Biology subjects

Marco, S.

Publications and source records attributed to Marco, S..

4 recordsLinked to original sources

bioRxiv2025

Rapid quantification of short-chain fatty acids by Fourier-transform infrared spectroscopy for microbiota quality assessment

Short-chain fatty acids (SCFAs) are bacterial metabolites with crucial roles in host homeostasis and immune system modulation. Given their benefits, they have been proposed as markers of a healthy microbiota. Their quantification, however, is time-consuming, expensive and requires specialized personal and equipment. Thus, their use for quality assessment of stool samples in clinical contexts is limited. In this study we explored the use of Fourier-transform infrared (FT-IR) spectroscopy as an alternative method for metabolomic quality assessment of stool samples. FT-IR identifies the chemical bonds present in SCFAs and allows clear discrimination between healthy and dysbiotic stool samples (caused by Clostridioides difficile infection) through Principal Component Analysis (PCA). Overall, FT-IR provides a rapid, cost-effective and simple method for stool samples quality assessment. Combined with the widespread availability of this technology in most hospitals, these advantages highlight its potential application for routine implementation in clinical laboratories.

microbiology↗

bioRxiv2022

Mechanical control of the mammalian circadian clock via YAP/TAZ and TEAD

Circadian rhythms are a key survival mechanism that dictates biological activity according to the day-night cycle. In animals, cell-autonomous circadian clocks can be found in nearly every cell type and are subjected to multi-layered regulation. Although these peripheral clocks are remotely controlled by the master clock in the brain, they are also sensitive to their immediate mechano-chemical microenvironment. Whereas the mechanisms by which biochemical signalling controls the circadian clock at the single cell level are increasingly well understood, mechanisms underlying regulation by mechanical cues are still unknown. Here we show that the circadian clock in fibroblasts is regulated mechanically through YAP/TAZ and TEAD. We use high-throughput analysis of single-cell circadian rhythms and apply controlled mechanical, biochemical, and genetic perturbations to study the expression of the clock gene Rev-erb. We observe that Rev-erb circadian oscillations are disrupted concomitantly with the translocation of YAP/TAZ to the nucleus. By targeted mutations and tuning expression levels of YAP we identify TEAD as the transcriptional effector of this mechanosensitive regulatory pathway. Our findings establish a mechanism that links cell mechanobiology and the circadian clock, which could contribute to explain the circadian impairment observed in cancer and ageing, where the regulation of the mechanical environment and YAP/TAZ is lost.

cell biology↗

bioRxiv2020

Improvements on marker-free images alignment for electron tomography

Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.

molecular biology↗

bioRxiv2018

Bidirectional intraflagellar transport is restricted to only two microtubule doublets in the trypanosome flagellum

Intraflagellar transport (IFT) is the rapid bidirectional movement of large protein complexes driven by kinesin and dynein motors along microtubule doublets of cilia and flagella. Here we used a combination of high-resolution electron and light microscopy to investigate how and where these IFT trains move within the flagellum of the protist Trypanosoma brucei. Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) analysis of trypanosomes showed that trains are found almost exclusively along two sets of doublets (3-4 and 7-8) and distribute in two categories according to their length. High-resolution live imaging of cells expressing mNeonGreen::IFT81 or GFP::IFT52 revealed for the first time IFT trafficking on two parallel lines within the flagellum. Anterograde and retrograde IFT occur on each of these lines. At the distal end, a large individual anterograde IFT train is converted in several smaller retrograde trains in the space of 3-4 seconds while remaining on the same side of the axoneme.

cell biology↗