Biology subjects

Anderson, D.

Publications and source records attributed to Anderson, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Investigating the Effects of Psilocybin on Cognitive Flexibility in Touchscreen and Naturalistic Variations of the Probabilistic Reversal Learning Task

RationalePsychedelic compounds such as psilocybin have attracted growing interest for their potential therapeutic effects in psychiatric disorders, with improvements in cognitive flexibility proposed as a possible mechanism of action. However, the effects of psychedelics on cognitive flexibility remain poorly understood. ObjectiveThis study aimed to examine the acute and post-acute effects of psilocybin (0.1, 0.3, 1 mg/kg) and lysergic acid diethylamide (LSD, (0.02, 0.04, 0.08 mg/kg) on cognitive flexibility in male rats. MethodsThis was tested using two variants of the probabilistic reversal learning task (PRLT): a touchscreen-based operant task and a more ethological foraging-based task. ResultsIn the touchscreen PRLT, acute psilocybin disrupted task engagement, with animals completing fewer trials and showing increased trial initiation latency, although psilocybin also showed a trend toward faster initial rule acquisition. However, psilocybin did not significantly alter the number of rule changes achieved, a canonical measure of cognitive flexibility, or feedback sensitivity. LSD similarly produced limited acute effects, although the highest dose reduced lose-shift probability, suggesting decreased sensitivity to negative feedback under some conditions. Post-acute effects of psilocybin were minimal in both PRLT variants and, where LSD effects were observed these occurred across different doses and timepoints without a consistent pattern. ConclusionsOverall, these findings suggest that serotonergic psychedelics do not robustly enhance reversal learning in these paradigms and that apparent learning effects may reflect transient disruptions in task engagement rather than improvements in cognitive flexibility. These results also highlight potential limitations of these PRLT paradigms for detecting psychedelic-induced changes in cognitive flexibility in rodents.

animal behavior and cognition↗

bioRxiv2026

Stress-Related Transcriptional Regulators Dominate the Conserved Core GRN for Three Cyanobacteria: Network Topology Maps the Highest-Influence Nodes as Promising Engineering Targets

Cyanobacteria manage photosynthetic and environmental stresses through transcriptional programs controlled by regulators also affecting carbon flux, growth states, and metabolic output that bioproduction seeks to optimize. This regulatory architecture and its most influential nodes remain incompletely characterized. We hypothesized two influential regulator layers: a conserved core responding to common stresses, and species-specific regulators mediating strain-level niche adaptations. Mapping both layers underpins understanding genome[->]regulatory-network[->]phenotype flow, enabling global transcription machinery engineering for reliable bioproduction. To test our hypothesis, we constructed conserved-core and species-specific gene regulatory networks (GRNs) for three cyanobacteria, Synechococcus elongatus PCC 7942, Synechocystis sp. PCC 6803 and Picosynechococcus sp. PCC 7002, integrating a manually curated multi-pipeline regulator inventory with 1,098 harmonized transcriptome states for the 1,362-gene tri-homolog core genome. We quantified each regulator influence using local (degree, k-core), global (betweenness, closeness), and community-aware (eigenvector) centrality measures, and an Integrated Centrality score aggregating influence across complementary topological measures. High-influence regulators are predicted to exert broad metabolic effects when manipulated, making them priority candidates for single-target engineering interventions that modulate multiple genes and reprogram complex phenotypes. Across the three cyanobacteria, the two GRN layers proved topologically distinct: the conserved core concentrated influence in stress-related hubs (11 of its top 15 by Integrated Centrality were stress-related), while species-specific networks spread influence across functionally diverse regulators. Stress-coupled enrichment also held per individual centrality measure: regulators ranking top in both the core and species-specific GRNs by the same measure were mostly stress-related (15 of 19 instances), including the multi-stress regulators RpaB, Rre1, and BolA, the heat-shock HrcA, and the nitrogen NtcA. In species-specific GRNs, stress-related regulators remained the leading category alongside circadian, carbon-metabolism, morphology, and housekeeping regulators, including PlmA, Pex, TetR, and SrrB in PCC 7942; KaiC3, Sycrp1, Rre28, and Bhl in PCC 6803; and Zur, Sycrp1, and NarL in PCC 7002. High-influence putative regulators included the iron-stress AraC-family paralogs IutR1-IutR3, OmpR-family paralogs OmpR1-OmpR2, and chromosome- or plasmid-encoded Xre-family, AraC, and HypP. Stress regulation emerges as a recurring high-influence axis across these networks. The conserved core identifies universal regulatory programs, and species-specific layers reveal strain-level innovations for cross-strain transfer to support engineering of robust bioproduction. ImportanceCyanobacteria are studied as platforms for sustainable, carbon-recycling production of fuels and chemicals from sunlight, water, and atmospheric carbon dioxide. Their reliable deployment in industrial settings is limited by environmental stresses that depress photosynthetic efficiency and product yields. The same regulatory proteins that govern stress responses also control how cells partition carbon, switch growth states, and direct metabolic output, making them natural levers for engineering robust production strains. Yet systematic, cross-species maps of these regulators have been missing. We present the first comparative regulatory map spanning three biotechnologically important model cyanobacteria, Synechococcus elongatus PCC 7942, Synechocystis sp. PCC 6803, and Picosynechococcus sp. PCC 7002, and identify the conserved regulators most influential across all three. The resulting catalog prioritizes candidate targets for experimental validation, and the supporting datasets and analytical framework are released for reuse to support efforts to engineer cyanobacterial strains for reliable industrial bioproduction.

