Biology subjects

Alves, T. C.

Publications and source records attributed to Alves, T. C..

8 recordsLinked to original sources

bioRxiv2026

MAFA drives pancreatic islet maturation through coordination of cell growth, metabolic maturation, and resilience to stress.

Stem cell-derived islets (SC-islets) are a promising source for replacing the loss of insulin-secreting {beta} cells in insulin-dependent diabetes patients, but compared to their primary human counter parts, SC-islets are considered functionally immature and do not immediately regulate blood glucose after transplantation. To better understand the molecular underpinnings of {beta} cell maturation, we genetically engineered human pluripotent stem cells (hPSCs) to control the induction of the {beta} cell-maturing transcription factor MAFA or a MAFA S64F mutant variant associated with premature {beta} cell aging and senescence in SC-islets. We employ a combination of in vitro assays, multi-omics analyses, and murine in vivo transplantation studies to demonstrate that MAFA remodeling of the SC-islet transcriptional landscape promotes SC-islet biogenesis and metabolic maturation giving rise to greater SC-islet resilience and insulin secretory capacity. Parallel MAFA S64F studies highlight the importance for compensatory mechanisms for sustaining accelerated oxidative metabolism and enhanced insulin secretion without inducing intracellular stress responses and islet dysfunction. Overall, these results reveal MAFA-governed transcriptional changes that drive SC-islet functional maturation, which provides the foundation for maturing SC-islets in vitro, preserving {beta} cell integrity, and improving SC-islet cell replacement therapies.

cell biology↗

bioRxiv2026

Optimizing Signal Acquisition and Chemometric Pipelines for Micro NIR Plant Identification: Evaluating Spectral Backgrounds and Data Processing in Herbarium Specimens

PremiseRapid and accurate plant species identification is a critical challenge exacerbated by the taxonomic impediment. Although portable near-infrared (Micro NIR) spectroscopy represents a promising solution, the current absence of standardized protocols and a fundamental understanding of how critical acquisition and analysis parameters influence accuracy remain significant barriers. This study focused on the systematic optimization and validation of a comprehensive workflow designed to maximize the reliability of plant identification using this technology. To ensure methodological robustness across diverse foliar matrices, four vascular plant species were strategically selected as a representative test set to encompass morphological extremes, including significant variations in leaf thickness, pubescence, and surface texture. MethodsUsing a portable spectrometer on herbarium specimens (exsiccate) of four vascular plant species, we systematically tested five spectral backgrounds, seven pre-processing methods, and four classification models. Subsequently, we optimized the number of spectral readings and evaluated the influence of the leaf scanning surface (adaxial vs. abaxial) on model accuracy. ResultsThe highest-performing combination was a Shiny Aluminum background, Second Derivative pre-processing, and a Random Forest model, which achieved a mean cross-validated accuracy of 99%. An average of just three spectral readings from the adaxial (upper) leaf face was sufficient to saturate model performance, proving statistically superior to other approaches (p < 0.001). DiscussionThis study establishes a validated, high-accuracy protocol for plant species identification from herbarium specimens using portable NIR, offering a powerful tool for biodiversity studies. Direct applicability to fresh plants in the field requires future validation to account for the spectral influence of moisture variability.

ecology↗

bioRxiv2025

Disruption of Plasma Membrane Lipid Asymmetry Alters Cellular Energetics

Biological membranes often feature an unequal and actively maintained concentration gradients of lipids between bilayer leaflets, termed lipid asymmetry.1-3 Lipid asymmetry has been linked to many cellular processes4,5, but the mechanisms that connect lipid trans-bilayer concentration gradients to cellular functions are poorly understood. Here we systematically map the cellular processes affected by dysregulation of lipid asymmetry by knocking out flippases, floppases, and scramblases in mammalian cells. We identify broad alterations to core metabolic pathways including nutrient uptake, neutral lipid turnover, pentose phosphate pathway and glycolysis. Lipidomics, respirometry, lipid and metabolic imaging, and live-cell calorimetry revealed elevated neutral lipid and ATP consumption rates which are coupled with increased heat loss per unit of biomass synthesized despite slower growth. This suggests that compensatory maintenance of lipid asymmetry strains the cellular energy budget, inducing a shift from a growth-promoting anabolic to a more energy-using catabolic state. Our data indicate that lipid asymmetry and its active maintenance is key for proper cell energetics, highlighting its putative role as a cellular store of potential energy akin to proton and ion transmembrane gradients.

cell biology↗

bioRxiv2023

Unveiling the phenology and associated floral regulatory pathways of Humulus lupulus L. in subtropical conditions

