Biology subjects

Crippa, D.

Publications and source records attributed to Crippa, D..

3 recordsLinked to original sources

bioRxiv2026

Adaptive-optics lattice light-sheet microscopy enables correlative single-molecule imaging of endogenous proteins in native environments

Resolving molecular organization and dynamics in native environments remains challenging, as single-molecule imaging requires high sensitivity and spatiotemporal resolution while preserving 3D cellular context. Here, we present ALPINE (Adaptive-optics Lattice light-sheet microscopy for endogenous Protein Imaging in Native Environments), a modular framework for quantitative single-molecule imaging into complex biological samples. ALPINE combines adaptive-optics lattice light-sheet microscopy, programmable PSF shaping and acquisition stabilization, an engineered cell-specific labelling toolkit for endogenous cell-surface proteins and analysis pipelines assigning molecular localizations and trajectories to 3D cellular compartments. Labelling endogenous AMPA receptors in intact brain tissue, we demonstrate aberration-corrected 3D single-molecule localization and nanoscale organization within neuronal compartments. Importantly, fast optical sectioning of lattice light-sheet illumination further enables 3D single-molecule tracking in live tissue and quantification of molecular dynamics within native cellular environment. Together, ALPINE provides a modular approach to investigate how endogenous molecules are organized and dynamically regulated in complex biological systems, with components adaptable to diverse biological questions and imaging modalities.

neuroscience↗

bioRxiv2026

Virus {Psi}M2 enters a non-lytic lifecycle alternative to lysogeny during infection of Methanothermobacter marburgensis

Methanogens, a diverse group of archaea that produce methane during energy metabolism, are prevalent in anoxic habitats where they are exposed to viral infections. The head-tailed virus {Psi}M2 is one of few virus isolates that infect a methanogen host and was described as a lytic virus that lyses its host, Methanothermobacter marburgensis. Here, we present evidence that {Psi}M2 does not exclusively follow the classic lytic lifecycle but can also enter an alternative, chronic infection-like state. Growth experiments showed that infected cultures in minimal medium, optimized for the methanogen host (MS medium) did not exhibit complete lysis but continuously released infective virions. In contrast, in a suboptimal complex medium (SAB medium), the {Psi}M2-infected culture released virions in the exponential growth phase and eventually lysed after 14 hours post infection. Although the genome of {Psi}M2 encodes a putative integrase, a prerequisite for lysogeny, whole genome sequencing of {Psi}M2-infected M. marburgensis cultures revealed that the viral DNA remained extrachromosomal rather than integrating into the host genome, likely due to a mutation in the integrase gene. These findings suggest that {Psi}M2 enters a non-lytic lifecycle alternative to lysogeny under suboptimal host growth conditions. Sequencing further identified a heterogeneous viral population including previously undescribed variants. A high density of non-synonymous mutations and frameshift-inducing insertions was observed within ORFs predicted to encode a capsid protein and a major spike protein, suggesting these viral variants to differ in host recognition and infectivity. Overall, our results show more complex viral behavior and greater genetic variability than previously described.

microbiology↗

bioRxiv2023

Quantifying nutrient colimitation of microbial growth

Resource availability dictates how fast and how much microbial populations grow. Quantifying the relationship between microbial growth and resource concentrations makes it possible to promote, inhibit, and predict microbial activity. Microbes require many resources, including macronutrients (e.g., carbon and nitrogen), micronutrients (e.g., metals), and complex nutrients like vitamins and amino acids. When multiple resources are scarce, as occurs in nature, microbes may experience resource colimitation in which more than one resource limits growth simultaneously. Despite growing evidence for colimitation, the data is difficult to interpret and compare due to a lack of quantitative measures of colimitation and systematic tests of resource conditions. We hypothesize that microbes experience a continuum of nutrient limitation states and that nutrient colimitation is common in the laboratory and in nature. To address this, we develop a quantitative theory of resource colimitation that captures the range of possible limitation states and describes how they can change dynamically with resource conditions. We apply this approach to clonal populations of Escherichia coli to show that colimitation occurs in common laboratory conditions. We also show that growth rate and growth yield are colimited differently, reflecting their different underlying biology. Finally, we analyze environmental data to provide intuition for the continuum of limitation and colimitation conditions in nature. Altogether our results provide a quantitative framework for understanding and quantifying colimitation of microbes in biogeochemical, biotechnology, and human health contexts.

microbiology↗