Biology subjects

Thompson, N.

Publications and source records attributed to Thompson, N..

11 recordsLinked to original sources

bioRxiv2026

An Implantable Wireless Battery-Free Selective Vagus Nerve Stimulator

Objective. Vagus nerve stimulation (VNS) is an established clinical therapy for drug-resistant epilepsy and other inflammatory conditions. However, off-target stimulation can produce unwanted side effects that limit therapeutic stimulation and hinder the development of new neuromodulation therapies. Selective VNS (sVNS) offers a strategy to reduce off-target organ activation; however, this approach is not available in humans, and no implantable or portable devices exist to trial sVNS in the clinical setup. This work aimed to design, manufacture, and validate an implantable wireless, battery-free stimulator with a selectively addressable output stage for targeted current delivery to specific regions of the human vagus nerve (VN). Approach. We developed a near-field communication-controlled, wirelessly powered, battery-free, temporary implantable multichannel stimulation device, compatible with a 15-channel sVNS cuff electrode (14 selective electrode pairs and one circumferential whole-nerve channel). The device was encapsulated for short-term implantation and evaluated through benchtop characterisation, accelerated ageing, and validation in an acute porcine and a pilot human study. Main result. The sVNS device was evaluated in a porcine (n = 4) trial and a first-in-human pilot study (n = 1). Selective bradycardia of 23.28 {+/-} 12.91% was observed in pigs and 7.5% in the human participant. In the human, a clear separation of bradycardic and tachycardic effects was observed, with additional selectivity in laryngeal activity. Cardiac and laryngeal responses were separated by 231{degrees} around the circumference of the nerve. Significance. This work demonstrates the feasibility of wireless battery-free sVNS for cardiac applications using a temporary implantable device. Geometrically selective stimulation has the potential to improve therapeutic efficacy while reducing stimulation-related side effects, and may facilitate future therapies for heart failure and other autonomic disorders.

bioengineering↗

bioRxiv2025

Substrate recognition and cleavage by mucin degrading O-glycopeptidases from the gut microbe Bacteroides caccae.

O-glycopeptidases are enzymes that hydrolyze the peptide bonds in glycoproteins by a mechanism that involves specific recognition of O-linked glycans on the substrate. Bacteroides caccae, an accomplished mucin degrader, is a member of the human gut microbiota with sixteen genes encoding putative O-glycopeptidases in the peptidase_M60 family. At present, the diversity of substrate selective in O- glycopeptidases is not well-understood nor is the rationale behind their expansion in bacteria such as B. caccae. Here we reveal the activity and diversity of the peptidase_M60 O-glycopeptidases encoded in the B. caccae genome. At least thirteen of the sixteen peptidase_M60 genes are active mucinases. Targeted functional studies by a high-throughput FRET screen combined with detailed kinetic analyses reveal that five examples in an uncharacterized clade of peptidase_M60 proteins have different substrate selectivities despite their relatively high degree of relatedness. Structural analyses of these enzymes, including bound complexes, reveal new insight into the molecular underpinnings of O-glycopeptidase diversity. This highlights the larger context of how varied the selectivity of peptidase_M60 O-glycopeptidases can be for the glycan moiety and/or the peptide portion of the substrates, and why mucin degraders like B. caccae diversify O-glycopeptidase substrate repertoires to potentially maximize breakdown of this extraordinarily complex polymer.

biochemistry↗

bioRxiv2025

The genetic architecture of ecotypic differentiation in Chinook salmon of the California Central Valley

Understanding the genomic details underlying complex behavioral traits is a foundational pursuit in biology. We use genomic and genetic techniques to dissect the heritable underpinnings of adult migration timing of Chinook salmon in the California Central Valley (CCV), home to several ecotypes not found elsewhere. We find that a previously described genomic region contributes to the seasonal shift in adult freshwater migration in the CCV, as in other river basins, but we further identify two functional domains in this locus that separately and additively influence the trait, with each allele copy affecting timing by [~]two weeks. We show how the evolution of a unique ecotype in the CCV is partially due to an allele derived from the more widespread early-migrating haplotype. However, the genomic background of the evolutionarily differentiated ecotypes contributes a similar amount to trait variation. We show how a relatively simple five-allele genetic system, in concert with genomic backgrounds, can create a remarkable diversity of phenotypes and ecotypes for this iconic species. TeaserA diverse complex of salmon ecotypes is explained by a simple two-locus system and evolutionarily derived genomic backgrounds.

