Biology subjects

Pierce, D. M.

Publications and source records attributed to Pierce, D. M..

6 recordsLinked to original sources

bioRxiv2025

Methods for Quantitative Analyses of Nerve Fiber Deformation in the Myenteric Plexus Under Loading of Mouse Distal Colon and Rectum

Visceral pain in the large bowel is a hallmark of irritable bowel syndrome (IBS) and the primary reason patients seek gastroenterological care. Notably, mechanical distension of the distal colon and rectum (colorectum) reliably evokes abdominal pain and thus understanding mechanotransduction of sensory nerve endings (nerve fibers) in the colorectum is crucial for understanding and treating IBS-related bowel pain. To facilitate such understanding we aimed to establish novel methods to mechanically test, image, and analyze large-strain deformations of networks of nerve fibers in the myenteric plexus of the colorectum, and thus enable quantitative analyses. We successfully delivered circumferential deformation (force or displacement driven) to intact segments of colorectum while maintaining the myenteric plexus in focus during fluorescent imaging to capture the deforming nerve fibers. We also established a semi-automated method to recapitulate the network morphology and a code to calculate the stretch ratios of individual nerve fibers deforming within the myenteric plexus of mouse colorectum. Our code allows plotting of stretch ratios for each fiber, stretch ratios vs. fiber angle, and stretch ratios vs. fiber length. Our methods not only facilitate analyses of deformations of networks of colorectal nerve fibers in the context of visceral nociception but are also applicable to analyzing the in-plane deformation of other two-dimensional fiber networks. We provide free, public access to our analysis code for MATLAB, including input files for a simple test case, at github.uconn.edu/imLab/Fiber-Network_Analyses.

bioengineering↗

bioRxiv2025

Colorectum and Embedded Networks of Nerve Fibers Present Auxetic Responses During Uniaxial Circumferential Extension

Understanding the multiscale mechanics of the colorectum is essential for uncovering the mechanotransductive pathways underlying visceral nociception. Intraluminal distension of the large intestine reliably evokes pain in disorders of gut-brain interaction (DGBIs), yet the tissue-level and nerve fiber-level responses to mechanical loading remain poorly defined. Here, we present results from a novel biomechanical testing framework that integrates uniaxial circumferential extension with high-resolution optical imaging to quantify deformation in both bulk colorectal tissue and embedded sensory nerve fibers. We tested intact, cylindrical colorectal segments from mice using a custom 3-D-printed chamber with intraluminal stainless-steel rods to apply circumferential stretch while maintaining a planar imaging field. We measured bulk-tissue deformation via Digital Image Correlation (DIC), while we assessed stretch in nerve fibers through fluorescence imaging of VGLUT2-labeled afferents analyzed using a custom fiber-network analyses. Across specimens, we observed a consistent auxetic response-characterized by positive axial strain during circumferential extension-at both the macroscale and microscale. Five out of six colorectal specimens exhibited positive axial Green-Lagrange strain (Exx), with an average median Exx of 0.0177, during circumferential extension generating an average median Eyy of 0.1273. Nerve fiber analysis across nine specimens revealed an average median stretch ratio of 1.0631, indicating 6.31% elongation, with substantial heterogeneity driven by fiber orientation. These findings demonstrate that the colorectum and its embedded network of nerve fibers exhibit auxetic behavior, a property that may amplify mechanical signaling and influence nociceptive signaling. Our methods and results provide foundational insight into structure-function relationships of colorectum and inform design of bioinspired auxetic materials.

bioengineering↗

bioRxiv2023

Insights into polyprotein processing and RNA-protein interactions in foot-and-mouth disease virus genome replication.

Foot-and-mouth disease affects cloven hoofed animals and is caused by foot-and-mouth disease virus (FMDV), a picornavirus with a positive-sense RNA genome. The FMDV genome contains a single open reading frame, which is translated to produce a polyprotein that is cleaved by viral proteases to produce the viral structural and non-structural proteins. Initial processing of the polyprotein occurs at three main junctions to generate four primary products; Lpro and the P1, P2 and P3 precursors (also termed 1ABCD, 2BC and 3AB1,2,3CD). The 2BC and 3AB1,2,3CD precursors undergo subsequent proteolysis to generate non-structural proteins that are required for viral replication, including the enzymes 2C, 3Cpro and 3Dpol. These precursors can be processed through both cis and trans (i.e., intra- and inter-molecular proteolysis) pathways, which are thought to be important for controlling virus replication. Our previous studies suggested that a single residue in the 3B3-3C junction had an important role in controlling 3AB1,2,3CD processing. Here, we use in vitro based assays to show that a single point mutation at the 3B3-3C boundary increases the rate of proteolysis to generate a novel 2C-containing precursor. Complementation assays showed that while this point mutation permitted production of some non-enzymatic non-structural proteins, those with enzymatic functions were inhibited. Interestingly, replication could only be supported by complementation with mutations in cis acting RNA elements, providing genetic evidence for a functional interaction between replication enzymes and RNA elements. ImportanceFoot-and-mouth disease virus (FMDV) is an economically important pathogen of animals that is responsible for foot-and-mouth disease (FMD). FMD is endemic in many parts of the world and can results in major economic losses. Replication of the virus is a highly coordinated event that occurs within membrane-associated compartments in infected cells and requires the viral non-structural proteins. These are all initially produced as a polyprotein that undergoes proteolysis likely through both cis and trans pathways (i.e., intra- and inter-molecular proteolysis). Alternative processing pathways can provide a mechanism to help coordinate viral replication by providing temporal control to protein production. Here, we analyse the consequences of mutations that change temporal control of FMDV polyprotein processing. Our data suggests that correct processing is required to produce key enzymes for replication in an environment in which they can interact with essential viral RNA elements. These data further the understanding of FMDV genome replication.

