Biology subjects

Archetti, A.

Publications and source records attributed to Archetti, A..

4 recordsLinked to original sources

bioRxiv2023

Generation of Bessel beam lattices by a single metasurface for neuronal activity recording in zebrafish larva

Bessel Beams (BBs) and BB lattices are structured-light excitation profiles frequently applied in material processing, nonlinear spectroscopy and in many fluorescence microscopy methods such as Light Sheet Microscopy (LSM). In LSM, BBs and BB-lattices offer wider excitation profiles, higher acquisition rate, enhanced resolution, and improved signal-to-noise ratio, while reducing the overall phototoxicity. However, this performance improvement typically comes at the cost of layout complexity and spatial constraints, originating from the optical arrangement required for obtaining BB features and for multiplexing the BB in a lattice of beamlets. Here, we introduce a novel method for encoding in a single flat element all the optical operations required to generate a BB lattice, including those of the excitation objective. We assessed the effective capabilities of this approach, using Meta-Surface (MS) technology to fabricate the corresponding flat optical element and to characterize its optical figures. Finally, we demonstrated its actual application in LSM, recording neuronal activity at cellular resolution in the zebrafish larval brain using fluorescence based neuronal activity reporters. In perspective, this approach, applied here for LSM, prompts a step forward in the BB versatility and in the BB application scenarios.

bioengineering↗

bioRxiv2019

Multi-phosphorylation reaction and clustering tune Pom1 gradient mid-cell levels according to cell size

Protein concentration gradients convey information at a distance from the source to both pattern developing organisms and organize single cells. In the rod-shaped cells of Schizosaccharomyces pombe, the DYRK-family kinase Pom1 forms concentration gradients with maxima at the cell poles. Pom1 controls the timing of mitotic entry by inhibiting the SAD-family kinase Cdr2, which forms stable membrane-associated nodes at mid-cell. Pom1 gradients rely on membrane association regulated by a phosphorylation-dephosphorylation cycle and lateral diffusion modulated by clustering. Whether the graded pattern directly alters Pom1 medial levels has been controversial. Here, using a combination of quantitative imaging approaches, including single particle tracking PALM and TIRF microscopy, we find that individual Pom1 molecules do not bind the membrane long enough to diffuse from cell pole to cell middle. Instead we propose they exchange within longer-lived clusters that form the functional gradient units. By creating an allelic series progressively blocking auto-phosphorylation, we show that multi-phosphorylation shapes and buffers the gradient to control the cortical mid-cell Pom1 levels, which represent the critical pool regulating Cdr2. Specific imaging of this cortical pool by TIRF microscopy demonstrates that more Pom1 overlaps with Cdr2 nodes in short than long cells, consistent with Pom1 inhibition of Cdr2 decreasing with cell growth. We conclude that Pom1 gradients modulate Pom1 mid-cell levels according to cell size.

cell biology↗

bioRxiv2018

Super-resolution fight club: A broad assessment of 2D & 3D single-molecule localization microscopy software

With the widespread uptake of 2D and 3D single molecule localization microscopy, a large set of different data analysis packages have been developed to generate super-resolution images. To guide researchers on the optimal analytical software for their experiments, we have designed, in a large community effort, a competition to extensively characterise and rank these options. We generated realistic simulated datasets for popular imaging modalities - 2D, astigmatic 3D, biplane 3D, and double helix 3D - and evaluated 36 participant packages against these data. This provides the first broad assessment of 3D single molecule localization microscopy software, provides a holistic view of how the latest 2D and 3D single molecule localization software perform in realistic conditions, and ultimately provides insight into the current limits of the field.

biophysics↗

bioRxiv2018

Constriction rate modulation can drive cell size control and homeostasis in C. crescentus

Rod-shaped bacteria typically grow first via sporadic and dispersed elongation along their lateral walls, then via a combination of zonal elongation and constriction at the division site to form the poles of daughter cells. Although constriction comprises up to half of the cell cycle, its impact on cell size control and homeostasis has rarely been considered. To reveal the roles of cell elongation and constriction in bacterial size regulation during cell division, we captured the shape dynamics of Caulobacter crescentus with time-lapse structured illumination microscopy and used molecular markers as cell-cycle landmarks. We perturbed constriction rate using a hyperconstriction mutant or fosfomycin inhibition. We report that constriction rate contributes to both size control and homeostasis, by determining elongation during constriction, and by compensating for variation in pre-constriction elongation on a single-cell basis.

biophysics↗