systems biology↗

bioRxiv2026

Coupling high-throughput protease enzymology with viral replication reveals biochemical constraints of viral fitness

Proteases govern essential biological processes and are key drug targets, yet how protease sequence variation quantitatively reshapes biochemical parameters and constrains biological fitness remains poorly understood. Here, we integrate high-throughput in vitro enzymology with cellular assays to link protease sequence, biochemistry, and fitness. We extend a microfluidic platform for high-throughput protease enzymology (HT-MEKpro), which is broadly applicable across protease families and catalytic classes, enabling measurement of catalytic turnover (kcat), Michaelis constant (KM), inhibitor potency (IC50), and relative substrate specificity for 102-103 variants. Applied to the SARS-CoV-2 main protease (Mpro), HT-MEKpro generated parallel catalytic and inhibitory landscapes for >400 variants. Integration with viral replication and in-cell cleavage assays reveals that variants with altered substrate specificity fail to support replication, suggesting imbalanced polyprotein processing as a constraint on viral fitness. More broadly, these data can enable mechanistically grounded modeling of protease sequence-property relationships and inform strategies for pharmacological modulation beyond active-site inhibition.

biochemistry↗

bioRxiv2026

A Course-Undergraduate Research Experience (CURE) to explore the effect of structural variants on gene expression in C. elegans balancers

Bioinformatics, a discipline at the crossroads of Biology and Computational Sciences, also referred to as Computational Biology, is nowadays widely spread in research programs. However, implementing any Bioinformatics projects requires the ability to comprehend biological concepts and apply computational approaches, and rare are the undergraduate programs offering such multi-disciplinary training. In addition, understanding the dynamic between Biology research projects and Bioinformatics analyses is challenging with no real-life experience. Course-based undergraduate research experience (CURE) courses are innovative programs that allow more students to acquire research experience and provide the perfect setting to introduce students to applied bioinformatics. As a part of the Bachelor of Health Sciences of the Cumming School of Medicine at the University of Calgary (Canada), a CURE applied bioinformatics was implemented in the Winter of 2023 to 2025. Students investigated the effect of structural variants (SVs, genetic variants larger than 50 bp) on gene expression in the model organism Caenorhabditis elegans (a hermaphrodite 1-mm long roundworm). The students detected and characterized SVs by analyzing genome and transcriptome sequencing data of C. elegans strains called balancers, as they are known to carry large genomic variations balancing regions of the genome by limiting recombination and allowing maintenance of lethal mutations. They used Galaxy, a public web-based supercomputing resource, but also a local High-Performance computing system, and R, to report different effects of SVs on gene expression and splicing. Students research explained the molecular mechanism behind the uncoordinated phenotype caused by the reciprocal translocation eT1(III;V) and uncovered unexpected effects on gene expression on an understudied gene. We evaluated the courses impact on student learning journeys and showed that the CURE favored students understanding of the Bioinformatics field and fostered their research interest. We provide here guidelines to facilitate the CURE implementations to improve access for undergraduate students to bioinformatics research experiences.

