Biology subjects

Craig, C.

Publications and source records attributed to Craig, C..

9 recordsLinked to original sources

bioRxiv2026

Distinct nigral and brainstem pathology markers map onto separable subthalamic electrophysiological signatures in Parkinson's disease

Subthalamic local field potentials (LFPs) are increasingly used as physiomarkers of the symptomatic state in Parkinsons disease, but their relationship to the underlying neurodegenerative pathology remains unclear. Here, we combined OFF-medication subthalamic LFP recordings with quantitative MRI markers of nigral and brainstem pathology in 33 people with Parkinsons disease. Distinct pathological markers mapped onto dissociable electrophysiological components. Substantia nigra pars compacta susceptibility was associated with increased occupancy, duration and rate of low-{beta} bursts, whereas nigral free water was associated with greater low-frequency aperiodic offset and a steeper slope. Pedunculopontine nucleus free-water- corrected axial diffusivity was selectively associated with high-frequency aperiodic activity, and this relationship strengthened with increasing nigral susceptibility, consistent with dopaminergic-state- dependent influences of extranigral pathology on subthalamic physiology. Only low-frequency aperiodic offset was also associated with contralateral bradykinesia. These findings indicate that the subthalamic LFP is not a unitary readout of dopamine loss or motor state, but an integrated physiological signal in which pathology across interconnected systems is expressed through separable oscillatory and aperiodic components. Chronically implanted devices may therefore provide physiological readouts of underlying disease biology alongside control signals for adaptive therapy.

neuroscience↗

bioRxiv2025

Knockout of Rab27b exacerbates neuropathology in alpha-synuclein mouse models

Parkinsons Disease (PD) and other synucleinopathies are characterized by the formation of inclusions comprised of alpha-synuclein (syn) among other proteins, but the mechanisms by which these inclusions form and cause toxicity are not well understood. We have previously reported that the small GTPase Rab27b modulates autophagic-lysosomal function in neurons and supports lysosomal degradation of syn across multiple syn cellular models. Knockout (KO) and knockdown of Rab27b damage lysosomal degradative capacity and exacerbate syn pathology, while Rab27b overexpression is conversely protective in cellular syn models. Elevations of Rab27b seen in human synucleinopathies suggest a compensatory role for Rab27b in these disorders. Here, we examined the role Rab27b plays in vivo in the context of both A53T genetic syn overexpression and viral AAV syn overexpression mouse models. Rab27b knockout in A53T+ mice did not alter motor behavior or survival. However, Rab27b knockout increased proteinase-K resistant syn in the cortex, striatum, and substantia nigra of A53T mice starting as early as six months of age. Additionally, Rab27b KO increased phosphorylated S129 syn in the cortex and nigra. Astrocyte and microglial activation were also observed upon Rab27b KO in the A53T model. In the AAV syn model, Rab27b KO resulted in accelerated dopaminergic cell loss in the nigra. Collectively, we report that loss of Rab27b results in elevated neuropathology in PD-relevant brain regions, validating its role as a therapeutic target in synucleinopathies.

neuroscience↗

bioRxiv2025

CandyCollect Open to Closed (O2C) Microfluidic System for Rapid and User-Centric Detection of Group A Streptococcus

We created CandyCollect, a lollipop-inspired, child-friendly saliva sampling device that provides enhanced comfort compared to common throat and mouth swabs. The device has an open microchannel and a functionalized surface that effectively captures and stores the saliva and pathogens. We recently demonstrated the ability to combine the CandyCollect with rapid antigen detection tests (RADTs) for fast and accessible detection of group A streptococcus (GAS). However, the current procedure necessitates manual steps to elute and transfer captured antigens from the lollipop to RADTs, which relies on the user to follow complex instructions, increasing the likelihood of error. In this work, we developed the CandyCollect Open to Closed (O2C) microfluidic system to automate antigen elution and streamline detection with RADTs. The O2C system securely seals the open microchannels of the CandyCollect device to create a continuous closed channel for seamless delivery of elution reagents to release antigens at the press of a button for subsequent lateral flow detection. Our system leverages and combines the unique benefits of both open channel and closed channel microfluidics into one platform, further enhancing the potential of both methods. We performed experiments with GAS bacteria spiked into saliva and compared the manual and O2C elution methods. Both the manual and O2C methods showed clear test lines on the RADT strips at clinically relevant GAS concentrations (between 5 x105 and 109 CFU/mL). The O2C provided comparable or better results than the manual procedure in a more convenient form factor. The O2C platform has the potential to enable user-friendly screening for respiratory pathogens by minimally trained users in decentralized settings.

