Biology subjects

Donnelly, J.

Publications and source records attributed to Donnelly, J..

9 recordsLinked to original sources

bioRxiv2026

Real-time electrochemical protein monitoring using molecular pendulum sensors

Continuous monitoring of proteins in complex biological fluids is essential for advancing personalized medicine, yet existing biosensors are often limited by instability, single-use designs, and insufficient sensitivity. Here, we describe a detailed protocol for the fabrication and operation of molecular pendulum (MP) electrochemical sensors integrated with an active-reset mechanism to enable real-time, reversible, and ultrasensitive protein detection. The protocol is described in two parts. First, we describe the microfabrication of gold microelectrodes and their nanostructured modification, followed by assembly of DNA-based pendulum probes with redox reporters and affinity receptors that translate binding into kinetic electron-transfer shifts. Second, we detail the sensing and active-reset approach, which detects the target analyte and applies tunable oscillatory potentials to accelerate its dissociation, regenerate sensor surfaces, and extend operational lifetime. The protocol includes detailed guidance on device fabrication, surface functionalization, sensing and reset cycles, and data analysis. When implemented, MP sensors with active-reset achieve pg/ml sensitivity, rapid equilibration, and robust performance across biofluids and in situ models, enabling continuous protein monitoring over extended periods. This combined technology represents a biosensing platform with significant potential, opening new avenues for wearable and implantable molecular monitoring, early disease detection, and personalized therapeutic guidance.

bioengineering↗

bioRxiv2025

Deconstructing natural products to develop synthetic small molecule attachment inhibitors with broad spectrum antiviral activity

The continuous emergence of new viruses and the number of viruses that are each highly consequential for few people raise a need for broad spectrum antivirals. Most human and emerging viruses first attach to cellular glycosaminoglycans (GAG) or sialylated glycans (SG), a potential target for broad spectrum antivirals. Attachment to the former is through polar interactions between the negatively charged glycans and positively charged domains in virion proteins and typically inhibited by negatively charged polymers. Attachment to the latter is through specific interactions at binding pockets and inhibited by molecules that bind to these pockets. Surprisingly, EGCG inhibits viruses that attach to GAG and SG. However, it does so with widely differing potencies, is not a pharmacologically desirable molecule, and is limited by solubility. We tested whether it was possible to develop small synthetic molecules to inhibit viruses that attach to SG or GAG. We first identified the EGCG moieties responsible for the antiviral activity. The two polyhydroxylated phenyl groups were essential while the central benzopyran linker was not. We thus designed a series of gallate compounds to explore the minimal pharmacophore required for broad-spectrum antiviral activity. By exploring the linkers and number of galloyls, we identified small molecule inhibitors of herpes simplex virus 1, influenza A virus, and the coronaviruses hCoV OC43 and SARS-CoV-2. These compounds have low micromolar to submicromolar potency and no limiting cytotoxicity. These molecules are still not pharmacologically optimized and limited by solubility, but they define a minimal pharmacophore that confers broad spectrum antiviral activity. ImportanceThe SARS-CoV-2 pandemic demonstrated the importance of antivirals in managing emerging viruses. Although vaccines were successfully developed in less than two years, there was resistance to vaccination while infected or sick people were far more willing to take antivirals. It is impossible to develop antivirals specific for unknown viruses, but broad spectrum antivirals could control viral spread until more specific and potent drugs are developed. Human pathogenic and emerging viruses commonly attach to glycans, providing a target for broad spectrum antivirals. However, inhibitors of attachment to glycosaminoglycans do not typically inhibit viruses attaching to sialylated glycans, and vice-versa. We had found that EGCG has the unique property of inhibiting viruses that attach both glycans, with quite different potencies. Here, deconstructed a natural compound, EGCG, to identify the moieties responsible for its antiviral activity to then produce broad spectrum antiviral compounds against established and emerging viruses that attach to either glycan.

microbiology↗

bioRxiv2024

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease

Mitochondrial disease encompasses untreatable conditions affecting tissues with high energy demands. A severe manifestation of mitochondrial disease is Leigh syndrome (Leigh), which causes defects in basal ganglia and midbrain regions, psychomotor regression, lactic acidosis, and early death. We previously generated isogenic pairs of Leigh cerebral organoids and uncovered defects in neuromorphogenesis. Here, we leveraged on this disease feature to devise drug discovery pipelines. We developed a deep learning algorithm tailored for cell type-specific drug repurposing to identify drugs capable of promoting neuronal commitment. In parallel, we performed a survival drug screen in yeast and validated the repurposable hits on branching capacity in Leigh neurons. The two approaches independently highlighted azole compounds, Talarozole and Sertaconazole, both of which lowered lactate release and improved neurogenesis and neurite organization in Leigh midbrain organoids. Hence, targeting neuromorphogenesis has led to identify potential new drugs for mitochondrial disease and could prove an effective strategy for further drug discovery.

