Biology subjects

Maida, A.

Publications and source records attributed to Maida, A..

8 recordsLinked to original sources

bioRxiv2025

Growth Cost and Transport Efficiency Tradeoffs Define Root System Optimization Across Varying Developmental Stages and Environments in Arabidopsis

Root system architecture (RSA) is central to plant adaptation and fitness, yet the design principles and regulatory mechanisms connecting RSA to environmental adaptation are not well understood. We developed Ariadne, a semi-automated software for quantifying cost-efficiency tradeoffs of RSA by mapping root networks onto a Pareto-optimality framework, which describes the balance between resource transport efficiency and construction cost. Applying Ariadne to Arabidopsis thaliana, we found that root architectures consistently assume Pareto-optimal forms across developmental stages, genotypes, and environmental conditions. Using the Discovery Engine, an engine that combines machine learning together with interpretability techniques, we found developmental stage, the hy5/chl1-5 genotype, and manganese availability as important determinants of the cost-efficiency tradeoff, with manganese exerting a unique influence not observed for other nutrients. These results reveal that RSA plasticity is genetically constrained to cost-efficiency optimal configurations and that developmental and environmental factors shift RSA on the pareto front, with manganese acting as a strong modulator of the transport efficiency and construction cost balance.

plant biology↗

bioRxiv2024

Low-pressure Isochoric Freezing as a scalable technique for fresh food preservation

Efficient means of reducing food waste are critically needed to meet the demands of a growing global population, while mounting consumer interest in minimally-processed food products has simultaneously driven renewed interest in non-chemical preservation modalities. Here, we investigate the potential of low-pressure isochoric freezing (LPIF) at -1.5{degrees}C / 15 MPa to simultaneously inhibit microbial growth and preserve fresh-like physiochemical and bioactive properties during storage. Using raw cows milk as a model product, we demonstrate synergistic effects of mild low temperature and mild enhanced pressure that significantly improve preservation for storage periods up to 5 weeks. Given the passive nature of the technique and the compatibility of the employed pressures with standard industrial compressed gas containers, these results suggest a route towards a scalable new cold storage modality.

bioengineering↗

bioRxiv2023

Effects of isochoric freezing on quality characteristics of raw bovine milk

This study investigated the effects of isochoric freezing (IF) on the shelf-life and quality of raw bovine milk over a 5-week period. The results were compared with conventional refrigeration (RF) and refrigeration after pasteurization (HTST). The IF treatment process entailed storing liquid raw milk in isochoric chambers in thermodynamic equilibrium at -5{degrees}C /77MPa and -10{degrees}C /96MPa. Several parameters were analyzed, including microbiology count, physicochemical properties, indigenous enzyme activity, protein content, volatile organic compounds profile, and lipid degradation. Both raw and pasteurized milk experienced microbial level increases past the acceptable threshold ([≥]5.5 log CFU/mL) after 2 weeks and 5 weeks, respectively, leading to the deterioration of other parameters during storage. In comparison, microbiology count decreased significantly during storage for both IF treatment conditions but was more pronounced for the higher pressure (96MPa) treatment, leading to undetectable levels of microorganism after 5 weeks. IF treatment maintained stable pH, titratable acidity, viscosity, lipid oxidation, volatile profiles, total protein content, and lactoperoxidase activity throughout the storage period. Color was preserved during IF treatment at -5{degrees}C/77MPa; however, color was impacted during IF treatment at -10{degrees}C/96MPa. Protein structures were also modified during pressurized storage in both IF treatments. Overall, the study demonstrated that isochoric freezing could significantly increase the shelf-life of milk by reducing microbiology activity, whilst maintaining its nutritional content. These results underscore the potential role of isochoric freezing as a valuable tool in eliminating pathogens while maintaining quality characteristics similar to raw milk over long storage periods.

