Biology subjects

Ruiz, E.

Publications and source records attributed to Ruiz, E..

5 recordsLinked to original sources

bioRxiv2023

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

Emerging spatial omics technologies continue to advance the molecular mapping of tissue architecture and the investigation of gene regulation and cellular crosstalk, which in turn provide new mechanistic insights into a wide range of biological processes and diseases. Such technologies provide an increasingly large amount of information content at multiple spatial scales. However, representing and harmonizing diverse spatial datasets efficiently, including combining multiple modalities or spatial scales in a scalable and flexible manner, remains a substantial challenge. Here, we present Giotto Suite, a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox. At its core, Giotto Suite is centered around an innovative and technology-agnostic data framework embedded in the R software environment, which allows the representation and integration of virtually any type of spatial omics data at any spatial resolution. In addition, Giotto Suite provides both scalable and extensible end-to-end solutions for data analysis, integration, and visualization. Giotto Suite integrates molecular, morphology, spatial, and annotated feature information to create a responsive and flexible workflow for multi-scale, multi-omic data analyses, as demonstrated here by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive ecosystem for spatial multi-omic data analysis.

bioinformatics↗

bioRxiv2022

Hydrothermal sulphur bacteria enhance mercury availability for coastal marine organisms

The hydrothermal compounds massively released into the sea by the geothermal power plant of Bouillante (Guadeloupe, Lesser Antilles) support the growth of sulphur-oxidising bacteria like around black smokers. Opportunistic animals of the bay were previously shown to actively seek and consume the bacterial biofilm. To investigate the role of these bacterial mats in enhancing the transfer of Hg, a highly toxic heavy metal, its concentrations were assessed in sediments, bacteria, and 6 low trophic levels animals from the Bouillante Bay and a Control Site nearby containing only natural sources of Hg. Concentrations of Hg in all samples from Bouillante were greater than those from the Control Site (2 to 627 times higher). A comparison with the Hg concentrations reported in the literature for similar samples types reveals that they are abnormally high in most Bouillante samples. Although bacterial biofilm contained high levels of Hg, the link between bacteria contribution to diet and Hg concentration was more complex than expected, which might be due to interspecific differences in Hg uptake and elimination rates. Species not consuming bacteria (i.e. filter feeders) still presented higher levels of Hg, suggesting that significant amounts of Hg are released along with discharge waters from the Bouillante geothermal plant, and are integrated through diffusion. Differences in Hg concentrations between tissues do not indicate that Hg contained in samples from animals was under the form of MeHg, lowering the biomagnification potential of Hg in the Bouillante Bay trophic food web. Overall, the Bouillante case study emphasises for the first time an important role played by sulphur bacteria mats as a vector of hydrothermal inorganic Hg, and potentially other trace metals emitted in vents area, through dietary pathways.

ecology↗

bioRxiv2021

Proton export drives the Warburg Effect

Aggressive cancers commonly ferment glucose to lactic acid at high rates, even in the presence of oxygen. This is known as aerobic glycolysis, or the "Warburg Effect". It is widely assumed that this is a consequence of the upregulation of glycolytic enzymes. Oncogenic drivers can increase the expression of most proteins in the glycolytic pathway, including the terminal step of exporting H+ equivalents from the cytoplasm. Proton exporters maintain an alkaline cytoplasmic pH, which can enhance all glycolytic enzyme activities, even in the absence of oncogene-related expression changes. Based on this observation, we hypothesized that increased uptake and fermentative metabolism of glucose could be driven by the expulsion of H+ equivalents from the cell. To test this hypothesis, we stably transfected lowly-glycolytic MCF-7, U2-OS, and glycolytic HEK293 cells to express proton exporting systems: either PMA1 (yeast H+-ATPase) or CAIX (carbonic anhydrase 9). The expression of either exporter in vitro enhanced aerobic glycolysis as measured by glucose consumption, lactate production, and extracellular acidification rate. This resulted in an increased intracellular pH, and metabolomic analyses indicated that this was associated with an increased flux of all glycolytic enzymes upstream of pyruvate kinase. These cells also demonstrated increased migratory and invasive phenotypes in vitro, and these were recapitulated in vivo by more aggressive behavior, whereby the acid-producing cells formed higher grade tumors with higher rates of metastases. Neutralizing tumor acidity with oral buffers reduced the metastatic burden. Therefore, cancer cells with increased H+ export increase intracellular alkalization, even without oncogenic driver mutations, and this is sufficient to alter cancer metabolism towards a Warburg phenotype.

cancer biology↗

bioRxiv2021

Age-related changes in Tau and Autophagy in human brain in the absence of neurodegeneration

Tau becomes abnormally hyper-phosphorylated and aggregated in tauopathies like Alzheimers disease (AD). As age is the greatest risk factor for developing AD, it is important to understand how tau protein itself, and the pathways implicated in its turnover, change during aging. We investigated age-related changes in total and phosphorylated tau in brain samples from two cohorts of cognitively normal individuals spanning 19-74 years, without overt neurodegeneration. One cohort utilised resected tissue and the other used post-mortem tissue. Total soluble tau levels declined with age in both cohorts. Phosphorylated tau was undetectable in the post-mortem tissue but was clearly evident in the resected tissue and did not undergo significant age-related change. To ascertain if the decline in soluble tau was correlated with age-related changes in autophagy, three markers of autophagy were tested but only two appeared to increase with age and the third was unchanged. This implies that in individuals who do not develop neurodegeneration, there is an age-related reduction in soluble tau which could potentially be due to age-related changes in autophagy. Thus, to explore how an age-related increase in autophagy might influence tau-mediated dysfunctions in vivo, autophagy was enhanced in a Drosophila model and all age-related tau phenotypes were significantly ameliorated. These data shed light on age-related physiological changes in proteins implicated in AD and highlights the need to study pathways that may be responsible for these changes. It also demonstrates the therapeutic potential of interventions that upregulate turnover of aggregate-prone proteins during aging.

neuroscience↗

bioRxiv2019

CReasPy-cloning: a method for simultaneous cloning and engineering of megabase-sized genomes in yeast using the CRISPR-Cas9 system

Over the last decade a new strategy was developed to bypass the difficulties to genetically engineer some microbial species by transferring (or \"cloning\") their genome into another organism that is amenable to efficient genetic modifications and therefore acts as a living workbench. As such, the yeast Saccharomyces cerevisiae has been used to clone and engineer genomes from viruses, bacteria and algae. The cloning step requires the insertion of yeast genetic elements within the genome of interest, in order to drive its replication and maintenance as an artificial chromosome in the host cell. Current methods used to introduce these genetic elements are still unsatisfactory, due either to their random nature (transposon) or the requirement for unique restriction sites at specific positions (TAR cloning). Here we describe the CReasPy-Cloning, a new method that combines both the ability of Cas9 to cleave DNA at a user-specified locus and the yeasts highly efficient homologous recombination to simultaneously clone and engineer a bacterial chromosome in yeast. Using the 0.816 Mbp genome of Mycoplasma pneumoniae as a proof of concept, we demonstrate that our method can be used to introduce the yeast genetic element at any location in the bacterial chromosome while simultaneously deleting various genes or group of genes. We also show that CReasPy-cloning can be used to edit up to three independent genomic loci at the same time with an efficiency high enough to warrant the screening of a small (<50) number of clones, allowing for significantly shortened genome engineering cycle times.

bioengineering↗