Biology subjects

Stoffel, C.

Publications and source records attributed to Stoffel, C..

5 recordsLinked to original sources

bioRxiv2026

Workflow for multiplex microsatellite panel development and sample preparation for robust amplicon sequencing of low-template and degraded DNA: validation for non-invasive genotyping in three large carnivore species

High-throughput amplicon sequencing has transformed microsatellite (STR) genotyping by overcoming many of the limitations of fragment-length analysis, enabling more accurate, cost-effective, and standardized genotyping. Yet, protocols specifically designed for high-throughput sequencing (HTS)-based STR genotyping from low-template and degraded DNA remain scarce, despite the prevalence of these challenging sample types in ecological and conservation contexts. We present a methodology for the de novo development of robust STR multiplex panels together with a laboratory protocol for efficient and reliable STR genotyping by sequencing with low quantity and quality DNA samples. The protocol comprises (i) an automated bioinformatic pipeline to design large sets of short tetranucleotide markers optimized for multiplex amplicon sequencing of degraded and low-template DNA; (ii) guidelines for efficient in vitro optimization of multiplex amplification using directly low quantity/quality template DNA; and (iii) a library preparation procedure that improves detection of low-level allele signal while enabling quality assessment of STR amplicon sequencing under limiting DNA conditions. We demonstrate the approach by developing and validating STR panels for non-invasive genotyping of three large carnivore species: a 44-plex for the grey wolf (Canis lupus), a 41-plex for the Eurasian lynx (Lynx lynx), and a 30-plex for the brown bear (Ursus arctos). Multiplex performance was high, with [≥]91% of samples successfully genotyped at [≥]50% of loci (allele size range 28-110 bp across panels) and correctly assigned to known individuals, negligible levels of noise in the controls, and high discriminatory power (PIDsibs [≤]2.4 x 1e-12), also owing to sequence variation among same-length alleles at 15-50% of loci. The approach is broadly applicable to animal and plant species, a wide range of sample types, and large-scale analysis such as genetic monitoring. Our study reinforces the value of STR amplicon sequencing for ecological and conservation applications while highlighting the importance of marker design and laboratory workflows tailored to HTS-based genotyping for accurate and efficient implementation.

ecology↗

bioRxiv2025

Sustaining the cell energy in dynamic environments requires photosynthetic electron flows with diverse bandwidths

All living cells depend on the dynamic balance between their energy supply and demand to survive and thrive in dynamic environments. In extreme cases, like for photosynthetic organisms, their energy source, light, can fluctuate dramatically in intensity over timescales of seconds to hours. While various photosynthetic electron flows (EF) are crucial for maintaining bioenergetic homeostasis, how EFs are modulated to respond to dynamic energy intake remains unclear. Here, we show in the model green alga Chlamydomonas reinhardtii that each EF is best suited to a specific domain of energetic fluctuation periodicity for which it can support the cells energetic needs, which we term bandwidth. By systematically exposing cells to a range of light periodicities, we show that while cyclic EF has a large bandwidth, pseudo-cyclic EF (PCEF) can only sustain the cells energetic needs for fast light fluctuations, and that the interplay between the chloroplast and the mitochondria (CMEF) has a limited bandwidth. We further show that the bandwidths of PCEF and CMEF, specialized for dynamic lights, are related to their capacity to generate ATP and protect the photosynthetic apparatus. Finally, we show that in wild-type cells, the activity level of PCEF matches its bandwidth, and we propose that cells tune the relative activity of AEFs depending on the light fluctuation frequency. Our work opens an avenue of research to characterize the molecular mechanisms that can sustain phototrophic growth in complex and dynamic energetic landscapes. It further provides a generalizable framework for understanding the physiological importance of molecular mechanisms in a dynamic environment.

plant biology↗

bioRxiv2025

N-terminal region of PetD is essential for cytochrome b6f function and controls STT7 kinase activity via STT7-dependent feedback loop phosphorylation

The cytochrome b6f complex (b6f) links photosystem I (PSI) and photosystem II (PSII) in the photosynthetic electron transport chain and is distributed across appressed and non-appressed thylakoid membranes. The b6f also activates the state-transition 7 kinase (STT7), which phosphorylates light-harvesting complex proteins, triggering their migration to enable energy redistribution between PSII and PSI. STT7-dependent phosphorylation has also been observed at T4 in the N-terminal domain of the b6f subunit-IV (PetD), though its functional significance has remained unclear. To investigate its role, we generated several chloroplast mutants. The phosphomimic mutation PetD T4E - but not T4A - inhibited STT7 kinase activity, as indicated by the absence of STT7-dependent phosphorylation and a State 1-locked phenotype. This reveals a novel feedback mechanism regulating STT7-dependent phosphorylation. Deletion of the first five N-terminal amino acids similarly inhibited STT7 activity and additionally disrupted electron transfer, underscoring a crucial role of the PetD N-terminus in b6f function.

plant biology↗

bioRxiv2023

Algal CO2 capture is powered by alternative electron pathways of photosynthesis

On Earth, microalgae contribute to about half of global net photosynthesis. During photosynthesis, sunlight is converted into chemical energy (ATP and NADPH) used by metabolism to convert CO2 into biomass. Alternative electron pathways of photosynthesis have been proposed to generate additional ATP that is required for sustaining CO2 fixation, but the relative importance of each pathway remains elusive. Here, we dissect and quantify the contribution of cyclic, pseudo-cyclic and chloroplast to mitochondria electron flows for their ability to sustain net photosynthesis in the microalga Chlamydomonas reinhardtii. We show that each pathway has the potential to energize substantial CO2 fixation, can compensate each other, and that the additional energy requirement to fix CO2 is more than 3 times higher than previous estimations. We further show that all pathways have very different efficiencies at energizing CO2 fixation, with the chloroplast-mitochondria interaction being the most efficient, thus laying bioenergetic foundations for biotechnological improvement of CO2 capture.

plant biology↗

bioRxiv2018

Molecular evolution of juvenile hormone esterase-like proteins in a socially exchanged fluid

Socially exchanged fluids are a direct means for organisms to influence conspecifics. When orally feeding larval offspring via trophallaxis, Camponotus floridanus ant workers were shown to transfer Juvenile Hormone (JH), a key developmental regulator, as well as paralogs of JH esterase (JHE), an enzyme that hydrolyzes JH. We combine proteomic, phylogenetic and selection analyses to investigate the evolution of this esterase subfamily. We show that Camponotus JHE-like proteins have sustained multiple duplications, positive selection, and changed localization to become abundantly and selectively present in trophallactic fluid. To assess their potential role in larval development, we fed workers a JHE-specific inhibitor to introduce it into the trophallactic network. This increased the proportion larvae reared to metamorphosis by these workers, similar to supplementation with JH. Together these findings suggest that JHE-like proteins have evolved new roles in inter-individual regulation of larval development in Camponotus.

evolutionary biology↗