Biology subjects

Hunter, R.

Publications and source records attributed to Hunter, R..

8 recordsLinked to original sources

bioRxiv2026

Simultaneous Denoising and Baseline Correction of Microplate Raman Spectra Using a Dual-Branch U-Net

In this paper, we present a novel dual-branch U-Net architecture for the simultaneous execution of Raman baseline correction and denoising. The network features a shared encoder that diverges into two specialized decoding heads for the Raman signal and for the baseline. The two heads are coupled with a cross-attention gating mechanism. The model offers a way to cross-confirm the peaks by comparing the recovered Raman signal with the baseline corrected spectrum. Moreover, the model offers a new method for quantitative analysis by counting the overall number of photons at a deep Raman decoder block. The model was trained entirely using a custom synthetic data engine explicitly designed to emulate automated HTS acquisitions from microplates via the RamanBot platform. Comprehensive validation demonstrates robust peak recovery on synthetic spectra with signal-to-noise ratios (SNR) as low as 5. Crucially, the model successfully extracts high-fidelity signals from highly noisy glycerol and moderately noisy adenine sulfate experimental samples. Furthermore, quantitative analysis is conducted on guanine samples with different concentrations by counting the Raman photons.

biophysics↗

bioRxiv2025

RamanBot: Versatile high throughput Raman system

Raman spectroscopy is a powerful tool for qualitative and quantitative analysis in various scientific and industrial fields. However, the development of multisample automated screening remains relatively unexplored. In this paper, we develop RamanBot, a low-cost, easy-to-assemble, and automated Raman spectroscopy system designed for efficient signal collection from samples stored in different types of containers. For the first time, the proposed device introduces the Cartesian motion system, commonly used in 3D printers, to Raman spectroscopy automation. This is achieved by replacing the extrusion head of a commercially available 3D printer with a novel designed "Raman Head". The Raman head integrates all the necessary optical components required for in-place sample excitation and signal collection. A multimode fiber is used to deliver the excitation laser to the Raman head, whereas the collected Raman signal is delivered to the spectrometer via a fiber bundle. The motion system is programmed to scan predefined sample arrangements using the standard programming language for computer numerical control (G-code). The effect of movement precision on the Raman signal is studied. The introduced device is used in the quantitative analysis of ethanol and methanol. In addition, RamanBot is used to screen six eggs in their commercial packaging with minimal human intervention. The results show that the system is highly stable and capable of delivering reliable Raman measurements, making it a promising solution for high-throughput Raman spectroscopy applications.

bioengineering↗

bioRxiv2025

Transport stress induces paradoxical increases in airway inflammatory responses in beef stocker cattle

The development of Bovine Respiratory Disease (BRD) in beef cattle is associated with stressful events, including auction and transport. In addition to the effects of commingling on pathogen exposure, stress also impacts immune function and has classically been associated with an immunosuppressed state. Much of the research on cattle immunity in stress has focused on peripheral blood immune functionality rather than mucosal immune responses. To characterize immunity at the primary site of pathogen colonization in BRD, we evaluated stress responses in lung cells from beef stocker cattle to understand mucosal immune changes. Stocker calves were sampled via bronchoalveolar lavage fluid collection within 24 hours of auction and transport to a new facility (Stressed, n=12), or allowed to acclimate for 2 months at the new facility before sampling (Acclimated, n=7). Lavage cellular RNA was extracted and sequenced for bulk RNA-seq gene expression. Differential gene expression analysis of RNA sequencing data demonstrated a profound upregulation of inflammatory genes in Stressed calves compared to Acclimated calves, including expression of CXCL8, CSF3R, IL1B, and CCL22. Top pathway upregulation in Stressed calves involved neutrophil migration and chemotaxis, and cytokine signaling. To predict cellular population proportions from the data, CIBERSORTx was used to deconvolute bulk RNA-seq gene counts. This analysis showed that Stressed calves had significantly increased BALF neutrophils compared to Acclimated calves (p =0.003). Neutrophilic infiltration occurred in the absence of pathogen colonization of the lungs in most calves, as demonstrated by a multi-pathogen respiratory qPCR screen. As such, the stress induced an inflammatory response in lungs not explained by pathogen exposure. This study provides strong evidence that shipping stress in beef stocker calves can paradoxically trigger increased rather than suppressed inflammatory pulmonary mucosal immune responses, which has important implications for the pathogenesis of BRD.

immunology↗

bioRxiv2024

TcCARP3 modulates compartmentalized cAMP signals involved in osmoregulation, infection of mammalian cells, and colonization of the triatomine vector in the human pathogen Trypanosoma cruzi

