Biology subjects

Roth, M. S.

Publications and source records attributed to Roth, M. S..

4 recordsLinked to original sources

bioRxiv2026

Behavior of downstream swimming brown trout in accelerating and high flow velocity - Movement matters

Studies on active and sedated fish passing through turbines and pumps show different mortality and injury rates for both cases. Consequently, fish behavior appears to play a substantial role in these outcomes. However, direct behavioral observations in hydraulic machines using quantitative parameters to draw conclusions about the underlying mechanisms are hardly possible and remain understudied. In this study, we examined the behavior of adult brown trout (Salmo trutta) in an experimental flume under hydraulic conditions characterized by strong flow acceleration and high velocities typical of turbine and pump intakes. Fish movement behavior was analyzed based on a quantitative approach to enable the analysis of swimming behavior even in flow velocities exceeding the sprint swimming speed of fish. The application of Hidden Markov Models (HMM) to analyze activity states and movement modes of fish from video tracking data demonstrated significant effects of the spatial velocity gradient (SVG) and flow velocity on fish behavior. Notably, SVG emerged as the primary trigger for avoidance reactions when exceeding a threshold of [Formula]. Fish exhibited distinct movement patterns under dark and daylight conditions, with more avoidance reactions in darkness. Whereas a considerable proportion of fish in daylight increased their swimming activity in the zone were flow velocity exceeded sprint swimming speed, in dark conditions no activity peak occurred in the same zone. The results illustrate how hydraulic conditions and lighting influence fish behavior. Integrating the behavioral rules identified in this study into numerical mortality-risk models could substantially improve their predictive accuracy. Thus, the findings allow for the development of less fish harming engineering solutions for hydropower facilities and pumping stations.

animal behavior and cognition↗

bioRxiv2025

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae

Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central metabolic regulator in eukaryotes that integrates carbon and nitrogen to maintain homeostasis and promote growth and development through protein synthesis. While TOR regulatory mechanisms of amino acid accumulation are well known in yeast and mammals, they remain unknown in photosynthetic organisms. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler model system for understanding TOR function. Multiomics experiments showed that TOR inhibition leads to an increase in amino acid levels independent of hexokinase-mediated glucose signaling. We observed upregulation of selective amino acid biosynthesis pathways at the transcript and protein levels as potential mechanisms driving the increase in amino acids. Transcriptomics and proteomics experiments identified a basic helix-loop-helix (bHLH) transcription factor with rapid upregulation during TOR inhibition. DAP-seq analysis demonstrated that bHLH can bind directly to the promoters of amino acid biosynthesis genes, potentially regulating their transcription in response to TOR inhibition. We found high conservation of the bHLH-binding motif in the genomes of other green algae and plants, suggesting a conserved regulatory mechanism for amino acid biosynthesis across Viridiplantae. Phosphoproteomics experiments also revealed novel conserved targets that are not currently recognized as part of the TOR pathway. Altogether, our findings elucidate the transcriptional regulation of amino acid metabolism and explain how TOR regulates nitrogen metabolism to support growth and development in photosynthetic organisms. Significance StatementCarbon and nitrogen metabolism play key roles in enhancing plant yield and reducing fertilizer use. Thus, improving nitrogen utilization can significantly boost crop productivity and algal biotechnology. From yeast to plants to mammals, the protein target of rapamycin (TOR) kinase is an essential metabolic regulator. Here, we developed the unicellular green alga Chromochloris zofingiensis as a simpler system to study conserved mechanisms in TOR signaling. Using a multiomics approach, we showed transcriptional regulation of amino acid accumulation upon TOR inhibition and identified a transcription factor with evolutionarily conserved DNA binding sites in nitrogen metabolism genes. We also discovered novel conserved targets of TOR. Our study demonstrates the role of TOR in regulating nitrogen metabolism to support growth and development in photosynthetic organisms.

plant biology↗

bioRxiv2024

An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation

Microalgae are promising sources to sustainably meet the global needs for energy and products. Algae grow under different trophic conditions, where nutritional status regulates biosynthetic pathways, energy production, and growth. The green alga Chromochloris zofingiensis has strong economic potential because it co-produces biofuel precursors and the high-value antioxidant astaxanthin while accumulating biomass when grown mixotrophically. As an emerging reference alga for photosynthesis, metabolism, and bioproduction, C. zofingiensis needs a defined, optimized medium to standardize experiments during fast growth. Because the interplay of glucose consumption (+Glc) and mineral deficiency influences photosynthesis, growth, and the production of lipids and astaxanthin, we designed a replete nutrient medium tailored to the C. zofingiensis cellular ionome. We combined inductively coupled plasma mass spectrometry (ICP-MS) and +Glc growth curves to determine a medium that is nutrient replete for at least 5 days of +Glc logarithmic growth. We found that there are high nutritional needs for phosphorus and sulfur during mixotrophy. Iron was the only element measured for which the cellular concentration correlated with exogenous concentration and was iteratively adjusted until the internal ionome was consistent through the logarithmic growth phase. This Chromochloris-Optimized Ratio of Elements (CORE) medium supports fast growth and high biomass without causing excess nutrient toxicity. This defined, nutrient-replete standard is important for future C. zofingiensis investigations and can be adapted for other species to support high biomass. The method used to develop CORE medium shows how ionomics informs replicable media design and may be applied in industrial settings to inform cost-effective biofuel production. Significance StatementStudying how carbon sources and mineral nutrients interplay to regulate algal metabolism can be exploited to discover and control pathways in photosynthesis and biofuel production. Here we design a medium from the cellular ionome of Chromochloris zofingiensis, a powerful algal model for photosynthesis, metabolism, and bioproducts, to provide a defined, replete standard for mixotrophic and heterotrophic growth of green algae. These media design principles show how accounting for increased nutritional demands based on carbon substrate can ensure experimental replicability when probing diverse algal metabolisms.

plant biology↗

bioRxiv2023

Iron rescues glucose-mediated photosynthesis repression during lipid accumulation in the green alga Chromochloris zofingiensis

Energy status and nutrients regulate photosynthetic protein expression. The unicellular green alga Chromochloris zofingiensis switches off photosynthesis in the presence of exogenous glucose (+Glc) in a process that depends on hexokinase (HXK1). Here, we show that this response requires that cells lack sufficient iron (-Fe). Cells grown in -Fe+Glc accumulate triacylglycerol (TAG) while losing photosynthesis and thylakoid membranes. However, cells with an iron supplement (+Fe+Glc) maintain photosynthesis and thylakoids while still accumulating TAG. Proteomic analysis shows that known photosynthetic proteins are most depleted in heterotrophy, alongside hundreds of uncharacterized, conserved proteins. Photosynthesis repression is associated with enzyme and transporter regulation that redirects iron resources to (a) respiratory instead of photosynthetic complexes and (b) a ferredoxin-dependent desaturase pathway supporting TAG accumulation rather than thylakoid lipid synthesis. Combining insights from diverse organisms from green algae to vascular plants, we show how iron and trophic constraints on metabolism aid gene discovery for photosynthesis and biofuel production.

plant biology↗