The Humulus lupulus L. (hops) is traditionally produced in temperate regions, historically attributed to the belief that vernalization was necessary for reproductive transition. Nevertheless, recent studies have revealed the potential for hop plants to flower in tropical and subtropical climates, thereby reshaping cultivation prospects once the developmental disparities are understood and adapted for optimized production. Here, we delved into the hop phenological cycle and the underlying floral regulatory pathways ultimately, seeking to devise strategies to modulate development and enhance production in regions with low latitudes. In contrast to cultivation in temperate regions, hops grown in the subtropical climate of Minas Gerais, Brazil, flower multiple times throughout the year, independently of the season. Hop is a short-day plant, and in Brazil, the photoperiod is consistently inductive due to daylight hours always being below the described threshold (16,5 h of light critical point). We observed that the reproductive transition of hop initiates after a specific number of nodes, 25 to 28, leading us to hypothesize that this process is primarily controlled by endogenous factors. To explore this issue, we first identified in the hop genome families of miRNAs related to reproductive transition, such as the families MIR156 and MIR172, and the PEBP family which includes the FLOWERING LOCUS T (FT). The expression of miR156 decreased along development inversely to miR172 and in synchrony with the upregulation of HlFT3 and HlFT5. These findings strongly support that the reproductive transition in hops under inductive photoperiodic conditions is primarily regulated by endogenous factors related to development and aging throughout the miRNA and FT-associated pathways. Thus, our study shedded light on the intricate molecular mechanisms that underlie hop floral development paving the way for potential advancements in hop production on a global scale.

plant biology↗

bioRxiv2021

GLS-driven glutamine catabolism contributes to prostate cancer radiosensitivity by regulating the redox state, stemness and ATG5-mediated autophagy

Radiotherapy is one of the curative treatment options for localized prostate cancer (PCa). The curative potential of radiotherapy is mediated by irradiation-induced oxidative stress and DNA damage in tumor cells. However, PCa radiocurability can be impeded by tumor resistance mechanisms and normal tissue toxicity. Metabolic reprogramming is one of the major hallmarks of tumor progression and therapy resistance. Here, we found that radioresistant PCa cells and prostate cancer stem cells (CSCs) have a high glutamine demand. Glutaminase (GLS)-driven catabolism of glutamine serves not only for energy production but also for the maintenance of the redox state. Consequently, glutamine depletion or inhibition of critical regulators of glutamine utilization, such as glutaminase (GLS) and the transcription factor MYC results in PCa radiosensitization. On the contrary, we found that a combination of glutamine metabolism inhibitors with irradiation does not cause toxic effects on nonmalignant prostate cells. Glutamine catabolism contributes to the maintenance of CSCs through regulation of the alpha-ketoglutarate (-KG)-dependent chromatin-modifying dioxygenase. The lack of glutamine results in the inhibition of CSCs with a high aldehyde dehydrogenase (ALDH) activity, decreases the frequency of the CSC populations in vivo and reduces tumor formation in xenograft mouse models. Moreover, this study shows that activation of the ATG5-mediated autophagy in response to a lack of glutamine is a tumor survival strategy to withstand radiation-mediated cell damage. In combination with autophagy inhibition, the blockade of glutamine metabolism might be a promising strategy for PCa radiosensitization. High blood levels of glutamine in PCa patients significantly correlate with a shorter prostate-specific antigen (PSA) doubling time. Furthermore, high expression of critical regulators of glutamine metabolism, GLS1 and MYC, is significantly associated with a decreased progression-free survival in PCa patients treated with radiotherapy. Our findings demonstrate that GLS-driven glutaminolysis is a prognostic biomarker and therapeutic target for PCa radiosensitization.

cancer biology↗

bioRxiv2020

Pharmacologic activation of the mitochondrial phosphoenolpyruvate cycleenhances islet function in vivo

The mitochondrial GTP (mtGTP)-dependent phosphoenolpyruvate (PEP) cycle is an anaplerotic-cataplerotic mitochondrial shuttle utilizing mitochondrial PEPCK (PCK2) and pyruvate kinase (PK). PEP cycling stimulates insulin secretion via OxPhos-independent lowering of ADP by PK. We assess in vivo whether islet PCK2 is necessary for glucose sensing and if speeding the PEP cycle via pharmacological PK activators amplifies insulin secretion. Pck2-/- mice had severely impaired insulin secretion during islet perifusion, oral glucose tolerance tests and hyperglycemic clamps. Acute and chronic pharmacologic PK activator therapy improved islet insulin secretion from normal, high-fat diet (HFD) fed, or Zucker diabetic fatty (ZDF) rats, and glucolipotoxic or diabetic humans. A similar improvement in insulin secretion was observed in regular chow and HFD rats in vivo. Insulin secretion and cytosolic Ca2+ during PK activation were dependent on PCK2. These data provide a preclinical rationale for strategies, such as PK activation, that target the PEP cycle to improve glucose homeostasis. HighlightsO_LILoss of mitochondrial phosphoenolpyruvate (PEP) impairs insulin release in vivo. C_LIO_LIPyruvate kinase (PK) activators stimulate beta-cells in preclinical diabetes models. C_LIO_LIPEP cycling in vivo depends on PK and mitochondrial PEPCK (PCK2) for insulin release. C_LIO_LIAcute and 3-week oral PK activator amplifies insulin release during hyperglycemia. C_LI eTOC BlurbAbudukadier et al. show that small molecule pyruvate kinase activation in vivo and in vitro increases insulin secretion in rodent and human models of diabetes. The phosphoenolpyruvate (PEP) cycling mechanism and its amplification are dependent on mitochondrial PEPCK (PCK2).