genetics↗

bioRxiv2025

A multipurpose microhaplotype panel for genetic analysis of California Chinook salmon

Genetic methods have become an essential component of ecological investigation and conservation planning for fish and wildlife. Among these methods is the use of genetic marker data to identify individuals to populations, or stocks, of origin. More recently, methods that involve genetic pedigree reconstruction to identify relationships between individuals within populations have also become common. We present, here, a novel set of multi-allelic microhaplotype genetic markers for Chinook salmon which provide unprecedented resolution for population discrimination and relationship identification from a rapidly and economically assayed panel of markers. We show how this set of microhaplotypes provides definitive power to identify all known lineages of Chinook salmon in California. The inclusion of genetic loci that have known associations with phenotype and that were identified as outliers in examination of whole genome sequence data, allows resolution of stocks that are not highly genetically differentiated but are phenotypically distinct and managed as such. This same set of multiallelic genetic markers have ample variation to accurately identify parent-offspring and full-sibling pairs in all California populations, including the genetically depauperate winter-run lineage. Validation of this marker panel in coastal salmon populations not previously studied with modern genetic methods, also reveals novel biological insights, including the presence of a single copy of a haplotype for a phenotype that has not been documented in that part of the species range, and a clear signal of mixed ancestry for a salmon population that is on the geographic margins of the primary evolutionary lineages present in California.

genetics↗

bioRxiv2024

Anatomical and functional organization of cardiac fibers in the porcine cervical vagus nerve allows spatially selective efferent neuromodulation

Cardiac disease progression reflects the dynamic interaction between adversely remodeled neurohumoral control systems and an abnormal cardiac substrate. Vagal nerve stimulation (VNS) is an attractive neuromodulatory option to dampen this dynamic interaction; however, it is limited by off-target effects. Spatially-selective VNS (sVNS) offers a promising solution to induce cardioprotection while mitigating off-target effects by specifically targeting pre-ganglionic parasympathetic efferent cardiac fibers. This approach also has the potential to enhance therapeutic outcomes by eliminating time-consuming titration required for optimal VNS. Recent studies have demonstrated the independent modulation of breathing rate, heart rate, and laryngeal contraction through sVNS. However, the spatial organization of afferent and efferent cardiac-related fibers within the vagus nerve remains unexplored. By using trial-and-error sVNS in vivo in combination with ex vivo micro-computed tomography fascicle tracing, we show the significant spatial separation of cardiac afferent and efferent fibers (179{+/-}55{degrees} SD microCT, p<0.05 and 200{+/-}137{degrees} SD, p<0.05 sVNS - degrees of separation across a cross-section of nerve) at the mid-cervical level. We also show that cardiac afferent fibers are located in proximity to pulmonary fibers consistent with recent findings of cardiopulmonary convergent neurons and circuits. We demonstrate the ability of sVNS to selectively elicit desired scalable heart rate decrease without stimulating afferent-related reflexes. By elucidating the spatial organization of cardiac-related fibers within the vagus nerve, our findings pave the way for more targeted neuromodulation, thereby reducing off-target effects and eliminating the need for titration. This, in turn, will enhance the precision and efficacy of VNS therapy in treating cardiac pathology, allowing for improved therapeutic efficacy. Condensed AbstractSpatially-selective vagus nerve stimulation (sVNS) presents a promising approach for addressing chronic heart disease with enhanced precision. Our study reveals significant spatial separation between cardiac afferent and efferent fibers in the vagus nerve, particularly at the mid-cervical level. Utilizing trial-and-error sVNS in vivo and micro-computed tomography fascicle tracing, we demonstrate the potential for targeted neuromodulation, achieving therapeutic effects like scalable heart rate decrease without stimulating afferent-related reflexes. This spatial understanding opens avenues for more effective VNS therapy, minimizing off-target effects and eliminating the need for titration, thereby expediting therapeutic outcomes in myocardial infarction and related conditions. TweetWith functional and structural imaging, we found organization of vagal efferent & afferent cardiac regions. We can selectively activate only cardiac efferents to achieve bradycardia; desired to reduce the effects of sympathetic overactivation associated with heart disease #VNS #Cardiac #VagusNerve Key PointsO_LISpatially-selective vagus nerve stimulation (sVNS) presents a promising approach for addressing chronic heart disease with enhanced precision. C_LIO_LIOur study reveals significant spatial separation between cardiac afferent and efferent fibers in the vagus nerve, particularly at the mid-cervical level. C_LIO_LIUtilizing trial-and-error sVNS in vivo and micro-computed tomography fascicle tracing, we demonstrate the potential for targeted neuromodulation, achieving therapeutic effects like scalable heart rate decrease without stimulating afferent-related reflexes. C_LIO_LIThis spatial understanding opens avenues for more effective VNS therapy, minimizing off-target effects and eliminating the need for titration, thereby expediting therapeutic outcomes in myocardial infarction and related conditions. C_LI

neuroscience↗

bioRxiv2023

Human vagus nerve fascicular anatomy: a microCT segmentation and histological study

