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Kelly, T.

Publications and source records attributed to Kelly, T..

At least 19 recordsLinked to original sources

WildAlert: A Real-Time, AI-Driven Early Warning System for Wildlife Health and Ecological Threat Detection

Emerging infections and environmental disruptions increasingly threaten wildlife and ecosystem health. Free-ranging wildlife often serve as early indicators of ecological instability, making timely detection of morbidity and mortality events critical for early warning. Yet, existing systems lack the analytical capacity for real-time outbreak detection. We present WildAlert, an AI-driven early warning system that integrates fine-tuned BERT-based natural language processing models with unsupervised anomaly detection framework to identify unusual wildlife health events using real-time pre-diagnostic clinical data from wildlife rehabilitation organizations. The NLP module achieved high accuracy across clinical classifications and circumstances of admissions, enabling a pre-diagnostic syndromic surveillance framework. Retrospective validation demonstrated that WildAlert anomalies frequently coincided with or preceded confirmed morbidity events, including highly pathogenic avian influenza (HPAI), harmful algal bloom-associated toxicosis, cold-stunning in sea turtles, mass stranding events, West Nile virus, and mycoplasmosis. WildAlert establishes the worlds largest standardized, near real-time wildlife health surveillance system, transforming wildlife rehabilitation clinical records into actionable intelligence capable of detecting anomalies across taxa and regions, often before other surveillance methods. WildAlert provides a transferable analytical framework and scalable One Health model linking biodiversity monitoring, zoonotic disease preparedness, and ecosystem-linked environmental threats, with implications for conservation, public health and environmental hazard response.

ecology↗

The effect of chronic, latent Toxoplasma gondii infection on human behavior: Testing the parasite manipulation hypothesis in humans

Parasitism is one of the key, structural, interspecific interactions in ecology. One remarkable parasitic strategy that has been documented in multiple systems is the behavioral manipulation of hosts to increase parasite fitness. While not yet documented in humans, we propose that a ubiquitous zoonotic parasite - Toxoplasma gondii - may change human behavior to favor the parasite by increasing the fitness of the parasites definitive host - cats. Specifically, we assess the possibility that human behavioral changes resulting from chronic, latent T. gondii infection lead to measurable changes in attitudes, actions and dopaminergic responses towards cats that function to increase domestic cat fitness. We assessed the potential role of humans in the T. gondii lifecycle by identifying and testing behavioral changes in humans that benefit the parasite; specifically, human affection for cats. We assessed T. gondii infection status in 68 participants using T. gondii serum antibody testing, and assessed their attitudes towards cats in three ways: i) surveys, ii) participant behavior in the presence of domestic cats, and iii) participant oxytocin levels before and after interactions with cats to assess dopaminergic changes. Only 2 of 68 participants were positive for T. gondii antibodies, limiting statistical power. However, our results indicated that T. gondii-positive participants both reported a greater affection for cats in surveys, and spent more time engaged with cats during behavioral trials than T. gondii-negative participants (87% of study time engaging with cats vs 75%). Oxytocin results were inconclusive.

evolutionary biology↗

Targeting epilepsy with photopharmacology in human brain tissue

Photo-activatable drugs (PDs) are rapidly emerging as precision therapeutics across biomedical research, yet their potential in epilepsy treatment has remained understudied. Given that 30% of epilepsies are medically refractory, and anti-seizure medications often cause multi-organ side-effects, PDs could break new ground. Here, we evaluate light-switchable ion-channel blockers QAQ and CQAQ, and a newly developed caged propofol (CaP), in murine brain slices, and postsurgical brain tissue from patients with epilepsy or brain tumors. In mice, we show that QAQ/CQAQ reversibly suppress neuronal firing, while photo-activated CaP prolonged inhibitory post-synaptic currents and enhanced leak current. While QAQ caused identical effects in human tissue, CQAQ unexpectedly increased firing. Activated CaP robustly suppressed epileptiform activity across species. This work establishes CaP as a tool for neuroscience and disease-related studies. Our results highlight the necessity for early human model testing in biomedical research, and showcase photopharmacology as a potential powerful approach to control human epilepsy.

pharmacology and toxicology↗

Partial retention of ancient function increases genetic pleiotropy in grass evolution