physiology↗

bioRxiv2020

Pyruvate kinase controls signal strength in the insulin secretory pathway

Pancreatic {beta}-cells couple nutrient metabolism with appropriate insulin secretion. Here, we show that pyruvate kinase (PK), which converts ADP and phosphoenolpyruvate (PEP) into ATP and pyruvate, underlies {beta}-cell sensing of both glycolytic and mitochondrial fuels. PK present at the plasma membrane is sufficient to close KATP channels and initiate calcium influx. Small-molecule PK activators increase {beta}-cell oscillation frequency and potently amplify insulin secretion. By cyclically depriving mitochondria of ADP, PK restricts oxidative phosphorylation in favor of the mitochondrial PEP cycle with no net impact on glucose oxidation. Our findings support a compartmentalized model of {beta}-cell metabolism in which PK locally generates the ATP/ADP threshold required for insulin secretion, and identify a potential therapeutic route for diabetes based on PK activation that would not be predicted by the {beta}-cell consensus model. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=164 HEIGHT=200 SRC="FIGDIR/small/907790v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1f6503forg.highwire.dtl.DTLVardef@e9393org.highwire.dtl.DTLVardef@fab08borg.highwire.dtl.DTLVardef@5c7c55_HPS_FORMAT_FIGEXP M_FIG C_FIG The consensus model for {beta}-cell glucose sensing supports a dominant role for OxPhos. This model doesnt fully explain the observed metabolic and electrophysiologic oscillations associated with glucose-stimulated insulin secretion. Lewandowski et al. challenge this model by mechanistically connecting the anaplerotic PEP cycle to the electrically silent triggering phase, and OxPhos to the electrically active secretory phase. Here, the allosteric recruitment of pyruvate kinase directs metabolic traffic between the two cycles and identifies potential therapeutic strategies for diabetes based on pharmacologic pyruvate kinase activation. HIGHLIGHTSO_LICompartmentalized pyruvate kinase (PK) activity underlies {beta}-cell fuel sensing C_LIO_LIMembrane-associated PK closes KATP channels and controls calcium influx C_LIO_LIBy lowering ADP, PK toggles mitochondria between OxPhos and PEP biosynthesis C_LIO_LIPharmacologic PK activation increases oscillatory frequency and amplifies secretion C_LI

cell biology↗

bioRxiv2018

Optimization of Experiment Design for Mass Spectrometric Isotopic Labeling Kinetics

Determination of metabolic fluxes by measurement of time-dependent sampling of isotopic enrichments during the administration of labeled substrates provides rich information. Because such experiments are resource-intensive and frequently push the limits of sensitivity of the measurement techniques, optimization of experiment design can improve feasibility with respect to financial and labor costs, time to completion, and increase precision and accuracy of the results. Here we used a previously published set of data acquired in cultured insulinoma cells to evaluate contributions to the sensitivity and variability of the rate of citrate synthase (CS). Specifically, we calculated changes in uncertainty in CS if sample times were dropped or new ones were added, and we observed that some sampling times can be dropped with little effect, while improvements can be made with a strategic choice of when to add samples. We measured the contributions of data sampled at different times on the sensitivity of CS, finding that CS had greater sensitivity at early time points. We tested the concept that if two estimated parameters are correlated significantly, then refining one might constrain the other. In this case, the rate of Beta-oxs was found to be correlated with CS, and narrower variability in Beta-ox did indeed improve the sensitivity of CS. The tests described here might be applied at the initial design stage and then after a pilot phase to improve sensitivities of targeted fluxes and the reduction of materials, time, labor, and other experimental resources. The correlation analyses can be used to consider what orthogonal measurements might be beneficial for further improvement of measurements. While this study used a specific example of a set of time-dependent kinetic isotopic measurements, the results illustrate some generalizable behaviors that can be tested in other experimental systems.

bioinformatics↗