Biology subjects

Agrawal, D. K.

Publications and source records attributed to Agrawal, D. K..

6 recordsLinked to original sources

bioRxiv2025

A New Model of Heart Failure with Preserved Ejection Fraction Induced by Metabolic Syndrome in Ossabaw Miniature Swine

A major obstacle to progress in heart failure with preserved ejection fraction (HFpEF) is the paucity of clinically relevant animal models. We developed a large, translationally relevant model in Ossabaw minipigs, which are genetically predisposed to the metabolic syndrome (MetS). Pigs were fed a "Western diet" high in calories, fructose, fat, cholesterol, and salt and received 1-2 deoxy-corticosterone acetate (DOCA) depots (n=10). After 6 months, they exhibited liver function abnormalities and marked increases in body weight, arterial blood pressure, serum cholesterol and triglycerides, and plasma glucose and insulin levels (glucose tolerance test), indicating the development of a full MetS. Echocardiography demonstrated no change in LV ejection fraction but progressive concentric LV hypertrophy and left atrial dilatation. Doppler echocardiography showed increased E/e ratio and increased peak early (E) and peak late atrial (A) transmitral inflow velocities, with no change in E/A ratio. Right heart catheterization demonstrated increased central venous pressure, pulmonary arterial systolic pressure, and pulmonary capillary wedge pressure. Clinically, pigs exhibited impaired exercise capacity, assessed by treadmill tests, associated with chronotropic incompetence. Pathologic examination showed significant myocardial fibrosis, myocyte hypertrophy, and liver fibrosis. In contrast, lean pigs fed a standard diet (n=3) did not show any changes at 6 months. The Ossabaw porcine model described herein is unique in that it recapitulates the entire constellation of major multiorgan comorbidities and hemodynamic, clinical, and metabolic features of MetS-driven human HFpEF: obesity, arterial hypertension, hyperlipidemia, glucose intolerance, insulin resistance, liver fibrosis and dysfunction, pulmonary hypertension, increased LV filling pressures, concentric LV hypertrophy, LV diastolic dysfunction with preserved systolic function, and impaired exercise capacity. Because of its high clinical relevance, this model is well-suited for exploring the pathophysiology of MetS-driven HFpEF and the efficacy of new therapies.

developmental biology↗

bioRxiv2020

A damaged-informed lung model for ventilator waveforms

Motivated by desire to understand pulmonary physiology and pathophysiology, scientists have developed models of pulmonary physiology. However, pathophysiology and interactions between human lungs and ventilators, e.g., ventilator-induced lung injury (VILI), present problems for modeling efforts. Real-world injury is too complex for simple models to capture, and while complex models tend not to be estimable with clinical data, limiting both the clinical utility with existing approaches. To address this gap, we present a damaged-informed lung ventilator (DILV) model to model and quantify patient-ventilator interactions and lung health. This approach relies on systematically mathematizing the pathophysiologic knowledge clinicians use to interpret lung condition from ventilator waveform data. This is achieved by defining clinically relevant features in the ventilator waveform data that contain hypothesis-driven information about pulmonary physiology, patient-ventilator interaction, and ventilator settings. To capture these features, we develop a modelling framework where the model has enough flexibility to reproduce commonly observed variability in waveform data. We infer the model parameters with clinical (human) and laboratory (mouse) data. The DILV model can reproduce essential dynamics of differently damaged lungs for tightly controlled measurements in mice and uncontrolled human intensive care unit data in the absence and presence of respiratory effort. Estimated parameters correlate with known measures of lung physiology, including lung compliance. This method has the potential to translate laboratory physiology experiments to clinical applications, including pathways for high fidelity estimates of lung state and sources of VILI with an end goal of reducing the impact of VILI and acute respiratory distress syndrome.