bioengineering↗

bioRxiv2024

Expanding the capillarics toolbox: 3D-printed microfluidic phaseguides and self-coalescence modules

Capillarics are microfluidic circuits that are assembled from individual fluidic elements, powered by surface tension forces encoded by microchannel geometry and surface chemistry, and enable instrument-free pre-programmed automation of multi-step liquid handling processes. 3D printing has recently transformed capillarics by enabling rapid and cost-effective prototyping, provided addition geometric degrees of freedom in multi-level fabrication, and facilitated new design paradigms with greater capabilities than traditional cleanroom fabrication. Despite widespread interest in 3D printing and development of custom high-resolution stereolithography printers for microfluidic applications, fluidic elements that require precise and tunable control over capillary pinning lines -- such as fluidic phaseguides and self-coalescence modules (SCMs) -- have so far only been manufactured with centralized and expensive cleanroom methods. Not only does this limit access to versatile capillaric features to only well-resourced settings, but it also slows innovation and widespread application of these fluid handling technologies. Here we expand the toolbox of 3D-printed capillarics to include phaseguides and SCMs, demonstrating their potential for precise instrument-free control over multi-step liquid handling and reagent rehydration. We employed benchtop stereolithography printers to prototype (up to 50X) scaled-up phaseguides and SCMs and integrated them into a capillaric circuit for inline reagent reconstitution, dynamic fluid control, and sequential drainage. We showcased scalable designs, customizable geometries, and robust self-coalescing flow for larger liquid volumes -- up to 50 L compared with 1.25 L in cleanroom-fabricated SCMs. This work represents a significant advance in democratizing access to microfluidics, with potential for broad applications in diagnostics, assay automation, and organ-on-chip systems.

bioengineering↗

bioRxiv2024

REverse transcriptase ACTivity (REACT) assay for point-of-care measurement of established and emerging antiretrovirals for HIV treatment and prevention

Maintaining adequate levels of antiretroviral (ARV) medications is crucial for the efficacy of HIV treatment and prevention regimens. Monitoring ARV levels can predict or prevent adverse health outcomes like treatment failure or drug resistance. However, conventional ARV measurement using liquid chromatography-tandem mass spectrometry (LC-MS/MS) is slow, expensive, and centralized delaying clinical and behavioral interventions. We previously developed a rapid enzymatic assay for measuring nucleotide reverse transcriptase inhibitors (NRTIs) - the backbone of HIV treatment and prevention regimens - based on the drugs termination of DNA synthesis by HIV reverse transcriptase (RT) enzyme. Here we expand our work to include non-nucleoside reverse transcriptase inhibitors (NNRTIs) - an ARV class used in established and emerging HIV treatment and prevention regimens. We demonstrate that the REverse Transcriptase ACTivity (REACT) assay can detect NNRTIs including medications used in oral and long-acting/extended-release HIV treatment and prevention. We demonstrate that REACT can measure NNRTIs spiked in either buffer or diluted plasma, and that fluorescence can be measured on both a traditional plate reader and an inexpensive portable reader that can be deployed in point-of-care (POC) settings. REACT measured clinically relevant concentrations of five NNRTI spiked in aqueous buffer. REACT measurements showed excellent agreement between the plate reader and the portable reader, with a high correlation in both aqueous buffer (Pearsons r=0.9807, P < 0.0001) and diluted plasma (Pearsons r = 0.9681, P < 0.0001). REACT has the potential to provide rapid measurement of NNRTIs in POC settings and may help to improve HIV treatment and prevention outcomes.

