Biology subjects

Giordano, M.

Publications and source records attributed to Giordano, M..

5 recordsLinked to original sources

bioRxiv2024

Effect of Sulfate Availability on Phytoplankton Stoichiometry

O_LISulfur is a key element in multiple metabolic pathways of phytoplankton cells. The effect of environmental S availability on phytoplankton elemental quotas and stoichiometry has been addressed in few studies, using a limited number of species and with contradictory results. C_LIO_LIUsing high-temperature combustion oxidation and X-ray fluorescence methods, we measured the concentrations of micro- and trace elements in monocultures of 20 phytoplankton species, grown with different sulfate concentrations representing those of early and modern oceans. C_LIO_LIThe red lineage species, with higher S requirement and metabolic S fluxes, have higher S content than those of the green lineage, resulting in lower C:S (93) and higher S:P (1.06) than the green lineage species (226 and 0.76, respectively). Zn was the only trace element affected by the environmental concentration of sulfate. C_LIO_LIPhytoplankton cells respond to different sulfate availability by either increasing Zn or decreasing P quotas, where the P response is more characteristic in the red lineage, and the Zn response is independent of genotypic constraints or plastid type. This study sheds light on a metabolic basis for the expansion of the red lineage algae and their current dominance in ocean waters. C_LI Plain language summaryMicroalgae assimilate dissolved sulfate as a source of sulfur, an element that takes part in multiple biochemical pathways and cellular functions. Changes in the concentration of dissolved sulfate in the environment have an effect on the cellular dynamics of several essential biological elements, essencially phosphorus and zinc. The results of this study help to understand the biogeochemical cycling of these elements in the ocean and the dominance of certain phytoplankton lineages.

ecology↗

bioRxiv2024

HELP: A computational framework for labelling and predicting human context-specific essential genes

Machine learning-based approaches are particularly suitable for identifying essential genes as they allow the generation of predictive models trained on features from multi-source data. Gene essentiality is neither binary nor static but determined by the context. The databases for essential gene annotation do not permit the personalisation of the context, and their update can be slower than the publication of new experimental data. We propose HELP (Human Gene Essentiality Labelling & Prediction), a computational framework for labelling and predicting essential genes. Its double scope allows for identifying genes based on dependency or not on experimental data. The effectiveness of the labelling method was demonstrated by comparing it with other approaches in overlapping the reference sets of essential gene annotations, where HELP demonstrated the best compromise between false and true positive rates. The gene attributes, including multi-omics and network embedding features, lead to high-performance prediction of essential genes while confirming the existence of essentiality nuances. Author summaryEssential genes (EGs) are commonly defined as those required for an organism or cells growth and survival. The essentiality is strictly dependent on both environmental and genetic conditions, determining a difference between those considered common EGs (cEGs), essential in most of the contexts considered, and those essential specifically to one or few contexts (context-specific EGs, csEGs). In this paper, we present a library of tools and methodologies to address the identification and prediction of cEGs and csEGs. Furthermore, we attempt to experimentally explore the statement that essentiality is not a binary property by identifying, predicting and analysing an intermediate class between the Essential (E) and Not Essential (NE) genes. Among the multi-source data used to predict the EGs, we found the best attributes combination to capture the essentiality. We demonstrated that the additional class of genes we defined as "almost Essential" shows differences in these attributes from the E and NE genes. We believe that investigating the context-specificity and the dynamism of essentiality is particularly relevant to unravelling crucial insights into biological mechanisms and suggesting new candidates for precision medicine.

bioinformatics↗

bioRxiv2023

Contribution and functional connectivity between cerebrum and cerebellum on sub-lexical and lexical-semantic processing of verbs

Language comprehension requires sub-lexical (e.g., phonological) and lexical-semantic processing. We designed a task to compare the sub-lexical and lexical-semantic processing of verbs during functional magnetic resonance imaging (fMRI). Likewise, we were interested in the dichotomous representation of concrete-motor versus abstract-non-motor concepts, so two semantic categories of verbs were included: motor and mental. The findings support the involvement of the left dorsal stream of the perisylvian network for sub-lexical processing during the reading of pseudo-verbs and the ventral stream for lexical-semantic representation during the reading of verbs. According to the embodied or grounded cognition approach, modality-specific mechanisms, i.e.,, sensory-motor systems, and the well-established multimodal left perisylvian network contribute to semantic representation for concrete and abstract verbs. The present study detected a preferential modality-specific system for abstract-mental verbs. The visual system was recruited by mental verbs and showed functional connectivity with the right crus I/lobule VI from the cerebellum, suggesting the existence of this network to support the semantic representation of abstract concepts. These results confirm the dissociation between sub-lexical and lexical-semantic processing and provide evidence about the neurobiological basis of semantic representations for abstract verbs.

neuroscience↗

bioRxiv2022

The cognitive and neural correlates of irony

It has been suggested that irony is one of the most challenging forms of communication, consequently, it can be a valuable indicator of communication abilities. An ironic statement transmits the opposite meaning of its literal counterpart. The cognitive processes that may support the interpretation of irony include the Theory of Mind (ToM), executive functions, and processing style. The brain areas associated with irony detection are the medial prefrontal cortex, inferior frontal gyrus (IFG), posterior superior temporal gyrus (pSTG), precuneus, and inferior parietal lobule, among others. This study aims to analyze the cognitive processes and neural correlates involved in irony detection in Mexican adults. Forty-five participants underwent a cognitive assessment and performed a contextual discrepancy task during fMRI acquisition. The behavioral results showed that the detection of nonliteral statements (irony, unrelated, and white lies) requires ToM and verbal abilities. In addition, white lies detection seemed to involve inhibitory control. Ironic statements were the hardest intention to detect, having the lowest percentage of classification and the slowest latency of classification. Irony detection involved brain areas associated with the ToM (i.e., precuneus) and language (i.e., IFG and pSTG) as was expected based on the results of previous studies. The detection of literal and unrelated statements recruited motor areas. No differential activation pattern was found for detection of white lies. Finally, a global perceptual processing style predicted the percent change in the BOLD signal in the IFG for all the nonliteral and literal statements.

neuroscience↗

bioRxiv2020

Changes in ATP sulfurylase activityin response to altered cyanobacteria growth conditions.

Here we investigated variations in cell growth and ATP sulfurylase activity when two cyanobacterial strains - Synechocystis sp. PCC6803 and Synechococcus sp. WH7803 - were grown comparatively between conventional media and media with low ammonium, low sulfate and a controlled high CO2/low O2 atmosphere, which might resemble some Precambrian environments. In both organisms, a transition and adaptation to the reconstructed environmental media resulted in a decrease in ATPS specific activity. This decrease in activity appears to be decoupled from growth rate, suggesting the enzyme is not rate-limiting in S assimilation and raising questions about the role of ATPS redox regulation in cell physiology and thorughout history.

physiology↗