Biology subjects

Edelmann, M.

Publications and source records attributed to Edelmann, M..

5 recordsLinked to original sources

bioRxiv2026

Carbon source-dependent metabolic states govern redox homeostasis and cofactor biosynthesis in Propionibacterium freudenreichii

Microbial adaptation to fluctuating nutrient and oxygen conditions requires coordinated regulation of metabolic networks to maintain redox homeostasis within physicochemical and energetic constraints. While oxygen-dependent responses in Propionibacterium freudenreichii (PFR) have been characterized at the transcriptomic level, the role of carbon source in defining system-level metabolic states remains unclear. Here, we investigated carbon source-dependent metabolic reprogramming and cofactor biosynthesis in PFR strain DSM 20271 using label-free quantitative proteomics integrated with physiological and metabolite analyses. Distinct carbon sources defined discrete metabolic states shaped by redox balance and flux distribution. Lactate supported a comparatively balanced physiological state characterized by enhanced respiratory metabolism, amino acid biosynthesis, and riboflavin metabolism, enabling high specific vitamin B12 yields ([~]100 {micro}g g-1 wet biomass). In contrast, hexose metabolism (glucose and fructose) imposed a redox-constrained state marked by upregulation of transport systems, glycolysis, and the pentose phosphate pathway, resulting in increased biomass but reduced biosynthetic efficiency. A defining feature of the hexose-driven state was activation of aspartate metabolism. Proteomic and metabolite data, together with functional assays, support a model in which aspartate is converted to fumarate and subsequently reduced to succinate, providing an alternative electron sink that facilitates NADH reoxidation under redox-constrained conditions. Together, these findings establish that carbon source shapes physiological state through flux distribution, redox homeostasis, and resource allocation, with cofactor biosynthesis emerging as a system-level property rather than a simple consequence of biosynthetic enzyme abundance. IMPORTANCEPropionibacterium freudenreichii is a central bacterium used in food fermentations and one of the few microorganisms able to synthesize biologically active vitamin B12, making it valuable for industry and biotechnology. Yet the metabolic principles that govern its performance under different growth conditions remain poorly understood. Here, we show that carbon source is a key determinant of metabolic state, dictating how cells resolve redox constraints and allocate biosynthetic resources. We uncover a previously unrecognized adaptation in sugar-grown cells, where aspartate functions as an alternative electron sink to sustain redox balance under constrained conditions. By contrast, lactate supports a physiological state that promotes efficient vitamin B12 biosynthesis. These findings reveal a central role for carbon source in shaping metabolic configuration and identify redox balancing as a critical lever linking environmental inputs to biosynthetic output. More broadly, this work provides mechanistic insight into redox-constrained metabolism and a framework for improving vitamin B12 production and other microbial bioprocesses.

microbiology↗

bioRxiv2025

Multiplexed Brain and Visceral Two-Photon Imaging Using a Simulation-Guided Ultrafast Three-Color Fiber Laser

Multicolor two-photon microscopy is an essential tool in modern life sciences, enabling simultaneous, high-resolution imaging of multiple cellular structures and dynamic processes within complex biomedical systems. Realizing its full potential demands light sources that combine multiplexed spectral flexibility, high pulse quality, and practical implementation for efficient excitation of diverse cellular targets. Here, we present a novel ultrafast fiber laser platform that enables efficient three-color multiplexed two-photon imaging through numerically optimized nonlinear spectral shaping in a photonic crystal fiber (PCF). The system is driven by a nonlinear Yb-doped fiber amplifier with tailored dispersion and gain characteristics to generate clean sub-50 fs pulses at 1030 nm with over 40 nJ pulse energy. Subsequent, simulation-guided PCF-based spectral broadening enables controlled formation of three distinct high-energy bands centered at 940 nm, 1,080 nm, and 1,175 nm, overlapping with key fluorescent probes and biomolecular markers. The resulting pulses, isolated with high spectral and time-domain pulse quality, provide sub-115 fs duration and 2.5 - 6 nJ energy per channel. Multiplexed imaging is validated in labeled mouse brain, kidney, and liver tissue slices using spectrally independent multi-fluorophore targeting to visualize e.g., astrocytes, neuronal structures, and nuclei in triple-stained mouse hippocampus. The demonstrated fiber-optic laser platform provides a practical alternative to conventional single-color sources and more complex multi-laser systems, supporting robust and high-resolution three-color two-photon imaging for a range of biomedical applications.

biophysics↗

bioRxiv2025

Deep-Tissue Two-Photon Brain Imaging Enabled by a Tunable Fiber-Optic Dispersive Wave Generator

Here, we present a fiber-optic dispersive wave generator for highly-efficient, wavelength-tunable ultrashort pulse generation, enabling multicolor deep-tissue two-photon imaging of neuronal and vascular structures in labeled mouse brain. Guided by comprehensive numerical simulations, a compact Yb:fiber laser-driven system is constructed that utilizes precisely parameter- and phase-matching-controlled dispersive wave generation in a photonic crystal fiber. The system delivers sub-100 fs pulses with over [~]6.7 nJ of energy across a continuously tunable spectral range of 880-950 nm, achieving a record-high optical conversion efficiency of up to 65%. Optimizing the output for two-photon excitation of enhanced Green Fluorescent Protein and SYTOX Orange enables high-resolution structural imaging in mouse hippocampus and cerebellum at depths exceeding 450 {micro}m. This technique for wavelength-tunable, high-energy and ultrashort pulse generation with record optical efficiency represents a significant advancement in ultrafast fiber laser technology for versatile biomedical two-photon imaging applications.

bioengineering↗

bioRxiv2024

Aerobic Adaptation and Metabolic Dynamics of Propionibacterium freudenreichii DSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Propionibacterium freudenreichii (PFR) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271 to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of B12 vitamin, pseudovitamin-B12, propionate and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, TCA cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for sensing and adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and -ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFRs physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications. ImportanceThe study of the response of Propionibacterium freudenreichii to aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding of P. freudenreichii responses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.

microbiology↗

bioRxiv2017

SQANTI: extensive characterization of long read transcript sequences for quality control in full-length transcriptome identification and quantification

High-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel transcripts, even in very well annotated organisms as mice and humans. Nonetheless, there is a need for studies and tools that characterize these novel isoforms. Here we present SQANTI, an automated pipeline for the classification of long-read transcripts that computes 47 descriptors that can be used to assess the quality of the data and of the preprocessing pipelines. We applied SQANTI to a neuronal mouse transcriptome using PacBio long reads and illustrate how the tool is effective in readily describing the composition of and characterizing the full-length transcriptome. We perform extensive evaluation of ToFU PacBio transcripts by PCR to reveal that an important number of the novel transcripts are technical artifacts of the sequencing approach, and that SQANTI quality descriptors can be used to engineer a filtering strategy to remove them. Most novel transcripts in this curated transcriptome are novel combinations of existing splice sites, result more frequently in novel ORFs than novel UTRs and are enriched in both general metabolic and neural specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short-read based quantification algorithms. By comparing our iso-transcriptome with public proteomics databases we find that alternative isoforms are elusive to proteogenomics detection and are variable in protein changes with respect to the principal isoform of their genes. SQANTI allows the user to maximize the analytical outcome of long read technologies by providing the tools to deliver quality-evaluated and curated full-length transcriptomes. SQANTI is available at https://bitbucket.org/ConesaLab/sqanti.

bioinformatics↗