Biology subjects

Uetz, P.

Publications and source records attributed to Uetz, P..

3 recordsLinked to original sources

bioRxiv2026

Biodiversity material remains where capacity and governance are strong, but taxonomic resources concentrate with geopolitical power

AimBiodiversity-rich regions often lack the scientific infrastructure needed to document and curate their own biodiversity, creating inequalities in access to taxonomic reference material. We investigated how biological, institutional, and geopolitical factors shape the retention, extraction, and appropriation of reptile holotypes, the name-bearing specimens upon which species descriptions are based. LocationGlobal. TaxonReptiles. MethodsWe compiled a historical dataset of reptile holotype origins and destinations spanning 1758-2024 to reconstruct long-term patterns of retention and international specimen flows. We then quantified species-level holotype retention, holotype flows between country pairs, and country-level patterns of retention, appropriation, and network centrality for the period 1990-2024, and used generalised linear mixed models to assess the biological, institutional, and geopolitical determinants of these contemporary circulation processes. ResultsAlthough nearly 90% of reptile species described originated in the Global South, less than a quarter of their holotypes remain housed there. Historically, exported holotypes consistently outnumbered retained holotypes on a decadal basis until the early twenty-first century. Retention was promoted by local scientific capacity, institutional infrastructure, collector involvement in species descriptions, and environmental governance. In contrast, extraction was concentrated in highly endemic regions with limited scientific infrastructure and was associated with taxonomic revisions, socioeconomic interest, and disparities in political stability and colonial history. Appropriation of foreign holotypes was greatest in countries with high research investment, strong environmental governance, and historical geopolitical influence. Main conclusionsGlobal patterns of holotype circulation reflect a persistent geography of scientific inequality. The distribution of taxonomic reference material emerges from the interaction of retention, extraction, and appropriation processes, linking local biodiversity discovery to uneven global scientific capacity. Reducing these inequalities will require investments in taxonomic expertise, institutional infrastructure, and governance frameworks that promote more equitable stewardship of biodiversity knowledge and its material foundations.

ecology↗

bioRxiv2024

The protein interactome of Escherichia coli carbohydrate metabolism.

Carbohydrate metabolism is strictly regulated by multiple mechanisms to meet cellular needs (i.e. energy production). Several mechanisms modulate the amount and activity of metabolic enzymes. Here, we investigate how carbohydrate metabolism (CHM) in E. coli is regulated by their interaction properties with other proteins and their quantities. We computationally analyze 378 protein-enzyme interactions (PEIs) potentially involved in carbohydrate metabolism. We identified 20 enzymes and 19 interactors that occur at stoichiometries that are highly likely to affect CHM and 174 interactions that are possibly conserved across thousands of bacteria. These PPIs are predicted to be of global importance, including pathogens. Author summaryIn systems biology, "big" data are used to reconstruct biological networks which are then investigated in detail to uncover their functional dynamics. Understanding functional dynamics finally helps in identifying biomarkers in the big networks. We apply this concept to the biological network which is a crosstalk of protein-protein interaction network and carbohydrate metabolic pathway in Escherichia coli K-12. We investigate if proteins regulate enzymes when they bind them and we predict that protein-enzyme interactions (PEIs) regulate carbohydrate metabolism in E. coli.

systems biology↗

bioRxiv2021

YhcB (DUF1043), a novel cell division protein conserved across gamma-proteobacteria

YhcB, an uncharacterized protein conserved across gamma-proteobacteria, is composed predominantly of a single Domain of Unknown Function (DUF 1043) with an N-terminal transmembrane -helix. Here, we show that E. coli YhcB is a conditionally essential protein that interacts with the proteins of the cell divisome (e.g., FtsI, FtsQ) and elongasome (e.g., RodZ, RodA). We found 7 interactions of YhcB that are conserved in Yersinia pestis and/or Vibrio cholerae. Furthermore, we identified several point mutations that abolished interactions of YhcB with FtsI and RodZ. The yhcB knock-out strain does not grow at 45{degrees}C and is hypersensitive to cell-wall acting antibiotics even in stationary phase. The deletion of yhcB leads to filamentation, abnormal FtsZ ring formation, and aberrant septa development. The 2.8 [A] crystal structure for the cytosolic domain from Haemophilus ducreyi YhcB shows a unique tetrameric -helical coiled-coil structure that combines parallel and anti-parallel coiled-coil intersubunit interactions. This structure is likely to organize interprotein oligomeric interactions on the inner surface of the cytoplasmic membrane, possibly involved in regulation of cell division and/or envelope biogenesis/integrity in proteobacteria. In summary, YhcB is a conserved and conditionally essential protein that is predicted to play a role in cell division and consequently or in addition affects envelope biogenesis. ImportanceOnly 0.8 % of the protein annotations in the UniProt are based on experimental evidence and thus, functional characterization of unknown proteins remains a rate-limiting step in molecular biology. Herein, the functional properties of YhcB (DUF1043) were investigated using an integrated approach combining X-ray crystallography with genetics and molecular biology. YhcB is a conserved protein that appears to be needed for the transition from exponential to stationary growth and is involved in cell division and/or envelope biogenesis/integrity. This study will serve as a starting point for future studies on this protein family and on how cells transit from exponential to stationary survival.

microbiology↗