biochemistry↗

bioRxiv2022

Fasting-sensitive SUMO-switch on Prox1 controls hepatic cholesterol metabolism

The liver is the major metabolic hub, ensuring appropriate nutrient supply during fasting and feeding. In obesity, accumulation of excess nutrients hampers proper liver function and is linked to non-alcoholic fatty liver disease. Understanding the signaling mechanisms that enable hepatocytes to quickly adapt to dietary cues, might help to restore balance in liver diseases. Post-translational modification by attachment of the Small Ubiquitin-like Modifier (SUMO), allows for a dynamic regulation of numerous processes including transcriptional reprograming. Here, we demonstrate that the specific SUMOylation of transcription factor Prox1 represents a nutrient-sensitive determinant of hepatic fasting metabolism. Prox1 was highly modified by SUMOylation on lysine 556 in the liver of ad libitum and re-fed mice, while this modification was strongly abolished upon fasting. In a context of diet-induced obesity, Prox1 SUMOylation became insensitive to fasting cues. Hepatocyte-selective knock in of a SUMOylation-deficient Prox1 mutant into mice fed a high fat/high fructose diet led to reduction of systemic cholesterol levels, associated with the induction of bile acid detoxifying pathways in mutant livers during fasting. As appropriate and controlled fasting protocols have been shown to exert beneficial effects on human health, tools to maintain the nutrient-sensitive SUMOylation switch on Prox1 may thus contribute to the development of "fasting-based" approaches for the maintenance of metabolic health.

physiology↗

bioRxiv2021

Hepatocyte-specific activity of TSC22D4 triggers progressive NAFLD by impairing mitochondrial function

ObjectiveFibrotic organ responses have recently been identified as long-term complication in diabetes. Indeed, insulin resistance and aberrant hepatic lipid accumulation represent driving features of progressive non-alcoholic fatty liver disease (NAFLD), ranging from simple steatosis and non-alcoholic steatohepatitis (NASH) to fibrosis. Effective pharmacological regimens to stop progressive liver disease are still lacking to-date. MethodsBased on our previous discovery of transforming growth factor beta-like stimulated clone (TSC)22D4 as a key driver of insulin resistance and glucose intolerance in obesity and type 2 diabetes, we generated a TSC22D4-hepatocyte specific knockout line (TSC22D4-HepaKO) and exposed mice to control or NASH diet models. Mechanistic insights were generated by metabolic phenotyping and single cell liver sequencing. ResultsHepatic TSC22D4 expression was significantly correlated with markers of liver disease progression and fibrosis in both murine and human livers. Indeed, hepatic TSC22D4 levels were elevated in human NASH patients as well as in several murine NASH models. Specific genetic deletion of TSC22D4 in hepatocytes led to reduced liver lipid accumulation, improvements in steatosis and inflammation scores and decreased apoptosis in mice. Single cell RNA sequencing revealed a distinct gene signature identifying an upregulation of mitochondrial-related processes. An enrichment of genes involved in the TCA cycle, mitochondrial organization, and triglyceride metabolism underscored the hepatocyte-protective phenotype and overall decreased liver damage as seen in mouse models. ConclusionsTogether, our data uncover a new connection between targeted depletion of TSC22D4 and intrinsic metabolic processes in progressive liver disease. Cell-specific reduction of TSC22D4 improves hepatic steatosis, inflammation and promotes hepatocyte survival thus paving the way for further preclinical therapy developments.