bioengineering↗

bioRxiv2024

Saturation transposon mutagenesis enables genome-wide identification of genes required for growth and fluconazole resistance in the human fungal pathogen Cryptococcus neoformans

Fungi can cause devastating invasive infections, typically in immunocompromised patients. Treatment is complicated both by the evolutionary similarity between humans and fungi and by the frequent emergence of drug resistance. Studies in fungal pathogens have long been slowed by a lack of high-throughput tools and community resources that are common in model organisms. Here we demonstrate a high-throughput transposon mutagenesis and sequencing (TN-seq) system in Cryptococcus neoformans that enables genome-wide determination of gene essentiality. We employed a random forest machine learning approach to classify the Cryptococcus neoformans genome as essential or nonessential, predicting 1,465 essential genes, including 302 that lack human orthologs. These genes are ideal targets for new antifungal drug development. TN-seq also enables genome-wide measurement of the fitness contribution of genes to phenotypes of interest. As proof of principle, we demonstrate the genome-wide contribution of genes to growth in fluconazole, a clinically used antifungal. We show a novel role for the well-studied RIM101 pathway in fluconazole susceptibility. We also show that 5 insertions of transposons can drive sensitization of essential genes, enabling screenlike assays of both essential and nonessential components of the genome. Using this approach, we demonstrate a role for mitochondrial function in fluconazole sensitivity, such that tuning down many essential mitochondrial genes via 5 insertions can drive resistance to fluconazole. Our assay system will be valuable in future studies of C. neoformans, particularly in examining the consequences of genotypic diversity.

microbiology↗

bioRxiv2023

Spies of the deep: an animal-borne active sonar and bioluminescence tag to characterise mesopelagic prey size and behaviour in distinct oceanographic domains

Mesopelagic fish, a central component of marine trophic networks, play a fundamental role in marine ecosystems. However, as they live in highly inaccessible environments, little information is currently available on their ecology, especially on the influence of oceanographic parameters on their distribution. The emergence of biologging technologies has made it possible to use deep-diving predators as bio-samplers of their environment in under-sampled regions. In this work, we deployed an innovati ve miniaturised sonar tag that combines active acoustics with high-resolution GPS, pressure, movement and light sensors on Southern elephant seals, a deep-diving predator feeding on mesopelagic prey. Seals were also equipped with oceanographic tags, allowing us to explore the functional relationships between oceanographic parameters, distribution and ecology of mesopelagic prey targeted by seals and the seals foraging behaviour. We highlighted strong vertical differences in prey characteristics and behaviour, with larger, more evasive and less bioluminescent prey in deeper waters. Moreover, prey encountered in warmer waters were found deeper, were more evasive and displayed a more marked diel vertical migration behaviour compared to prey encountered in colder waters, suggesting that prey accessibility and characteristics differ according to oceanographic domains. This study highlights the usefulness of the sonar-bioluminescence tag to infer mesopelagic prey distribution and habitat when deployed on deep-diving predators such as elephant seals.

ecology↗

bioRxiv2021

Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages from livestock. Porcine and bovine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages. Pig PSCdMs were productively infected by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and African Swine Fever Virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, Pig PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied in parental stem cells, or directly by lentiviral vector transduction. PSCs and differentiated derivatives therefore provide a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in livestock.

immunology↗

bioRxiv2017

High Frequency Actionable Pathogenic Exome Mutations in an Average-Risk Cohort

Whole exome sequencing (WES) is increasingly utilized in both clinical and non-clinical settings, but little is known about the utility of WES in healthy individuals. In order to determine the frequency of both medically actionable and non-actionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multi-omics profiling study at Stanford University. We assessed exomes for rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We used American College of Medical Genetics (ACMG) guidelines were used for the classification of rare sequence variants, and additionally we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes, including 6 (9%) with mutations in genes not currently included in the ACMGs list of 59 actionable genes. This number is higher than that reported in previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 60 participants (89%) had non-actionable findings identified including 57 who were found to be mutation carriers for recessive diseases and 21 who have increased Alzheimers disease risk due to heterozyg ous or homozygous APOE e4 alleles (18 participants had both). These results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.

genomics↗