Biology subjects

Ai, W.

Publications and source records attributed to Ai, W..

5 recordsLinked to original sources

bioRxiv2026

Energetic analysis of Na+/K+-ATPase using bond graphs

The sodium-potassium ATPase (NKA) accounts for 19-28% of the total ATP consumption in mammals and is critical for maintaining ion homeostasis. Understanding its energetic efficiency is essential for comprehending cellular physiology and pathophysiology. We develop bond graph models of the NKA that ensure thermodynamic consistency by enforcing conservation of mass, charge, and energy. A simplified 6-state model captures biophysics comparable to a 15-state model while remaining computationally tractable. Through detailed energetic analysis, we demonstrate that under physiological conditions for the mammalian cardiac cell, approximately 66% of the energy from ATP hydrolysis is stored as chemical energy in ion gradients, 12% as electrical energy in the membrane potential, and 22% is dissipated as heat, yielding an overall efficiency of ~78%. We investigate how the free energy of ATP hydrolysis ({Delta}GATP), intracellular Na+, and extracellular K+ affect NKA efficiency and activity. A critical threshold exists at {Delta}GATP {approx} -48 kJ/mol below which chemoelectrical transduction drops dramatically, consistent with NKA inhibition under ischemic conditions. The bond graph framework enables quantitative comparison of different NKA models and provides a systematic approach for analyzing ion pumps. SIGNIFICANCEThe sodium-potassium ATPase is one of the bodys most energy-consuming enzymes, yet its energetic efficiency and mechanisms remain incompletely understood. This study presents the first comprehensive energetic analysis using bond graph modeling, guaranteeing thermodynamic consistency. By demonstrating that simplified 6-state models capture essential energetic behaviors of complex 15-state models, we establish bond graphs as a powerful, tractable tool for energetic analysis, model comparison, model selection and validation. The bond graph approach can be applied to other transporters, offering a powerful tool for systems physiology and drug discovery.

biophysics↗

bioRxiv2026

The biophysical basis of enterocyte homeostasis

We present an approach to analysing cell homeostasis using a bond graph modelling approach that ensures that the conservation laws of physics (conservation of mass, charge, and energy, respectively) are satisfied for the interdependent biochemical, electrical, mechanical, and thermal energy storage mechanisms operating within the cell. We apply the bond graph approach to several cell membrane transport mechanisms and then consider how physics constrains intracellular electrolyte homeostasis for enterocytes (the epithelial absorptive cells of the gut). The model includes the electrogenic sodium-potassium ATPase pump (NKA), the glucose transporter (GLUT2), and an inwardly rectifying potassium channel, all in the basolateral membrane, and the electrogenic sodium-driven glucose transporter (SGLT1) in the apical membrane. Glycolysis converts the imported glucose to ATP to drive NKA. For specified levels of sodium, potassium, and glucose in the blood, the model demonstrates how enterocytes absorb sodium and glucose from the gut and transfer glucose to the blood while maintaining the membrane potential and homeostasis of intracellular sodium and potassium. The Gibbs free energy available from the ATP hydrolysis ensures that the cell operates as a sodium battery with a high external to internal ratio of sodium concentration in order to provide the energy for many other cellular transport processes. We show that the 3:2 stoichiometry of Na+/K+ exchange in NKA, coupled with 2:1 Na+/glucose cotransport in SGLT1, a 1:2:2 ratio between glucose consumption and ATP and water production in glycolysis, and K+ and glucose efflux through Kir and GLUT2, respectively, provides a balanced system that maintains homeostasis of intracellular Na+, K+, glucose, ATP and water, and homeostasis of the membrane potential, under varying levels of transport of glucose from the gut to the blood. We also show how the flux expressions for SLC transporters, ATPase pumps and ion channels can all be expressed in a consistent and thermodynamically valid way.

bioengineering↗

bioRxiv2025

Chromosome-Specific Aneuploidy Engineering via dCas9-Induced Centromeric Chromatin Relaxation