BackgroundPrevious research has revealed the logical mapping of fascicles in both human somatic and pig vagus nerves, but the organization of fascicles within the human vagus nerve remains largely unknown. Understanding its fascicular arrangement would significantly advance our knowledge of the autonomic nervous system and facilitate studies and application of selective vagus nerve stimulation to avoid off-target effects. The purpose of this study was to trace the thoracic branches of human vagus nerves, investigate their fascicular organization, and analyze the nerves histologically and morphologically. MethodsBoth left and right vagus nerves were dissected from human cadavers, preserving the cardiac, recurrent laryngeal, and pulmonary branches. The nerves were prepared, scanned using microCT, and the fascicles segmented and traced from their branching points. Histology and immunohistochemistry were performed for morphological analysis and validation of the microCT segmentation. The data was then analyzed and compared between nerves. ResultsThe organization of the cardiac, pulmonary, and recurrent laryngeal fascicles was observed for a short distance from their entry point into the nerves. Initially, left vagus nerves showed merging of cardiac and pulmonary fascicles, while the recurrent laryngeal fascicles remained separate. In right vagus nerves, the cardiac fascicles merged with both pulmonary and recurrent laryngeal fascicles. MicroCT imaging limitations prevented visualization and tracing of fiber organization within merged fascicles. Immunohistochemistry and morphological analysis revealed that right vagus nerves were larger and had more fascicles than the left and fascicle counts varied along the nerve, indicating anastomoses. The superior cardiac branch was separate from other fascicles near the VNS cuff placement. ConclusionsIt is possible that organ-specific fibers may still retain some spatial organization despite most fascicles being merged at cervical level. However, fiber tracing and in vivo studies could provide valuable information beyond microCT to resolve this further. The separate superior cardiac fascicles offer potential for targeted neuromodulation of the heart, benefiting conditions like myocardial infarction, heart failure, and atrial fibrillation. Overall, the study provides insights into the morphology and anatomy of human vagus nerves. Our findings thereby contribute to the development of selective vagus nerve stimulation strategies for more precise autonomic regulation.

neuroscience↗

bioRxiv2022

Attenuation of polysialic acid biosynthesis in cells by the small molecule inhibitor 8-keto-sialic acid

Sialic acids are key mediators of cell function, particularly with regards to cellular interactions with the surrounding environment. Reagents that modulate the display of specific sialyl glycoforms at the cell surface would be useful biochemical tools and potentially allow for therapeutic intervention in numerous challenging chronic diseases. While multiple strategies are being explored for the control of cell surface sialosides, none that shows high selectivity between sialyltransferases or that targets a specific sialyl glycoform has yet to emerge. Here we describe a strategy to block the formation of 2,8-linked sialic acid chains (oligo- and polysialic acid) through the use of 8-keto-sialic acid as a chain-terminating metabolic inhibitor that, if incorporated, can not be elongated. 8-Keto-sialic acid is non-toxic at effective concentrations and serves to block polysialic acid synthesis in cancer cell lines and primary immune cells, with minimal effects on other sialyl glycoforms.

biochemistry↗

bioRxiv2022

Organotopic organisation of the cervical vagus nerve

Despite detailed characterization of fascicular organization of somatic nerves, the functional anatomy of fascicles evident in human and large mammal cervical vagus nerve is unknown. The vagus nerve is a prime target for intervention in the field of electroceuticals due to its extensive distribution to the heart, larynx, lungs, and abdominal viscera. However, current practice of the approved vagus nerve stimulation (VNS) technique is to stimulate the entire nerve. This produces indiscriminate stimulation of non-targeted effectors and undesired side effects. Selective neuromodulation is now a possibility with a spatially-selective vagal nerve cuff. However, this requires the knowledge of the fascicular organization at the level of cuff placement to inform selectivity of only the desired target organ or function. We imaged function over milliseconds with fast neural electrical impedance tomography and selective stimulation, and found consistent spatially separated regions within the nerve correlating with the three fascicular groups of interest, suggesting organotopy. This was independently verified with structural imaging by tracing anatomical connections from the end organ with microCT and the development of an anatomical map of the vagus nerve. This confirmed organotopic organization. Here we show, for the first time, localized fascicles in the porcine cervical vagus nerve which map to cardiac, pulmonary and recurrent laryngeal function (N=4). These findings pave the way for improved outcomes in VNS as unwanted side effects could be reduced by targeted selective stimulation of identified organ-specific fascicles and the extension of this technique clinically beyond the currently approved disorders to treat heart failure, chronic inflammatory disorders and more.

