Biology subjects

Riedel-Kruse, I.

Publications and source records attributed to Riedel-Kruse, I..

5 recordsLinked to original sources

bioRxiv2026

Methanogenic Ethanol Production from Acetate

Biological ethanol production is important for the circular carbon economy and makes up 73% of the U.S. biological fuels market. Previously, we produced ethanol by reversing methanogenesis and capturing methane by cloning methyl-coenzyme M reductase (Mcr) from an unculturable population of anaerobic methanotrophic archaea; this process was predicated on the generation of the intermediate acetate and its conversion by the methanogenic host to ethanol. Moreover, methanogens are generally thought to be detrimental for converting acetate to ethanol and are usually intentionally inhibited. Here, we demonstrate that direct growth on acetate as the sole carbon and energy source by the methanogen Methanosarcina acetivorans C2A results in 40% of the metabolized acetate becoming ethanol and that there is 430% more ethanol produced, compared to growth on methane via Mcr. In addition, we found growth on methanol results primarily in methane generation and low levels of ethanol. Therefore, acetate may be readily converted by the methanogen M. acetivorans to ethanol at high yields.

microbiology↗

bioRxiv2026

Engineering Methyl-Coenzyme M Reductase for Enhanced Methane and Carbon Dioxide Capture through Biofilm Growth

Methane is a potent greenhouse gas, nearly half of which is consumed anaerobically by anaerobic methanotrophic archaea (ANME) through methyl-coenzyme M reductase (Mcr). However, ANME cannot be grown as pure cultures, and obtaining active ANME Mcr in vitro remains extremely challenging, preventing previous efforts to engineer this key enzyme. Here, we used directed evolution in the methanogen Methanosarcina acetivorans to enhance ANME-1 Mcr (McrANME-1) activity for methane and carbon dioxide capture by selecting McrANME-1 variants with improved growth during methane-dependent cultivation. As a result, we discovered two beneficial substitutions in the catalytic -subunit of McrANME-1, S60P and I154V, that increased biofilm growth as well as acetate production and methane capture. AlphaFold structural predictions suggest possible mechanistic explanations for these beneficial substitutions. These findings demonstrate that Mcr can be engineered to enhance methane and carbon dioxide capture, establishing a foundation for biological greenhouse gas mitigation and carbon utilization technologies.

Synthetic Biology↗

bioRxiv2023

Flagellar beat state switching in microswimmers to select between positive and negative phototaxis

Microorganisms have evolved various sensor-actuator circuits to respond to environmental stimuli. However, how a given circuit can select efficiently between positive vs. negative taxis under desired vs. undesired stimuli is poorly understood. Here, we investigate how the cellular mechanism by which the chiral microswimmer Euglena gracilis can select between positive vs. negative phototaxis under low vs. high light intensity conditions, respectively. We propose three general selection mechanisms for microswimmer phototaxis. A generic biophysical model demonstrates the effectiveness of all mechanisms, but which varies for each depending on specific conditions. Experiments reveal that only a photoresponse in-version mechanism is compatible with E. gracilis phototaxis. Specifically, a light-intensity dependent transition on the sub-second time scale between two flagellar beat states responsible for forward swimming vs. sideway turning ultimately generates positive phototaxis at low light intensity via a run-and-tumble strategy and negative phototaxis at high light intensity via a helical klinotaxis strategy. More generally, a picture emerges where a variety of E. gracilis behaviors over a wide range of light intensities as reported in the literature can be explained by the coordinated switching between just these two flagellar beating states over time. These results provide design principles for simple two-state switching mechanisms in natural and synthetic microswimmers to operate under both noisy and saturated stimulus conditions. LAY ABSTRACTOur experimental and theoretical results explain how the single cell Euglena gracilis achieves both positive and negative phototaxis. Our insights are then able to synthesise a larger number of previously described observations on E. gracilis photoresponses and photobehaviors due to a concise two-state model of flagellar beating. These insight will likely inform the behaviors of other natural microswimmers as well as the design of synthetic ones.

biophysics↗

bioRxiv2017

A Model For Adult Organ Resizing Demonstrates Stem Cell Scaling Through A Tunable Commitment Rate

Many adult organs grow or shrink to accommodate different physiological demands. Often, as total cell number changes, stem cell number changes proportionally in a phenomenon called stem cell scaling. The cellular behaviors that give rise to scaling are unknown. Here we study two complementary theoretical models of the adult Drosophila midgut, a stem cell-based organ with known resizing dynamics. First, we derive a differential equations model of midgut resizing and show that the in vivo kinetics of growth can be recapitulated if the rate of fate commitment depends on the tissues stem cell proportion. Second, we develop a twodimensional simulation of the midgut and find that proportion-dependent commitment rate and stem cell scaling can arise phenomenologically from the stem cells exploration of physical tissue space during its lifetime. Together, these models provide a biophysical understanding of how stem cell scaling is maintained during organ growth and shrinkage.

systems biology↗

bioRxiv2017

Interactive Biology Cloud Lab Enables Authentic Inquiry-Based Science Learning At MOOC Scale

The Next Generation Science Standards (NGSS) and other national frameworks are calling for much more sophisticated approaches to STEM education, centered around the integration of complex experimentation (including real labs, not just simulations), data collection and analysis, modeling, and data-driven argumentation, i.e., students can behave like real scientists. How to implement such complex approaches in scalable ways is an unsolved challenge - both for presential and distance education. Here we report on the iterative design and large-scale deployment of an open online course with a \"biology cloud experimentation lab\" (using living cells) that engaged remote learners (> 300 students) in the scientific practices of experimentation, modeling and data analysis to investigate the phototaxis of a microorganism. We demonstrate (1) the robustness and scalability of the cloud lab technology (> 2, 300 experiments run), (2) the design principles and synergistic integration of multiple UI and learning activities and suitable data formats to facilitate NGSS-aligned science activities, and (3) design features that leverages the natural variability of real biology experiments to instigate authentic inquiry. This platform and course content are now suited for large-scale adaptation in formal K-16 education; and we provide recommendations for inquiry-based science learning in general.

scientific communication and education↗