Aneuploidy, the gain or loss of chromosomes, is prevalent in both normal and disease conditions, however, experimental approaches to engineer and study aneuploidy remain limited, leaving its functional significance under-characterized. Here, we present CRISPR-Taiji (CRISPRt), an efficient method for inducing chromosome-specific mis-segregation and aneuploidy generation across all 24 human chromosomes via dead Cas9 (dCas9)-induced centromeric chromatin relaxation. Using CRISPRt with scRNA-seq, we generated the first comprehensive transcriptomic alteration landscape of nearly all autosomal aneuploidies at chromosome-arm resolution. This genotype-phenotype map provides causal evidence linking recurrent aneuploidies in clear cell renal cell carcinoma (ccRCC) to molecular and clinical phenotypes observed in patient tumors. Notably, chromosome 3(p) loss, the ccRCC initiating event, specifically drives strong interferon signaling activation, offering novel insights into ccRCC tumorigenesis and immune modulation. Overall, we establish CRISPRt as a simple, efficient and scalable approach for chromosome-specific aneuploidy engineering and characterization in preclinical models to advance aneuploidy research across diverse biological contexts.

genomics↗

bioRxiv2024

Energy-based bond graph models of glucose transport with SLC transporters

The SLC (solute carrier) superfamily mediates the passive transport of small molecules across apical and basolateral cell membranes in nearly all tissues. In this paper we employ bond graph approaches to develop models of SLC transporters that conserve mass, charge and energy, respectively, and which can be parameterised for a specific cell and tissue type for which the experimental kinetic data is available. We show how analytic expressions that preserve thermodynamic consistency can be derived for a representative four- or six-state model, given reasonable assumptions associated with steady-state flux conditions. We present details on fitting parameters for SLC2A2 (a GLUT transporter) and SLC5A1 (an SGLT transporter) to experimental data and show how well the steady-state flux expressions match the full kinetic analysis. Since the bond graph approach will not be familiar to many readers, we provide a detailed description of the approach and illustrate its application to a number of familiar biophysical processes. SIGNIFICANCEPhysiological systems typically involve coupled mechanical, electrical and chemical processes, with energy acting as a universal currency across these domains. We propose a new visual representation for all components of these processes using bond graphs. Bringing all physical processes under one consistent framework greatly simplifies the task of understanding multiscale physiological processes. This energy-based framework, which is the 0D version of a more general 3D port-Hamiltonian theory, can be used to model all lumped parameter physiological processes. A small number of bond graph templates can be used to model all members of the large SLC transporter family, and reduced thermodynamically consistent steady-state flux models provide a useful simplification for many situations. Glucose transport is chosen here to illustrate the bond graph approach because it represents the first step in cell metabolic processes, where energy conservation needs to be a fundamental characteristic of quantitative models. Our future work on cell metabolism will build on the foundation established here.

biophysics↗

bioRxiv2023

ScRNA-seq of Diverse Pheochromocytoma Patients Reveals Distinct Microenvironment Characteristics and Supports an Informative Molecular Classification System

Pheochromocytomas (PCCs) are rare neuroendocrine tumors that originate from chromaffin cells in the adrenal gland. However, the cellular molecular characteristics and immune microenvironment of PCCs are incompletely understood. Here, we performed single-cell RNA sequencing (scRNA-seq) on 16 tissues from 4 sporadic unclassified PCC patients and 1 hereditary PCC patient with Von Hippel-Lindau (VHL) syndrome. We found that intra-tumoral heterogeneity was less extensive than the inter-individual heterogeneity of PCCs. Further, the unclassified PCC patients were divided into two types, metabolism-type (marked by NDUFA4L2 and COX4I2) and kinase-type (marked by RET and PNMT), validated by immunohistochemical staining. Trajectory analysis of tumor evolution revealed that metabolism-type PCC cells display phenotype of consistently active metabolism and increased metastasis potential, while kinase-type PCC cells showed decreased epinephrine synthesis and neuron-like phenotypes. Cell-cell communication analysis showed activation of the annexin pathway and a strong inflammation reaction in metabolism-type PCCs and activation of FGF signaling in the kinase-type PCC. Although multispectral immunofluorescence staining showed a lack of CD8+ T cell infiltration in both metabolism-type and kinase-type PCCs, only the kinase-type PCC exhibited downregulation of HLA-I molecules that possibly regulated by RET, suggesting the potential of combined therapy with kinase inhibitors and immunotherapy for kinase-type PCCs; in contrast, the application of immunotherapy to metabolism-type PCCs (with antigen presentation ability) is likely unsuitable. Our study presents a single-cell transcriptomics-based molecular classification and microenvironment characterization of PCCs, providing clues for potential therapeutic strategies to treat PCCs.

cancer biology↗