Changes in form are driven by the differential, context-dependent regulation of pleiotropic genes. How genetic pleiotropy itself emerges, however, remains unclear. The maize genes GRASSY TILLERS1 (GT1) and RAMOSA3 (RA3) are required for axillary meristem suppression, a deeply conserved trait across angiosperms, and for floral organ suppression, a trait which evolved within the grass family. To determine how these pleiotropic functions are regulated, we first established a high-throughput method for quantitative phenotyping of grass flowers. Using this method, we show that distinct environmental mechanisms regulate axillary meristem versus floral organ suppression. In line with these differences, we find upstream regulation of GT1 and RA3 has diverged, consistent with their redeployment in flowers. Our results show that, rather than wholesale adoption of genetic networks, developmental genes can retain ancient functions and be recruited into other programs in the evolution of form, thereby increasing genetic pleiotropy.

plant biology↗

Nanoscale dendritic shaft constrictions shape synaptic integration in fine caliber principal neuron dendrites

Traditionally, theoretical studies typically described dendritic morphology as optimized for efficient synaptic voltage transfer from spines to the soma, implemented as a tubular design respecting Ralls 3/2 rule for impedance matching at branch points. Here, we reveal that this view is an oversimplification. Using three high-resolution imaging techniques, we demonstrate that dendrites in cortical and hippocampal neurons contain nanoscale constrictions, comparable in diameter to spine necks. We provide theoretical and experimental evidence that these constrictions partition the dendrite into distinct electrical compartments, significantly shaping dendritic integration of synaptic potentials.

neuroscience↗

Monensin and Its Analogs Exhibit Activity Against Breast Cancer Stem-Like Cells in an Organoid Model

Monensin (MON) is a polyether ionophore antibiotic of natural origin and is an FDA-approved drug for veterinary use. Recent studies have highlighted its potential anti-cancer activity in various in vitro and in vivo models. In this study, we evaluated the anti-breast cancer activity of MON and 37 synthetic analog compounds using cell monolayer and organoid models. Through a mini-ring cell viability assay, several compounds were identified that were more potent and selective against breast cancer cells compared to non-cancerous cells, surpassing the activity of parent MON. MON and these compounds induced significant DNA fragmentation, reduced cell migration, and downregulated SOX2 expression. Furthermore, MON and the most potent analog, compound 12, reduced the percentage of CD44+/CD24-/low stem-like cells and diminished cell self-renewal properties. Proteomics analyses revealed that several pathways, including extracellular matrix organization, were significantly dysregulated by MON and compound 12 in breast cancer cells. Among these, TIMP2, a protein associated with the suppression of tumor growth and metastasis, was identified as one of the most prominently upregulated proteins by MON and compound 12 in MDA-MB-231 cells. This finding was also validated in other breast cancer and melanoma cell lines. To simulate breast cancer metastasis to the brain, a human Hybrid Organoid System: Tumor in Brain Organoid (HOSTBO) model was developed. MON and compound 12 significantly reduced Ki-67 expression within the HOSTBOs, and compound 12 significantly downregulated SOX2 expression. Collectively, MON and compound 12 significantly reduced the proliferation of breast cancer stem-like cells in the organoid models, inhibited their migration, and dysregulated markers associated with stemness, demonstrating their potential as anti-metastatic agents and warranting further clinical development. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/663311v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@388862org.highwire.dtl.DTLVardef@182072dorg.highwire.dtl.DTLVardef@1a55072org.highwire.dtl.DTLVardef@447150_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

Early postnatal CA3 hyperexcitability drives hippocampal development and epileptogenesis in SCN2A developmental and epileptic encephalopathy

Developmental and epileptic encephalopathies caused by pathogenic variants in SCN2A (SCN2A-DEE), encoding the voltage-gated sodium channel Nav1.2, present with early-life seizures, developmental delay, and increased mortality. Using a novel Scn2a p.A263V gain-of-function (GOF) mouse model, we demonstrate gene-dose and background-dependent phenotypes ranging from self-limited neonatal seizures to chronic epilepsy with high mortality. In vivo electrophysiology revealed hippocampal seizures as early as postnatal day 2.5, with CA3-driven gamma oscillations preceding seizure onset. CA3 and CA1 pyramidal neurons exhibited transient hyperexcitability during early postnatal development, resolving by P24-30. Single-cell RNA sequencing uncovered gene dose-dependent accelerated maturation of hippocampal networks, peaking at P7, alongside widespread transcriptional changes in excitatory and inhibitory neurons. In adulthood, persistent hippocampal network alterations emerged, marked by reduced mid-gamma oscillations and theta-gamma coupling. Our findings establish hippocampal CA3 hyperexcitability as an early driver of epileptogenesis in SCN2A-DEE and highlight it as a potential therapeutic target to mitigate disease progression.

