Surprisingly, we uncovered strong population structure and low gene-flow. We reject a stepwise, south to north, colonization history scenario and instead uncovered a complex demographic history with a putative eastern European origin. Analyzing the evolutionary history of the mitochondrial genome as well as X-linked and autosomal loci, we found evidence of a maternal colonialization of Germany, putatively from a western European population, followed by male-only migration from south of the Alps (Italy). Overall, investigating the demographic history and colonization patterns of a species should form part of an integrative approach of biodiversity research. Our results provide evidence of sex-biased migration which is important to consider for demographic, biogeographic and species delimitation studies.

evolutionary biology↗

bioRxiv2017

Synthetic single domain antibodies for the conformational trapping of membrane proteins

Single domain antibodies called nanobodies are excellent affinity reagents for membrane proteins. However, their generation relies on immunizations, which is only amenable to robust proteins and impedes selections in the presence of non-covalent or toxic ligands. To overcome these key limitations, we developed a novel in vitro selection platform, which builds on synthetic nanobodies called sybodies. Inspired by the shape diversity of natural nanobodies, three sybody libraries exhibiting different randomized surface shapes were engineered for high thermal stability. Using ribosome display, exceptionally large libraries were pre-enriched against membrane protein targets and subsequently funneled into a robust phage display process, thereby reducing selection bias. We successfully generated conformation-selective, high affinity sybodies against the human glycine transporter GlyT1, the human equilibrative nucleotide transporter ENT1 and a bacterial ABC transporter. Our platform builds exclusively on commercially available reagents and enables non-specialized labs to generate conformation-specific binders against previously intractable protein targets.

bioengineering↗