microbiology↗

bioRxiv2022

Processing of the hepatitis E virus polyprotein can be mediated by a cellular protease

The genomes of positive-sense RNA viruses encode polyproteins that are essential for controlling viral replication. These viral polyproteins must undergo proteolysis (also termed polyprotein processing) to generate functional protein units. This proteolysis can be performed by virally-encoded proteases as well as host cellular proteases, and is generally believed to be a key step in regulating viral replication. Hepatitis E virus (HEV), a leading cause of acute viral hepatitis, translates its positive-sense RNA genome to generate a polyprotein, termed pORF1, which is necessary and sufficient for viral genome replication. However, the mechanism of polyprotein processing in HEV remains to be determined. In this study, we aimed to understand processing of this polyprotein and its role in viral replication using a combination of in vitro translation experiments and HEV sub-genomic replicons. Our data suggest no evidence for a virally-encoded protease or auto-proteolytic activity as in vitro translation predominantly generates unprocessed viral polyprotein precursors. However, seven cleavage sites within the polyprotein (suggested by bioinformatic analysis) are susceptible to the host cellular protease, thrombin. Using a sub-genomic replicon system, we demonstrate that mutagenesis of these sites prevents replication, as does pharmacological inhibition of serine proteases. Overall, our data supports a model where HEV uses host proteases to support its replication and could have uniquely evolved not to rely on a virally-encoded protease for replication. Author summaryPositive-strand RNA viruses produce polyproteins that are cleaved by proteases that control viral replication. The polyproteins of all well studied positive-strand viruses undergo proteolysis in a highly controlled manner to generate functional proteins and regulate the transition from translation to RNA replication. Proteolysis of viral polyproteins is generally performed by virally-encoded proteases, although host cell proteases are used by some viruses. In this report, we provide evidence that suggests that hepatitis E virus, a medically important human pathogen, does not encode a protease and unlike other viral polyproteins cannot undergo auto-catalytic processing. Instead, we provide evidence that the polyprotein is susceptible to proteolysis by host cell proteases and that this is essential for viral replication. Our data contradict the previous dogma of positive-sense viral replication and suggests a model where this virus has evolved to use a host protease to control viral replication and tropism.

microbiology↗

bioRxiv2022

A Dual Role for LAR-RPTP in Regulating Long-distance Transport and Synaptic Retention of AMPARs, Essential for Long Term Associative Memory

The AMPA subtype of ionotropic glutamate receptors (AMPARs) plays an essential role in excitatory synaptic transmission, learning, and memory. The majority of AMPARs are made in the cell body and are transported by molecular motors to synapses. Maintaining the proper number of synaptic receptors requires coordinated regulation of receptor production, export from the soma and delivery at synapses. This major logistical process is essential for circuit function and behavior. Although recent studies have shown that long-distance synaptic transport is regulated by neuronal activity, little is known about the mechanisms that coordinate somatic export or synaptic delivery and removal. Here we show that loss of the PTP-3A isoform of the receptor tyrosine phosphatase PTP-3 (the C. elegans homologue of vertebrate LAR-RPTP) leads to a [~]60% decrease in AMPAR transport; this affects synaptic delivery of AMPARs and synaptic functions necessary for long-term associative olfactory memory in C. elegans. Interestingly, while complete loss of PTP-3A leads to defects in transport and local synaptic trafficking of AMPARs, loss of only PTP-3 phosphatase function affects local synaptic recycling and retention of AMPARs. Finally, we show that the N-terminus of PTP-3A regulates transport, whereas the C-terminal regulates synaptic retention of AMPARs. Altogether, our results suggest a model in which the two domains of PTP-3/LAR-RPTPs have specific, complementary roles in coordinating somatic export and local retention of AMPARs essential for long-term associative memory.

neuroscience↗

bioRxiv2020

A 3-D Constitutive Model for Finite Element Analyses of Agarose with a Range of Gel Concentrations

Hydrogels have seen widespread application across biomedical sciences and there is considerable interest in using hydrogels, including agarose, for creating in vitro three-dimensional environments to grow cells and study mechanobiology and mechanotransduction. Recent advances in the preparation of agarose gels enable successful encapsulation of viable cells at gel concentrations as high as 5%. Agarose with a range of gel concentrations can thus serve as an experimental model mimicking changes in the 3-D microenvironment of cells during disease progression and can facilitate experiments aimed at probing the corresponding mechanobiology, e.g. the evolving mechanobiology of chondrocytes during the progression of osteoarthritis. Importantly, whether stresses (forces) or strains (displacement) drive mechanobiology and mechanotransduction is currently unknown. We can use experiments to quantify mechanical properties of hydrogels, and imaging to estimate microstructure and even strains; however, only computational models can estimate intra-gel stresses in cell-seeded agarose constructs because the required in vitro experiments are currently impossible. Finite element modeling is well-established for (computational) mechanical analyses, but accurate constitutive models for modeling the 3-D mechanical environments of cells within high-stiffness agarose are currently unavailable. In this study we aimed to establish a 3-D constitutive model of high-stiffness agarose with a range of gel concentrations. We applied a multi-step, physics-based optimization approach to separately fit subsets of model parameters and help achieve robust convergence. Our constitutive model, fitted to experimental data on progressive stress-relaxations, was able to predict reaction forces determined from independent experiments on cyclical loading. Our model has broad applications in finite element modeling aimed at interpreting mechanical experiments on agarose specimens seeded with cells, particularly in predicting distributions of intra-gel stresses. Our model and fitted parameters enable more accurate finite element simulations of high-stiffness agarose constructs, and thus better understanding of experiments aimed at mechanobiology, mechanotransduction, or other applications in tissue engineering.

bioengineering↗