Commensal-derived acetylcholine enhances mucosal immune education - Nature

A diet–microbiome–host axis strengthens mucosal immune defences and reinforces host–microbiota mutualism.

nature.com

Reactive oxygen species stimulate Paneth cell plasticity and diminish antimicrobial function - The EMBO Journal

The gut epithelium faces constant environmental oxidative stresses. How it responds to pathological reactive oxygen species (ROS) is not fully understood. Using Paneth cell (PC) lineage reporters and ...

link.springer.com

Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning

During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...

cell.com

academicrenewal.substack.com

Restored clearance of senescent neutrophils by tissue-resident macrophages limits organ aging

Aging disrupts tissue homeostasis across organ systems. Here, we identify tissue-resident macrophages (TRMs) as central coordinators of age-related organ decline through impaired clearance of senescen...

science.org

A novel approach to quantify out-of-distribution uncertainty in Neural and Universal Differential Equations | npj Systems Biology and Applications

Dynamical systems play a central role across the quantitative sciences, offering a powerful mathematical framework to describe, analyze, and predict the evolution of complex processes over time. In systems biology, dynamical systems provide a foundation for modeling and predicting the intricate behaviors of biological systems. Recent advances in data-driven approaches, such as Neural Ordinary Differential Equations (NODEs) and Universal Differential Equations (UDEs), have enabled the development of models that are either fully or partially data-driven. Integrating data-driven components into dynamical systems amplifies the challenge of generalization beyond training data, highlighting the need for robust methods to quantify uncertainty in out-of-distribution (OOD) scenarios—i.e., conditions not encountered during training. In this work, we investigate the reliability of uncertainty quantification (UQ) based on ensembles of models in the reconstruction of dynamical systems. We show that standard ensembles (i.e., models trained independently with different random initializations) risk producing overconfident predictions in previously unseen scenarios, as the models in the ensemble tend to exhibit similar behaviors. To address this issue, we propose a novel ensemble construction method for NODEs and UDEs that fosters diversity in the reconstructed vector field across models within specific regions of the state space, while maintaining explicit control over the fit on the training set. We first evaluate our method on numerical test cases derived from three models commonly used as benchmarks for data-driven reconstruction of dynamical systems: the Lotka–Volterra model, the damped oscillator, and the Lorenz system. We then apply the method to a biologically motivated model of cell apoptosis, considering more realistic conditions such as partial observability of the system outputs and noise in the training dataset. Overall, our results show that the proposed method improves the reliability of UQ in previously unseen scenarios compared with standard ensembles, especially where the latter exhibit overconfidence.

nature.com

An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut

To colonize their host and cause disease, enteric pathogens must deploy their virulence factors to establish distinct nutrient niches. How anaerobic p…

doi.org

ChREBP-mediated regulation of lipid metabolism in liver and brown adipose tissue of long-lived mice

GeroScience - De novo lipogenesis (DNL) is a metabolic process by which carbohydrates are converted into fatty acids and used for immediate energy or stored as triglycerides for later use....

doi.org

Oxytocin signaling in adipocytes is required for normal milk fat production

Milk triglycerides, a crucial nutrient source for newborn mammals, can be derived from adipose lipolysis, dietary sources, or de novo synthesis in mam…

doi.org

Polyunsaturated lipid senolytics exploit a ferroptotic vulnerability in senescent cells

Cellular senescence is a key driver of the aging process and contributes to tissue dysfunction and age-related pathologies. Senolytics have emerged as…

doi.org

Hallucinated citations are polluting the scientific literature. What can be done?

Tens of thousands of publications from 2025 might include invalid references generated by AI, a Nature analysis suggests.

go.nature.com

From Data and Models to E-Health | SBMC 2026

Website of the 10th international conference on Systems Biology of Mammalian Cells SBMC 2026 on May, 4th – 6th in Mannheim.

lisym-cancer.org

From Data and Models to E-Health | SBMC 2026

Website of the 10th international conference on Systems Biology of Mammalian Cells SBMC 2026 on May, 4th – 6th in Mannheim.

lisym-cancer.org

Macrophages restrict tumor immune infiltration by controlling collagen topography | Science Immunology

During tumorigenesis, the extracellular matrix is extensively remodeled. Whereas the impact of such remodeling on tumor growth and invasion is well described, the consequences on immune infiltratio...

science.org

Weight loss with GLP-1 medicines does not result in a disproportionate loss of muscle mass or function in obese mice and humans

Langer et al. show that GLP-1 medicines mildly reduce absolute muscle mass but improve relative mass and running performance in mice. Despite similar changes to body weight, GLP-1RA affects the muscle proteome differently compared to calorie restriction. A human pilot trial shows that muscle strength is maintained during GLP-1RA treatment.

dlvr.it

Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids

Nature Microbiology - Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites...

nature.com

ER remodelling is a feature of ageing and depends on ER-phagy

Nature Cell Biology - Donahue et al. show that ageing is associated with changes in ER morphology. ER-phagy drives age-associated ER remodelling through tissue-specific factors.

nature.com

Lipid-dependent accrual of a subset of monocyte-derived macrophages is essential for tissue regeneration

Nature Metabolism - A distinct lipid-laden subset of monocyte-derived macrophages regulates hepatocyte proliferation and liver regeneration in injured livers, via CD36-mediated signalling.

nature.com