neuroscience↗

Overcoming lentiviral delivery limitations in hard-to-transduce suspension cells for genome-wide CRISPR screening

Lentiviral vectors are a cornerstone delivery modality of biomedical research, renowned for their ability to stably integrate genetic material into the host genome, enabling sustained transgene expression and long-term genetic manipulation. These properties make them indispensable tools in functional genomics and genome engineering, particularly for delivering molecular components in high-throughput CRISPR screening, a powerful approach for uncovering the genetic basis of complex cellular mechanisms and phenotypes. However, challenges such as lentiviral-induced recombination, unpredictable integration profiles, and variable susceptibility of target cells to transduction can introduce noise and compromise experimental outcomes. In this study, we selected two suspension-adapted mammalian cell lines, Chinese Hamster Ovary cells CHO-K1 and Human Embryonic Kidney cells HEK293-6E, due to their widespread use in recombinant protein production. Recognizing the influence of intrinsic cell line properties and transduction methodology, we compared two distinct procedures: spinoculation and static transduction. By implementing a two-step static transduction protocol, we achieved significantly higher transduction efficiencies while minimizing cellular stress, streamlining workflows, and eliminating scalability limitations inherent to large-scale lentiviral applications like genome-wide CRISPR screens. To further characterize the variation in lentiviral integration, we used droplet digital PCR (ddPCR) to quantify copy number variation (CNV) both at the pooled population level and within individual clonal isolates. This comprehensive analysis underscores the robustness of our optimized protocol in enhancing transduction efficiency in difficult-to-transduce suspension cell lines. It further emphasizes the importance of carefully modulating infection rates to limit multiple integrations, ensuring the accuracy and consistency required for large-scale functional genomics applications.

molecular biology↗

A genome-scale CRISPR deletion screen in Chinese Hamster Ovary cells reveals essential regions of the coding and non-coding genome

The biopharmaceutical sector relies on CHO cells to investigate biological processes and as the preferred host for production of biotherapeutics. Simultaneously, advancements in CHO cell genome assembly have provided insights for developing sophisticated genetic engineering strategies. While the majority of these efforts have focused on coding genes, with some interest in transcribed non-coding RNAs (e.g., microRNAs and lncRNAs), there remains a lack of genome-wide systematic studies that precisely examine the remaining 90% of the genome. This unannotated "dark matter" includes regulatory elements and other, poorly understood or characterized functionality of the genome that may be potentially critical for cell survival. In this study, we deployed a genome-scale CRISPR screening platform with 112,272 paired guide RNAs targeting 14,034 genomic regions for complete deletion of 150 kb long sections. This platform enabled the execution of a negative screen that selectively identified dying cells to determine regions essential for cell survival. By using paired gRNAs, we overcame the intrinsic limitations of traditional frameshift strategies, which will likely have little or no effect on the non-coding genome. This study revealed 427 regions essential for CHO survival, many of which currently lack gene annotation or known function. For these regions we present annotation status, transcriptional activity as well as annotated chromatin states such as enhancers. Selected regions, specifically those that were negative for all the above, were individually deleted for confirmation. This work sheds a novel light on a substantial part of the mammalian genome which is traditionally difficult to investigate and therefore, neglected.

cell biology↗

Chromatin Changes Associated with Neutrophil Extracellular Trap (NET) Formation in Whole Blood Reflect Complex Immune Signaling

BackgroundNeutrophils are key players in innate immunity, forming neutrophil extracellular traps (NETs) to defend against infections. However, excess NET formation is implicated in inflammatory conditions such as sepsis and immunothrombosis. Studying NET formation in isolated neutrophils provides important mechanistic insights but does not reflect the complexity of immune interactions in whole blood, limiting our understanding of neutrophil responses. MethodsThis study investigates chromatin accessibility changes using Assay for Transposase-Accessible Chromatin with sequencing (ATAC-Seq) during phorbol 12-myristate 13-acetate (PMA) induced NET formation in whole blood. We compared chromatin accessibility patterns in neutrophils following PMA treatment in isolation and whole blood to assess the impact of other immune cells and signaling environment. ResultsWhole blood PMA stimulation elicited consistent chromatin accessibility changes across donors, demonstrating organized chromatin decondensation during NET formation. The chromatin response was characterized by increased accessibility in genomic regions enriched for immune-specific pathways, highlighting the role of immune cell interactions in NET formation. Differentially accessible regions (DARs) present following PMA induction in whole blood and isolated neutrophils showed greater association with NET-related and inflammatory transcription factors, while DARs specific to isolated neutrophils showed fewer relevant motifs. Pathway analysis indicated that whole blood responses involved more robust activation of immune-specific pathways, such as interleukin and cytokine signaling, compared to isolated neutrophils. ConclusionsOur findings underscore the importance of studying NET formation within a whole blood environment to capture the complexity of neutrophil responses and immune cell interactions. This understanding is crucial for identifying effective therapeutic targets in NET-associated inflammatory diseases.

