Biology subjects

Braga, A.

Publications and source records attributed to Braga, A..

5 recordsLinked to original sources

bioRxiv2025

Reframing Sleep Architecture: A Compositional and Temporal Approach to Sleep Data Analysis

Significant progress has been made in developing sleep staging methodologies; however, less attention has been devoted to the analysis of sleep architecture. Two critical aspects remain underexplored: the choice of binning window (i.e., grouping data into time intervals) and the statistical treatment of the interdependencies among sleep phases. While one-hour bins are commonly used, this choice is often based on convention rather than empirical justification. Additionally, sleep architecture data are typically expressed as proportions of time spent in each sleep phase, forming compositional datasets, non-negative values that represent parts of a whole and are constrained by a constant sum (e.g., 100%). Such data violate the assumptions of traditional statistical methods, yet their compositional nature is often overlooked, compromising analytical validity. In this study, we address two key methodological challenges in sleep architecture analysis: (1) determining the optimal binning window through a data-driven approach that balances information retention and noise reduction, and (2) applying isometric log-ratio (ILR) transformation to account for the compositional structure of the data, enabling the use of conventional statistical tests. By addressing these issues, we propose a more rigorous and interpretable framework for analyzing sleep architecture, aiming to enhance the accuracy and reproducibility of findings in sleep research. Statement of SignificanceSleep architecture is typically analysed without accounting for the interdependent nature of sleep stages, leading to potentially misleading interpretations. This study introduces a compositional analytical framework that treats sleep data as interdependent, where changes in one phase necessarily impact the others. By integrating compositional data principles with a biologically grounded approach to temporal binning, we offer researchers a practical and interpretable method for analysing sleep structure. This work challenges conventional analysis practices and encourages a rethinking of how sleep-related biological questions are framed. These findings hold potential relevance for improving the design and interpretation of both experimental and clinical sleep studies, ultimately supporting more accurate insights into physiological and pathological studies involving altered sleep patterns.

neuroscience↗

bioRxiv2024

Adenosine deficiency facilitates CA1 synaptic hyperexcitability in the presymptomatic phase of a knock in mouse model of Alzheimer's disease.

The diseases trajectory of Alzheimers disease (AD) is associated with and worsened by hippocampal hyperexcitability. Here we show that during the asymptomatic stage in a knock in mouse model of Alzheimers disease (APPNL-G-F/NL-G-F; APPKI), hippocampal hyperactivity occurs at the synaptic compartment, propagates to the soma and is manifesting at low frequencies of stimulation. We show that this aberrant excitability is associated with a deficient adenosine tone, an inhibitory neuromodulator, driven by reduced levels of CD39/73 enzymes, responsible for the extracellular ATP-to-adenosine conversion. Both pharmacologic (adenosine kinase inhibitor) and non-pharmacologic (ketogenic diet) restorations of the adenosine tone successfully normalize hippocampal neuronal activity. Our results demonstrated that neuronal hyperexcitability during the asymptomatic stage of a KI model of Alzheimers disease originated at the synaptic compartment and is associated with adenosine deficient tone. These results extend our comprehension of the hippocampal vulnerability associated with the asymptomatic stage of Alzheimers disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/590882v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@cd128forg.highwire.dtl.DTLVardef@17d7701org.highwire.dtl.DTLVardef@100337org.highwire.dtl.DTLVardef@14333d0_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LISynaptic hyperexcitability spreads to the soma and manifests at low frequencies of stimulation C_LIO_LISynaptic hyperexcitability is associated with reduced adenosine tone in vitro and in vivo C_LIO_LIReduced adenosine tone is driven by reduced ATP-to-adenosine extracellular conversion C_LIO_LIRestoration of adenosine tone successfully normalizes neuronal excitability in the AD model C_LI

neuroscience↗

bioRxiv2024

Astrocytic metabolic control of orexinergic activity in the lateral hypothalamus regulates sleep and wake architecture

Neuronal activity undergoes significant changes during vigilance states, accompanied by an accommodation of energy demands. While the astrocyte-neuron lactate shuttle has shown that lactate is the primary energy substrate for sustaining neuronal activity in multiple brain regions, its role in regulating sleep/wake architecture is not fully understood. We manipulated the cell-specific expression of monocarboxylate transporters (MCTs), the major lactate transporters, to examine the involvement of astrocytic lactate supply in maintaining consolidated wakefulness. Our results demonstrate that reduced expression of MCT4 in astrocytes disrupts lactate supply to orexin neurons in the lateral hypothalamus (LH), impairing wakefulness stability. We also show that MCT2-mediated lactate uptake is necessary for maintaining tonic firing of orexinergic neurons and stabilizing wakefulness. Our findings provide both in vivo and in vitro evidence supporting the critical role of astrocyte-to-orexinergic neuron lactate shuttle in regulating proper sleep/wake stability-- a crucial step for maintaining physiological functions and overall well-being.

neuroscience↗

bioRxiv2023

Optimization of chondroitin production in E. coli using genome scale models

Chondroitin is a natural occurring glycosaminoglycan with applications as a nutraceutical and pharmaceutical ingredient and can be extracted from animal tissues. Microbial chondroitin-like polysaccharides emerged as a safer and more sustainable alternative source. However, chondroitin titers using either natural or recombinant microorganisms are still far from meeting the increasing demand. The use of genome-scale models and computational predictions can assist the design of microbial cell factories with possible improved titers of these value-added compounds. Genome-scale models have been used to predict genetic modifications in Escherichia coli engineered strains that would potentially lead to improved chondroitin production. Additionally, using synthetic biology approaches, a pathway for producing chondroitin has been designed and engineered in E. coli. Afterwards, the most promising mutants identified based on bioinformatics predictions were constructed and evaluated for chondroitin production in flask fermentation. This resulted in the production of 118 mg/L of extracellular chondroitin by overexpressing both superoxide dismutase (sodA) and a lytic murein transglycosylase (mltB). Then, batch and fed-batch fermentations at bioreactor scale were also evaluated, in which the mutant overexpressing mltB led to an extracellular chondroitin production of 427 mg/L and 535 mg/L, respectively. The computational approach herein described identified several potential novel targets for improved chondroitin biosynthesis, which may ultimately lead to a more efficient production of this glycosaminoglycan.

bioengineering↗

bioRxiv2020

Neural stem cells traffic functional mitochondria via extracellular vesicles to correct mitochondrial dysfunction in target cells

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs). EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs is yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics. Herein we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells. Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs (Mito-EVs) with conserved membrane potential and respiration. We found that the transfer of Mito-EVs to mtDNA-deficient L929 Rho0 cells rescued mitochondrial function and increased Rho0 cell survival. Furthermore, the incorporation of Mito-EVs into inflammatory professional phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits. Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via Mito-EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.

neuroscience↗