neuroscience↗

bioRxiv2024

A Genome-Wide CRISPR Screen Identifies Sortilin as the Receptor Responsible for Galectin-1 Lysosomal Trafficking

Galectins are a family of mammalian glycan-binding proteins that have been implicated as regulators of myriad cellular processes including cell migration, apoptosis, and immune modulation. Several members of this family, such as galectin-1, exhibit both cell-surface and intracellular functions. Interestingly, galectin-1 can be found in the endomembrane system, nucleus, or cytosol, as well as on the cell surface. The mechanisms by which galectin-1 traffics between cellular compartments, including its unconventional secretion and internalization processes, are poorly understood. Here, we determined the pathways by which exogenous galectin-1 enters cells and explored its capacity as a delivery vehicle for protein and siRNA therapeutics. We used a galectin-1-toxin conjugate, modelled on antibody-drug conjugates, as a selection tool in a genome-wide CRISPR screen. We discovered that galectin-1 interacts with the endosome-lysosome trafficking receptor sortilin in a glycan-dependent manner, which regulates galectin-1 trafficking to the lysosome. Further, we show that this pathway can be exploited for delivery of a functional siRNA. This study sheds light on the mechanisms by which galectin-1 is internalized by cells and suggests a new strategy for intracellular drug delivery via galectin-1 conjugation.

molecular biology↗

bioRxiv2023

Behavioural pharmacology predicts disrupted signalling pathways and candidate therapeutics from zebrafish mutants of Alzheimer's disease risk genes

By exposing genes associated with disease, genomic studies provide hundreds of starting points that should lead to druggable processes. However, our ability to systematically translate these genomic findings into biological pathways remains limited. Here, we combine rapid loss-of-function mutagenesis of Alzheimers risk genes and behavioural pharmacology in zebrafish to predict disrupted processes and candidate therapeutics. FramebyFrame, our expanded package for the analysis of larval behaviours, revealed that decreased night-time sleep was common to F0 knockouts of all four late-onset Alzheimers risk genes tested. We developed an online tool, ZOLTAR, which compares any behavioural fingerprint to a library of fingerprints from larvae treated with 3,677 compounds. ZOLTAR successfully predicted that sorl1 mutants have disrupted serotonin signalling and identified betamethasone as a drug which normalises the excessive day-time sleep of presenilin-2 knockout larvae with minimal side effects. Predictive behavioural pharmacology offers a general framework to rapidly link disease-associated genes to druggable pathways.

neuroscience↗

bioRxiv2023

Transdermal Electrophysiological Recordings of Diabetic Peripheral Neuropathy Using a Needle Electrode Array in Mice and Men

Diabetic peripheral neuropathy (DPN) is a common complication of diabetes. Proactive treatment options remain limited, which is exacerbated by a lack of sensitive and convenient diagnostics, especially early in disease progression or specifically to assess small fiber neuropathy (SFN), the loss of distal small diameter axons that innervate tissues and organs. We designed, fabricated, tested, and validated a first-of-its-kind medical diagnostic device for the functional assessment of transdermal small fiber nerve activity. This device, the Detecting Early Neuropathy (DEN), is an electrically conductive needle array designed to record nerve electrical activity in the skin and subdermal tissues. DEN recordings were validated across a time course of diet-induced DPN in mice, using statistical and computational analyses compared to other SFN measures. Based on these preclinical mouse data, the device design was adapted to obtain recordings in human with a flexible printed circuit board to mold to the leg or other skin regions. The DEN successfully recorded various types of neural activity in mouse and human, with or without stimulation, including validated action potentials and electromyography signals. New functional diagnostic tools like DEN offer a promising outlook for patients needing an earlier or more sensitive diagnosis of SFN/DPN, to allow for earlier and more effective treatment options, especially as more become available in the clinic in future years.