immunology↗

Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adenoviral expression of Ca2+ indicators

Genetically encoded calcium indicators (GECIs) such as GCaMP are invaluable tools in neuroscience to monitor neuronal activity using optical imaging. The viral transduction of GECIs is commonly used to target expression to specific brain regions, can be conveniently used with any mouse strain of interest without the need for prior crossing with a GECI mouse line and avoids potential hazards due to the chronic expression of GECIs during development. A key requirement for monitoring neuronal activity with an indicator is that the indicator itself minimally affects activity. Here, using common adeno-associated viral (AAV) transduction procedures, we describe spatially confined aberrant Ca2+ micro-waves slowly travelling through the hippocampus following expression of GCaMP6, GCaMP7 or R-CaMP1.07 driven by the synapsin promoter with AAV-dependent gene transfer, in a titre-dependent fashion. Ca2+ micro-waves developed in hippocampal CA1 and CA3, but not dentate gyrus (DG) nor neocortex, were typically first observed at 4 weeks after viral transduction, and persisted up to at least 8 weeks. The phenomenon was robust, observed across laboratories with various experimenters and setups. Our results indicate that aberrant hippocampal Ca2+ micro-waves depend on the promoter and viral titre of the GECI, density of expression as well as the targeted brain region. We used an alternative viral transduction method of GCaMP which avoids this artifact. The results show that commonly used Ca2+-indicator AAV transduction procedures can produce artefactual Ca2+ responses. Our aim is to raise awareness in the field of these artefactual transduction-induced Ca2+ micro-waves and we provide a potential solution. Impact statement: Common AAV transduction procedures induce artefactual spatially confined Ca2+ waves in the hippocampus.

neuroscience↗

A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies

Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.

genetics↗

In vivo Safety and Immunoactivity of Oncolytic Jurona Virus in Hepatocellular Carcinoma: A Comprehensive Proteogenomic Analysis

Oncolytic viruses can effectively unwrap a multimodal anti-tumor activity, encompassing a selective tumor cell killing and promoting a systemic anti-tumor immunity, making them a formidable foe against cancer. Among these, several members of the Rhabdoviridae family are particularly attractive as oncolytic agents due to their natural tumor selectivity and non-pathogenicity in humans. In this study, we demonstrated that intratumorally (IT) administration of Jurona virus (JURV), a novel oncolytic Rhabdovirus, induces dynamic tumor regression in human HCC xenograft and syngeneic models. Our data shows that IT injections of JURV trigger the recruitment and activation of cytotoxic T (CTLs) and decrease the tumor-associated macrophages (TAM) infiltration leading to tumor growth delay in both local and distant murine HCC tumors in a syngeneic model. Moreover, when administered concomitantly, JURV and anti-PD-1 therapy profoundly modulate the tumor microenvironment (TME) via enhanced infiltration of CTLs, suggesting that immune checkpoint blockade therapy could potentiate the immunomodulatory effect of JURV and potentially provide durable anti-tumor immunity. Our analysis of the molecular and cellular mechanism of JURV-medicated anti-cancer activity unveiled that JURV and anti-PD-1 antibodies activate different effectors of the immune system but have complementary anti-tumor activities. Furthermore, our results indicate that the abscopal effect induced by JURV is likely mediated by the mechanism regulating the T helper cell responses. Our work supports the further development of JURV as a novel immunovirotherapy platform for hepatocellular carcinoma.

immunology↗

Salp blooms increase carbon export 5-fold in the Southern Ocean

The Southern Ocean (SO) contributes substantially to the global biological carbon pump (BCP). Salps in the SO, in particular Salpa thompsoni, are keystone grazers that produce large, fast-sinking fecal pellets with high export potential. In a first study of this kind, we conducted Lagrangian experiments to quantify the salp bloom impacts on export pathways by contrasting locations differing in salp bloom presence/absence. We show that blooms increased particle export by ~5-fold, and exported up to 46% of net primary production out of the euphotic zone. BCP efficiency increased from 5% in non-salp areas to up to 28% in salp areas, which is among the highest recorded in the global ocean. Using SO salp abundances from KRILLBASE, we estimate they can consume ~ 13% of regional production, mediating 13-40% of the SO BCP. Consideration in models forecasting the SO BCP is recommended considering long-term increases in SO salp abundances.