neuroscience↗

bioRxiv2020

Imaging fascicular organization of peripheral nerves with fast neural Electrical Impedance Tomography (EIT)

Imaging of the compound action potential (CAP) in fascicles in peripheral nerves could help avoid side effects in neuromodulation by selective stimulation of identified fascicles. Existing methods have low resolution, limited imaging depth, or are invasive. We propose fast neural electrical impedance tomography (EIT), which allows fascicular CAP imaging with a high resolution of [~]200 m, <1 ms. This uses a non-penetrating flexible cuff electrode array with 14 circumferential electrodes. This has been validated in rat sciatic nerve by comparison to micro-computed tomography (microCT) and histology with fluorescent dextran tracers (n=5). With EIT, there were reproducible localized changes in tissue impedance in response to stimulation of individual fascicles (tibial, peroneal and sural). The reconstructed EIT images corresponded to microCT scans and neural tracer histology, with significant separation between the fascicles (p<0.01), and no significant difference between techniques. The standard deviation from the mean fascicle position for EIT was 86 m (6% of nerve diameter). This suggests fast neural EIT can reliably image the functional fascicular anatomy of the nerves and so aid selective neuromodulation.

bioengineering↗

bioRxiv2019

MicroCT optimisation for imaging fascicular anatomy in peripheral nerves

Vagus nerve stimulation (VNS) is a promising therapy for treatment of various conditions resistant to standard therapeutics. However, due to the lack of understanding of the fascicular organisation of the vagus nerve, VNS leads to unwanted off-target effects. Micro-computed tomography (microCT) can be used to trace fascicles from periphery and image fascicular anatomy. In this work we optimised the microCT protocol of the rat sciatic and subsequent pig vagus nerves.\n\nAfter differential staining, the optimal staining time was selected and scanning parameters were altered in subsequent scans. Scans were reconstructed, visualised in ImageJ and fascicles segmented with a custom algorithm in Matlab to determine ultimate parameters for tracking of the nerve. Successful segmentation for tracking of individual fascicles was achieved after 24 hours and 120 hours of staining with Lugols solution (1% total iodine) for rat sciatic and pig vagus nerves, respectively, and the following scanning parameters: 4 {micro}m voxel size, 35 kVp energy, 114 {micro}A current, 4 W power, 0.25 fps in 4 s exposure time, 3176 projections and a molybdenum target.\n\nThe optimised microCT protocol allows for segmentation and tracking of the fascicles within the nerve. This will be used to scan the full length of the pig, and possibly, the human vagus nerves. The resulting segmentation map of the functional anatomical organisation of the vagus nerve will enable selective VNS ultimately allowing for the avoidance of the off-target effects and improving its therapeutic efficacy.

neuroscience↗

bioRxiv2017

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

Despite recent therapeutic advances in the management of BRAFV600-mutant melanoma, there is still a compelling need for more effective treatments for patients who developed BRAF/NRAS wild type disease. Since the activity of single targeted agents is limited by innate and acquired resistance, we performed a high-throughput drug screen using 180 drug combinations to generate over 18,000 viability curves, with the aim of identifying agents that synergise to kill BRAF/NRAS wild type melanoma cells. From this screen we observed strong synergy between the tyrosine kinase inhibitor nilotinib and MEK inhibitors and validated this combination in an independent cell line collection. We found that AXL expression was associated with synergy to the nilotinib/MEK inhibitor combination, and that both drugs work in concert to suppress pERK. This finding was supported by genome-wide CRISPR screening which revealed that resistance mechanisms converge on regulators of the MAPK pathway. Finally, we validated the synergy of nilotinib/trametinib combination in vivo using patient-derived xenografts. Our results indicate that a nilotinib/MEK inhibitor combination may represent an effective therapy in BRAF/NRAS wild type melanoma patients.

cancer biology↗