Trypanosoma cruzi is the causative agent of Chagas disease, a zoonotic infectious disease considered a leading cause of cardiomyopathy, disability, and premature death in the Americas. This parasite spends its life between a mammalian host and an arthropod vector, undergoing essential transitions among different developmental forms. How T. cruzi senses microenvironmental changes that trigger cellular responses necessary for parasite survival has remained largely unknown. Cyclic AMP (cAMP) is a universal second messenger that has been shown to regulate key cellular processes in trypanosomes, in which cyclic AMP response proteins (CARPs) have been proposed to be modulators or effectors of a PKA-independent signaling pathway. In this study we aimed to investigate the role of TcCARP3 in cAMP signaling throughout T. cruzi life cycle. Our results show that TcCARP3 shares a dual localization (flagellar tip and contractile vacuole complex) with adenylate cyclase 1 (TcAC1) in the main developmental stages of the parasite. We also found that TcCARP3 directly interacts with several TcACs, modulating the intracellular content of cAMP. Through generation of TcCARP3 knockout, addback, and overexpression cell lines we showed that modulation of gene expression affects the parasites ability to differentiate, respond to osmotic stress, invade mammalian cells and replicate within them, and colonize the hindgut of the triatomine vector. In addition, we identified several signaling proteins interacting with TcCARP3 in what we propose are cAMP signaling microdomains. Our results unveil a key role for TcCARP3 as modulator of cAMP signals necessary for parasite differentiation and survival throughout T. cruzi life cycle. IMPORTANCECyclic AMP signaling pathways are poorly understood in the stercorarian parasite Trypanosoma cruzi. Specifically, the mechanisms driving the activation of TcACs in response to microenvironmental stress are completely unknown. This study unveils the role of TcCARP3 in modulating the content of cAMP through the interaction with several TcACs and putative cAMP effectors in T. cruzi. Particularly, TcCARP3 interacts with TcAC1 in the main developmental stages of this parasites life cycle, where both proteins display a dual localization pattern. These results provide new evidence supporting the compartmentalization of cAMP signals in trypanosomes. Moreover, our data unequivocally demonstrates that TcCARP3 is required for key cellular processes for parasite survival, such as response to osmotic stress, host cell invasion, intracellular replication, and the ability to colonize the hindgut of the triatomine vector. In summary, we found that TcCARP3 is an adenylate cyclase regulator, necessary for the life cycle progression of T. cruzi.

microbiology↗

bioRxiv2024

The T-cell niche tunes immune function through modulation of the cytoskeleton and TCR-antigen forces

Obesity is a major public health crisis given its rampant growth and association with an increased risk for cancer. Interestingly, patients with obesity tend to have an increased tumor burden and decreased T-cell function. It remains unclear how obesity compromises T-cell mediated immunity. To address this question, we modeled the adipocyte niche using the secretome released from adipocytes as well as the niche of stromal cells and investigated how these factors modulated T-cell function. We found that the secretomes altered antigen-specific T-cell receptor (TCR) triggering and activation. RNA-sequencing analysis identified thousands of gene targets modulated by the secretome including those associated with cytoskeletal regulation and actin polymerization. We next used molecular force probes to show that T-cells exposed to the adipocyte niche display dampened force transmission to the TCR-antigen complex and conversely, stromal cell secreted factors lead to significantly enhanced TCR forces. These results were then validated in diet-induced obese mice. Importantly, secretome-mediated TCR force modulation mirrored the changes in T-cell functional responses in human T-cells using the FDA-approved immunotherapy, blinatumomab. Thus, this work shows that the adipocyte niche contributes to T-cell dysfunction through cytoskeletal modulation and reduces TCR triggering by dampening TCR forces consistent with the mechanosensor model of T-cell activation.

bioengineering↗

bioRxiv2022

The matrisome of the murine and human dorsal root ganglion: a transcriptomal approach

