bioRxiv Science⌕ Search

Biology subjects

Huss, M.

Publications and source records attributed to Huss, M..

5 recordsLinked to original sources

DNA extracted from boiled archival fish bones yields high quality whole genome sequencing data

Archival samples provide a unique source of DNA, offering the potential to extend the temporal scale of genetic studies by decades to centuries. Fish hard structures, such as otoliths and scales, serve as records for fish collected during fisheries monitoring across a large spatiotemporal scale. Operculum bones are a type of fish hard structure that, although less commonly collected, have been utilized in genetic studies. However, the usefulness of archived operculum bones to provide high quality whole genome sequence information has not been thoroughly evaluated. Here, we applied a commercially available extraction protocol, with minor adjustments, to isolate genomic DNA from operculum bones of Eurasian perch collected up to 47 years ago, followed by standard short-read whole genome sequencing. By comparing the metrics of DNA and whole genome sequencing data of bones with contemporary muscle samples, we demonstrate that the application of a simple extraction protocol on boiled archival fish operculum bones yields high quality genomic information that is comparable to fresh tissue, highlighting the role of archival operculum bones as an overlooked repository of valuable genomic information.

molecular biology↗

Etomidate as an Effective Alternative Method of Euthanizing Adult Zebrafish (Danio Rerio)

We assessed the efficacy of etomidate in euthanizing adult zebrafish. The aims of this study were to investigate: 1) the efficacy of 2 concentrations and 2) the effects at 2 densities. Aim 1-Fish (n=10 fish/group) were immersed in either 6 mg/L (Eto-6) or 10 mg/L (Eto-10) etomidate. Aim 2- either 5 or 10 fish were immersed in Eto-6. Tanks were video recorded and scored by two blinded observers. The parameters monitored included: 1) loss of righting reflex (LORR); 2) undulation cessation; 3) cessation of operculation (COO); and 4) loss of startle reflex. After the 30 minute immersion, fish were transferred to recovery tanks and monitored once every 5 minutes for 60 minutes. Results - Aim 1, the time to undulation cessation, COO, and loss of startle reflex was significantly shorter in the Eto-10 group and there was no difference in LORR. Aim 2, the time to LORR and undulation cessation was significantly shorter in the 5 fish/L group and there was no significant difference in time to COO or loss of startle reflex. No aversive behaviors were noted and fish in all groups were effectively euthanized by 30 minutes. This study indicates that Eto-6 or Eto-10 effectively euthanizes adult zebrafish.

animal behavior and cognition↗

Multi-decadal warming alters predator's effect on prey community composition

Predator responses to warming can occur via phenotypic plasticity and evolutionary adaptation, resulting in changes in their prey communities. However, we lack evidence of how warming-induced evolutionary changes in predators can influence the food web. Here, we ask whether fish subject to long-term warming across multiple generations differ in their impacts on prey communities compared to their nearby conspecifics experiencing a natural thermal regime. We carried out a common garden mesocosm experiment with larval perch (Perca fluviatilis), originating from one heated or one reference coastal environment, feeding on zooplankton communities under a gradient of experimental temperatures. We found that fish thermal origin influenced the zooplankton communities, and differently so depending on the experimental temperature. In presence of fish of heated origin, there were less zooplankton and also fewer individuals of large size, except for at intermediate experimental temperatures. Our findings show that differences between fish populations, potentially representing adaptation to local thermal environment, caused by multi-generational warming can cascade down via trophic interactions to also affect their zooplankton prey communities. Considering climate warming, our results suggest that rapid evolution in predators might have indirect cross-generational ecological consequences propagating through food webs.

ecology↗

Size-based ecological interactions drive food web responses to climate warming

Predicting the impacts of climate change on animal populations and communities requires understanding of feedbacks between direct physiological responses and indirect effects via ecological interactions. Food-dependent body growth and within-species size variation have major effects on dynamics of populations and communities through feedbacks between individual performance and population size structure. Moreover, evidence suggests a link between temperature and population size structure, but we lack an understanding of how this is mediated by species interactions when life history processes are food-dependent. Here, we use a dynamic stage-structured biomass model with food-, size- and temperature-dependent life history processes to assess how temperature affects coexistence, stability and size structure in a tri-trophic food chain. We show that predator biomass densities decline with warming either gradually or in the form of collapses, depending on which consumer life stage they predominantly feed on. Collapses occur when warming destabilizes the community and induces alternative stable states via Allee effects, which emerge when predators promote their own food source through predation. By contrast, warming at low temperatures stabilizes the community as limit cycles turn to fixed point dynamics, unless predators feed only on juveniles. Elevated costs of being large in warmer environments accelerate the decline in predator persistence and mean body size of the community. These results suggest that predator persistence in warmer climates may be lower than previously acknowledged when accounting for size- and food-dependence of life history processes, and that interactions within and between species can mediate the effects of warming on food web stability.\n\nSignificanceClimate warming is altering the dynamics and structure of aquatic ecosystems worldwide. Predicting food web reorganization under rising temperatures requires an understanding of physiological responses and ecological interactions of organisms, both of which depend on body size. We show that size variation within species, food-dependent growth and ecological interactions critically affect how food chains respond to warming. Specifically, warming can stabilize or destabilize food chains and expose predators to increased risk of sudden collapses, resulting in alternative stable food web states. Increasing temperatures can cause abrupt reductions in mean community body size, primarily due to loss of top predators. The potential loss of biodiversity and shifts in ecosystem stability are among the major challenges caused by a warming climate.

ecology↗

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during trophectoderm and inner cell mass specification

The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and an outer functional epithelium called trophectoderm (TE). The lineage specific transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4) by inhibiting OCT4 from promoting its own expression. However its downstream network in the developing early embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify components of the CDX2-regulated network in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells, derived from the TE. In addition, we examined the dynamics of gene expression changes using an inducible CDX2 embryonic stem (ES) cell system, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we were able to identify novel regulatory elements that are likely to repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

cell biology↗