bioengineering↗

bioRxiv2018

Growth Factor Independent 1 is a tumor suppressor gene in colorectal cancer

Colorectal cancer (CRC) is the third most common cancer and the third leading cause of cancer death in the United States, causing about 50,000 deaths each year. Growth Factor-Independent 1 (GFI1) is a critical zinc finger transcriptional repressor responsible for controlling secretory cell differentiation in the small intestine and colon. GFI1 plays a significant role in the development of human malignancies, including leukemia, lung cancer and prostate cancer. However, the role of GFI1 in CRC progression is largely unknown. Our results demonstrate that RNA and protein expression of GFI1 are reduced in advanced stages of non-mucinous CRC. Subcutaneous tumor models demonstrated that the re-expression of GFI1 in 4 different human CRC cell lines inhibits tumor growth by 25-60%. To further investigate the role of Gfi1 in de novo colorectal tumorigenesis, we developed transgenic mice harboring a deletion of Gfi1 in the distal intestine driven by the CDX2cre (Gfi1F/F; CDX2cre/+) and crossed them with ApcMin/+ mice (ApcMin/+; Gfi1F/F; CDX2cre/+). Loss of Gfi1 significantly increased the total number of colorectal adenomas compared to littermate controls with an APC mutation alone. Furthermore, we found that compound (ApcMin/+; Gfi1F/F; CDX2cre/+) mice develop both adenomas as well as carcinoid-like tumors expressing the neuroendocrine marker chromogranin A, a feature that has not been previously described in APC-mutant tumors in mice. Collectively, these results demonstrate that Gfi1 deficiency promotes colorectal tumorigenesis, and suggest that loss of Gfi1 may promote formation of carcinoid cancers of the large intestines.\n\nSignificanceThese findings reveal that GFI1 functions as a tumor suppressor gene in colorectal tumorigenesis.

cancer biology↗

bioRxiv2018

Acute-stress impairs cytoprotective mechanisms through neural inhibition of the insulin pathway

Persistent activation of the \"fight-or-flight\" response accelerates aging and increases the susceptibility to disease. We show that repeated induction of the C. elegans flight response inhibits conserved cytoprotective mechanisms. This acute-stress response activates neurons that release tyramine, the invertebrate analog of adrenaline/noradrenaline. Tyramine stimulates the DAF-2/Insulin/IGF-1 pathway and precludes the nuclear translocation of the DAF-16/FOXO transcription factor through the activation of an adrenergic-like receptor TYRA-3 in the intestine. In contrast, environmental long-term stressors, such as heat or oxidative stress, reduce tyramine release allowing the induction of FOXO-dependent cytoprotective genes. These findings demonstrate how a neural stress-hormone signaling provides a state-dependent neural switch between acute and long-term stress responses, and provide mechanistic insights how acute stress impairs cellular defensive systems.\n\nOne Sentence Summary: The \"fight-or-flight\" response reduces resistance to environmental challenges.

neuroscience↗

bioRxiv2017

Cerebral Autoregulation, CSF outflow resistance and outcome following CSF diversion in Normal Pressure Hydrocephalus.

IntroductionNormal pressure hydrocephalus (NPH) is not simply the result of a disturbance in cerebrospinal fluid (CSF) circulation, but often includes cardiovascular comorbidity and abnormalities within the cerebral mantle. In this study, we have examined the relationship between the global autoregulation pressure reactivity index (PRx), the profile of disturbed CSF circulation and pressure-volume compensation, and their possible effects on outcome after surgery.\n\nMaterials and methodsWe studied a cohort of 131 patients, investigated for possible NPH. Parameters describing CSF compensation and circulation were calculated during the cerebrospinal fluid (CSF) infusion test and PRx was calculated from CSF pressure and arterial pressure recordings. A simple scale was used to mark the patients outcome 6 months after surgery (improvement, temporary improvement, and no improvement).\n\nResultsPRx was negatively correlated with Rout (R=-0.18; p=0.044); patients with normal CSF circulation tended to have worse autoregulation. The correlation for patients who were surgically-managed (N=83) was: R=-0.28; p=0.03, and stronger in patients who improved after surgery (N=64; R=-0.36; p=0.03). In patients who did not improve, the correlation was not significantly different from zero (N= 19; R=0.17; p=0.15). There was a trend towards higher values for PRx in non-responders than in responders (PRx =0.16+/- 0.04 vs 0.09 +/-0.02 respectively; p=0.061), associated with higher MAP values (107.2+/-8.2 in non-responders vs 89.5+/-3.5 in responders; p=0.195). The product of MAP* (1+PRx), proposed as a measure of combined arterial hypertension and deranged autoregulation, showed a significant association with outcome (greater value in non-responders; p=0.013).\n\nConclusionAutoregulation proves to associate with cerebrospinal fluid circulation, and appears strongest in shunt responders. Outcome following CSF diversion is possibly most favorable when CSF outflow resistance is increased and global cerebral autoregulation is intact, in combination with arterial normotension.

neuroscience↗