The extracellular matrix (ECM) is a dynamic structure composed of a large number of molecules that can be divided into six different categories and are collectively called the matrisome. The ECM plays pivotal roles in physiological and pathological processes in many tissues, including the nervous system. Intriguingly, alterations in ECM molecules/pathways are often associated with painful human conditions and murine experimental pain models. Nevertheless, mechanistic insight into the interplay of normal or defective ECM and pain is largely lacking. To expand the knowledge on ECM composition and synthesis in the peripheral nervous system, we used a transcriptomal approach to investigate the expression and cellular origin of matrisome genes in murine and human dorsal root ganglia (DRG), containing the cell bodies of sensory neurons. Bulk RNA sequencing data showed that over 60% of all matrisome genes were expressed in both murine and human DRG, with proportionally more core matrisome genes (glycoproteins, collagens, and proteoglycans) expressed compared to matrisome-associated genes (ECM-affiliated genes, ECM regulators and secreted factors). Examination of the cellular origin of matrisome expression by single cell RNA sequencing on murine DRG revealed that core matrisome genes, especially collagens, were expressed by vascular leptomeningeal-like (fibroblast) cell types whereas matrisome-associated genes were mainly expressed by neuronal cell types. We analyzed cell-cell communication networks with the CellChat R package and predicted an important role for the Collagen signaling pathway in connecting vascular cell types and nociceptors in murine tissue, which we confirmed by analysis of spatial transcriptomic data from human DRG. RNAscope in situ hybridization and immunohistochemistry confirmed expression of collagens in fibroblasts surrounding nociceptors in human DRG. This study supports the idea that the DRG matrisome may contribute to neuronal signaling in both mouse and human. The identification of the cellular distribution of murine and human matrisome genes provides a framework to study the role of the ECM in peripheral nervous tissue and its effects on pain signaling. HighlightsO_LITranscriptomal analyses of mouse and human dorsal root ganglia (DRG) revealed that over 60% of matrisome genes are expressed by murine and human dorsal root ganglia (DRG), with over 85% of the genes with orthologues overlapping between both species. C_LIO_LIMatrisome-associated genes had the highest expression in both species and included conserved expression of annexins, S100 calcium binding proteins and cathepsins. C_LIO_LICollagens and collagen receptors are expressed by distinct cell types in murine and human DRG, suggesting that the collagen signaling pathway could be involved in cell-cell signaling. C_LI

neuroscience↗

bioRxiv2022

Dynamic Compartmentalisation of Intracellular Sodium in collecting duct cells

In Principal cells (PC) of the cortical collecting duct (CCD), the highly regulated and coordinated reabsorption of sodium occurs through the epithelial sodium channel (ENaC) at the apical membrane and Na/K ATPase at the basolateral membrane. However, it is not known how sodium ions (Na+) are transported across the cell. We investigated intracellular transport in mCCDcl1 cells using a fluorescent sodium dye, CoroNa Green AM. Dye uptake was stimulated by aldosterone, blocked by amiloride (an ENaC inhibiter), and basolateral transport was prevented by ouabain (an Na/K ATPase blocker) thus validating the dyes apparently faithful replication of sodium transport. Cells exhibited a consistent pattern of sodium-containing vesicles, of various sizes, surrounded by cytoskeleton and lipid membrane. While the smallest vesicles ([~]0.5m) co-stained with lysotracker, larger vesicles (up to 6.4m) did not co-stain with either lysosomal- or mitochondrial-specific dyes and appeared to have internal structure, suggesting that they were multivesicular bodies. Time-lapse imaging showed a subset of these multivesicular bodies release or take up sodium dye in a controlled manner. Our novel data suggest that intracellular sodium compartmentalisation is highly regulated and offer new insights into intracellular sodium dynamics in the collecting duct, revealing potential new targets for control of sodium homeostasis. New and NoteworthyThe article shows for the first time, to our knowledge, intracellular sodium transport mechanism in mCCDcl1 cells in the form of dynamic vesicular bodies. These structures offer new targets for the regulation of sodium homeostasis and transport in the kidney collecting duct, with wider implications for blood pressure regulation.

cell biology↗

bioRxiv2020

Rapid Assembly and Screening of Multivalent Immune Cell-Redirecting Therapies for Leukemia

Therapies that bind with immune cells and redirect their cytotoxic activity towards diseased cells represent a promising and versatile approach to immunotherapy with applications in cancer, lupus, and other diseases; traditional methods for discovering these therapies, however, are often time-intensive and lack the throughput of related target-based discovery approaches. Inspired by the observation that the cytokine, IL-12, can enhance antileukemic activity of the clinically approved T cell redirecting therapy, blinatumomab, here we describe the structure and assembly of a chimeric immune cell-redirecting agent which redirects the lytic activity of primary human T cells towards leukemic B cells and simultaneously co-targets the delivery of T cell-stimulating IL-12. We further describe a novel method for the parallel assembly of compositionally diverse libraries of these bi-specific T cell engaging cytokines (BiTEokines) and their high-throughput phenotypic screening, requiring just days for hit identification and the analysis of structure-function relationships. Using this approach, we identified CD19 x CD3 x IL12 compounds that exhibit ex vivo lytic activity comparable to current FDA-approved therapies for leukemia and correlated drug treatment with specific cell-cell contact, cytokine delivery, and leukemia cell lysis. Given the modular nature of these multivalent compounds and their rapid assembly/screening, we anticipate facile extension of this therapeutic approach to a wide range of immune cells, diseased cells, and soluble protein combinations in the future.

bioengineering↗