physiology↗

bioRxiv2021

TSC22D4 interacts with Akt1 in response metabolic and stress signals

Transforming Growth Factor {beta} 1 Stimulated Clone 22 D4 (TSC22D4) is an intrinsically disordered protein that regulates cellular and physiological processes such as cell proliferation, cellular senescence as well as hepatic glucose and lipid metabolism. The molecular mechanism of TSC22D4 action in these cellular and metabolic functions, however, remains largely elusive. Here, we identified TSC22D4 as a novel protein kinase B/Akt1 interacting protein, a critical mediator of insulin/PI3K signaling pathway implicated in diverse set of diseases including type 2 diabetes, obesity and cancer. TSC22D4 interacts with Akt1 not constitutively but rather in a regulatory manner. While glucose and insulin stimulation of cells or refeeding of mice impair the hepatic TSC22D4-Akt1 interaction, inhibition of mitochondria and oxidative stress, promote it; indicating that extra- and intra-cellular cues play a key role in controlling TSC22D4-Akt1 interaction. Our results also demonstrate that together with its dimerization domain, i.e. the TSC box, TSC22D4 requires its intrinsically disordered region (D2 domain) to interact with Akt1. To understand regulation of TSC22D4 function further, we employed tandem mass spectrometry and identified 15 novel phosphorylation sites on TSC22D4. Similar to TSC22D4-Akt1 interaction, TSC22D4 phosphorylation also responds to environmental signals such as starvation, mitochondrial inhibition and oxidative stress. Interestingly, 6 out of the 15 novel phosphorylation sites lie within the TSC22D4 D2 domain, which is required for TSC22D4-Akt1 interaction. Characterization of the regulation and function of these novel phosphorylation sites, in the future, will shed light on our understanding of the role of TSC22D4-Akt1 interaction in both cell biological and physiological functions. Overall, our findings postulate a model whereby TSC22D4 acts as an environmental sensor and interacts with Akt1 to regulate cell proliferation, cellular senescence as well as maintain metabolic homeostasis.

molecular biology↗

bioRxiv2020

HAND2 is a novel obesity-linked adipogenic transcription factor regulated by glucocorticoid signaling

Adipocytes are critical cornerstones of energy metabolism. While obesity-induced adipocyte dysfunction is associated with insulin resistance and systemic metabolic disturbances, adipogenesis, the formation of new adipocytes and healthy adipose tissue expansion are associated with metabolic benefits. Understanding the molecular mechanisms governing adipogenesis is of great clinical potential to efficiently restore metabolic health in obesity. Here we show that Heart- and neural crest derivatives-expressed protein 2 (HAND2) is an obesity-linked adipocyte transcription factor regulated by glucocorticoids and required for adipocyte differentiation in vitro. In a large cohort of humans with obesity, white adipose tissue (WAT) HAND2 expression was correlated to body-mass-index (BMI). The HAND2 gene was enriched in white adipocytes, induced early in differentiation and responded to dexamethasone, a typical glucocorticoid receptor (GR, encoded by NR3C1) agonist. Silencing of NR3C1 in human multipotent adipose-derived stem cells (hMADS) or deletion of GR in a transgenic conditional mouse model results in diminished HAND2 expression, establishing that adipocyte HAND2 is regulated by glucocorticoids via GR in vitro and in vivo. Using a combinatorial RNAseq approach we identified gene clusters regulated by the GR-HAND2 pathway. Interestingly, silencing of HAND2 impaired adipocyte differentiation in hMADS and primary mouse adipocytes. However, a conditional adipocyte Hand2 deletion mouse model using Cre under control of the Adipoq promoter did not mirror these effects on adipose tissue differentiation, indicating that Hand2 was required at stages prior to Adipoq expression. In summary, our study identifies HAND2 as a novel obesity-linked adipocyte transcription factor, highlighting new mechanisms of GR-dependent adipogenesis in human and mice.

molecular biology↗

bioRxiv2017

A novel data-driven model for real-time influenza forecasting

We provide data-driven machine learning methods that are capable of making real-time influenza forecasts that integrate the impacts of climatic factors and geographical proximity to achieve better forecasting performance. The key contributions of our approach are both applying deep learning methods and incorporation of environmental and spatio-temporal factors to improve the performance of the influenza forecasting models. We evaluate the method on Influenza Like Illness (ILI) counts and climatic data, both publicly available data sets. Our proposed method outperforms existing known influenza forecasting methods in terms of their Mean Absolute Percentage Error and Root Mean Square Error. The key advantages of the proposed data-driven methods are as following: (1) The deep-learning model was able to effectively capture the temporal dynamics of flu spread in different geographical regions, (2) The extensions to the deep-learning model capture the influence of external variables that include the geographical proximity and climatic variables such as humidity, temperature, precipitation and sun exposure in future stages, (3) The model consistently performs well for both the city scale and the regional scale on the Google Flu Trends (GFT) and Center for Disease Control (CDC) flu counts. The results offer a promising direction in terms of both data-driven forecasting methods and capturing the influence of spatio-temporal and environmental factors for influenza forecasting methods.

epidemiology↗