ecology↗

A novel genomic DNA library preparation method with low GC bias

The amount of input DNA available to prepare next-generation sequencing (NGS) libraries is often limited, which can lead to GC content bias and enrichment of specific genomic regions with currently available protocols. In this study, we used breath capture technology to incorporate sequencing adapters into DNA to develop a novel cost-effective protocol for the preparation of genomic DNA libraries. We performed a benchmarking experiment comparing our protocol with common commercially available kits for genomic DNA library preparation with input DNA amount in the range of 1 to 50 ng. Our protocol can generate high-quality genomic sequence data with a marked improvement in coverage breadth and low GC bias, in contrast to standard protocols. Further, our protocol reduces sample handling time and reagent costs, and requires comparatively fewer enzymatic steps relative to other protocols, making it suitable for a range of genomics applications.

genomics↗

Integrative analysis of scRNAs-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator

Medullary thymic epithelial cells (mTECs) are critical for self-tolerance induction in T cells via promiscuous expression of tissue-specific antigens (TSAs), which are controlled by transcriptional regulator AIRE. Whereas AIRE-expressing (Aire+) mTECs undergo constant turnover in the adult thymus, mechanisms underlying differentiation of postnatal mTECs remain to be discovered. Integrative analysis of single-cell assays for transposase accessible chromatin (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) suggested the presence of proliferating mTECs with a specific chromatin structure, which express high levels of Aire and co-stimulatory molecules CD80 (Aire+CD80hi). Proliferating Aire+CD80hi mTECs detected by using Fucci technology express a minimal level of Aire-dependent TSAs and are converted into quiescent Aire+CD80hi mTECs expressing high levels of TSAs after a transit amplification. These data provide evidence for the existence of transit amplifying Aire+mTEC precursors during Aire+mTEC differentiation process of the postnatal thymus.

immunology↗

Ste20-like kinase is critical for inhibitory synapse maintenance and its deficiency confers a developmental dendritopathy

The size and structure of the dendritic arbor play important roles in determining how synaptic inputs of neurons are converted to action potential output. The regulatory mechanisms governing the development of dendrites, however, are insufficiently understood. The evolutionary conserved Ste20/Hippo kinase pathway has been proposed to play an important role in regulating the formation and maintenance of dendritic architecture. A key element of this pathway, Ste20-like kinase (SLK), regulates cytoskeletal dynamics in non-neuronal cells and is strongly expressed throughout neuronal development. However, its function in neurons is unknown. We show that during development of mouse cortical neurons, SLK has a surprisingly specific role for proper elaboration of higher, [≥] 3rd, order dendrites. Moreover, we demonstrate that SLK is required to maintain excitation-inhibition balance. Specifically, SLK knockdown caused a selective loss of inhibitory synapses and functional inhibition after postnatal day 15, while excitatory neurotransmission was unaffected. Finally, we show that this mechanism may be relevant for human disease, as dysmorphic neurons within human cortical malformations revealed significant loss of SLK expression. Overall, the present data identify SLK as a key regulator of both dendritic complexity during development and of inhibitory synapse maintenance.

neuroscience↗

Targeting aberrant dendritic integration to treat cognitive comorbidities of epilepsy

Memory deficits are a debilitating symptom of epilepsy, but little is known about mechanisms underlying cognitive deficits. Here, we describe a Na+ channel-dependent mechanism underlying altered hippocampal dendritic integration, degraded place coding, and deficits in spatial memory. Two-photon glutamate uncaging experiments revealed that the mechanisms constraining the generation of Na+ spikes in hippocampal 1st order pyramidal cell dendrites are profoundly degraded in experimental epilepsy. A selective Nav1.3 sodium channel blocker reversed this effect, and Nav1.3 channels were up-regulated selectively in principal neurons at the mRNA level. Finally, in-vivo two-photon imaging revealed that the Nav1.3 channel blocker improves degraded hippocampal spatial representations, and reverses hippocampal memory deficits. Thus, a dendritic channelopathy may underlie cognitive deficits in epilepsy and targeting it pharmacologically may constitute a new avenue to enhance cognition. One Sentence SummaryImpaired input computations via aberrant dendritic spikes in chronic epilepsy degrade neuronal place codes and spatial memory

neuroscience↗