physiology↗

bioRxiv2019

Modular protein-oligonucleotide signal exchange

The ability to detect a protein selectively and produce a predicted signal in real time is a long-lasting engineering challenge in the field of biochemistry. Such a mechanism typically requires a sensing module to recognize the input protein and a translation module to produce a programmable output signal that reflects the concentration of the input. Here we present a generic biomolecular reaction process that exchanges the concentration of an input protein with a DNA oligonucleotide. This approach uses the unique characteristic of DNA oligonucleotide aptamer that can either bind to a specific protein or to a complementary DNA oligonucleotide reversibly. We then pass the information of the protein concentration to the output signal through DNA strand displacement reactions. Using this strategy, we design and characterize four different exchange processes that can produce modular DNA oligonucleotides in response to different proteins such as clinically important human -thrombin and vascular endothelial growth factor (VEGF). These exchange processes are capable of real time sensing and are modular such that they can be used for concurrent detection of different proteins with well-defined input-output characteristics. The novelty and simplicity of our approach encourage to develop advanced biochemical systems for point-of-care testing of infectious diseases and treatments.

biochemistry↗

bioRxiv2019

Mathematical models of protease-based enzymatic biosensors

An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frame-works that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a timescale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.

synthetic biology↗

bioRxiv2019

In vitro implementation of robust gene regulation in a synthetic biomolecular integral controller

Feedback mechanisms play a critical role in the maintenance of cell homeostasis in the presence of disturbances and uncertainties. Motivated by the need to tune the dynamics and improve the robustness of synthetic gene circuits, biological engineers have proposed various designs that mimic natural molecular feedback control mechanisms. However, practical and predictable implementations have proved challenging because of the complexity of synthesis and analysis of complex biomolecular networks. Here, we analyze and experimentally validate a first synthetic biomolecular controller executed in vitro. The controller is based on the interaction between a sigma and an anti-sigma factor, which ensures that gene expression tracks an externally imposed reference level, and achieves this goal even in the presence of disturbances. Our design relies upon an analog of the well-known principle of integral feedback in control theory. We implement the controller in an Escherichia coli cell-free transcription-translation (TXTL) system, a platform that allows rapid prototyping and implementation. Modeling and theory guide experimental implementation of the controller with well-defined operational predictability.

synthetic biology↗

bioRxiv2018

Vitamin D and Macrophage Polarization in Epicardial Adipose Tissue of Atherosclerotic Swine

Vitamin D functions as a potent immunomodulator by interacting with many immune cells however, its role in regulating inflammation in the epicardial adipose tissue (EAT) is unclear. In the EAT of atherosclerotic microswine that were fed with deficient, sufficient or supplemented levels of vitamin D, we evaluated the phenotype of the macrophages. Vitamin D treatment was continued for 12 months and serum 25(OH)D levels were measured regularly. Infiltration of M1/M2 macrophage was investigated by immunostaining for CCR7 and CD206, respectively in conjunction with a pan macrophage marker CD14. Significant difference in the number of CCR7+ cells was observed in the EAT from vitamin D-deficient swine compared to vitamin D-sufficient or -supplemented swine. Expression of CD206 correlated with high levels of serum 25(OH)D indicating a significant increase in M2 macrophages in the EAT of vitamin D-supplemented compared to -deficient swine. These findings suggest that vitamin D-deficiency exacerbates inflammation by increasing pro-inflammatory M1 macrophages, while vitamin D-supplementation attenuates the inflammatory cytokines and promotes M2 macrophages in EAT. This study demonstrates the significance of vitamin D mediated inhibition of macrophage mediated inflammation in the EAT during coronary intervention in addition to its immunomodulatory role. However, additional studies are required to identify the cellular mechanisms that transduce signals between macrophages and smooth muscle cells during restenosis in the presence and absence of vitamin D.\n\nAuthor Contribution StatementDKA conceived and designed the experiments; PG, JPF, MMR performed the experiments; PG, JPF, VJS analyzed and interpreted the results; PG prepared the figures and wrote the initial draft of the manuscript; CSB, DKA revised and edited the revised manuscript.

immunology↗