bioinformatics↗

bioRxiv2026

Designing AI-programmable therapeutics with the EDEN family of foundation models

The ability to interpret, modify, and design DNA has driven many of the most significant advances in modern medicine, from diagnostics, biologics, and vaccines to cell and gene therapies. However, the inherent complexity of biological systems means that most modern medicines are still engineered using bespoke, labor-intensive processes. To address the need for a generalisable and programmable approach to therapeutic design, we introduce the EDEN (environmentally-derived evolutionary network) family of metagenomic foundation models, including a 28 billion parameter model trained on 9.7 trillion nucleotide tokens from BaseData1. This dataset, at the time of training, contained more than 10 billion novel genes from over 1 million new species, and is intentionally enriched for environmental and host-associated metagenomes, phage sequences, and mobile genetic elements, enabling the model to learn from diverse and novel cross-species evolutionary mechanisms and apply them to key challenges in human health. EDEN achieves state-of-the-art performance across a series of predictive and generative genomic and protein benchmarks. To demonstrate the models broad applicability across biology, we evaluate EDENs capacity for programmable therapeutic design by challenging a single architecture to design biological novelty across three distinct therapeutic modalities, disease areas and biological scales: (i) large gene insertion, (ii) antibiotic peptide design, and (iii) microbiome design. First, we demonstrate AI-programmable Gene Insertion (aiPGI), in which EDEN designs de novo large serine recombinases (LSRs) capable of inserting large pieces of DNA at desired target sites in the human genome when prompted only on 30 nucleotides of DNA sequence from the desired target site. In low-N experimental validation, EDEN generated multiple active recombinases for all tested disease-associated genomic loci (ATM, DMD, F9, FANCC, GALC, IDS, P4HA1, PHEX, RYR2, USH2A) and 4 potential safe harbor sites in the human genome. EDEN achieves an overall functional hit rate of 63.2% across diverse DNA prompts when prompted on only 30bp of DNA from outside the training data. 50% of EDEN-generated LSRs were active in human cells, achieving therapeutically relevant levels of CAR insertion in primary human T cells. We also show that EDEN can generate active bridge recombinases when prompted on the associated guide RNA alone, with sequence identities to training and public data as low as 65%. These results pave the way for a new generation of cell and gene therapies by opening the door to rapid, programmable and site-specific integration of large genetic payloads without double-strand breaks. This offers an alternative to the safety, efficiency and payload limitations inherent in viral or nuclease-based editing at thousands of currently intractable human therapeutic targets. Second, we use the same model to generate a focused low-N library of novel antimicrobial peptides where 97% showed activity, with top candidates achieving single-digit micromolar potency against critical-priority multidrug-resistant pathogens. Third, to demonstrate that EDEN captures inter-genomic features, we design a gigabase-scale microbiome with over 94,000 synthetic metagenomic assemblies, including prophage genomes and correct cross-species metabolic pathway completions. The EDEN-generated synthetic microbiome covers 9,067 species with a biome-specific taxonomic accuracy of 99%. Over 1,500 of the generated species were outside the fine-tuning dataset while retaining the correct microecological properties and biome association, thus significantly expanding genetic and taxonomic diversity. Together, these results establish a new strategic direction for AI-programmable therapeutics, in which a single foundation model architecture designs candidate therapeutics across diverse modalities and disease areas. This suggests that the combination of billions of years of evolutionary data with specific therapeutic records offers a clear, scaling-driven path to making therapeutic design a predictable engineering discipline. O_FIG O_LINKSMALLFIG WIDTH=141 HEIGHT=200 SRC="FIGDIR/small/699009v2_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@68c20borg.highwire.dtl.DTLVardef@19b8e8corg.highwire.dtl.DTLVardef@1ab9362org.highwire.dtl.DTLVardef@1592cb7_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Pre-clinical validation of a novel AAV-mediated gene therapy for KCNV2 retinopathy improves visual function in a mouse model and expression in patient organoids

Voltage-gated (Kv) potassium channels are critical for neuronal physiology, and their dysfunction can lead to serious consequences. For example, mutations in the silent modulatory Kv8.2 subunit are known to cause irreversible inherited blindness (KCNV2 retinopathy). This is a currently incurable condition that causes lifelong visual loss, reduced visual acuity, photoaversion, night blindness and abnormal colour vision, alongside a distinctive supernormal electrophysiological (ERG) retinal response to light. In this study, we demonstrate that AAV-mediated gene replacement therapy delivering a codon-optimised human KCNV2 gene subretinally into Kv8.2 knock-out mice significantly restores retinal function. Treated mice exhibited improved ERG responses and correct expression of KCNV2 and its encoded Kv8.2 protein in photoreceptors. Recovery of visually guided scotopic and photopic optomotor responses to wildtype levels was achieved at lower vector doses, highlighting dose-dependent efficacy. Furthermore, treatment of human retinal organoids derived from a KCNV2 patient iPSC line resulted in substantial Kv8.2 protein rescue. This work provides the first preclinical proof-of-concept for the safety and therapeutic potential of gene therapy for KCNV2 retinopathy, laying a strong foundation for future clinical trials.

neuroscience↗

bioRxiv2025

Bioactive Cationic Lipidated Oligomers (CLOs) as Antimicrobial Materials: Metabolomic Insights into MRSA Membrane Disruption

The escalating incidence of antimicrobial resistance in Staphylococcus aureus, particularly the methicillin-resistant strain (MRSA), necessitates the development of novel therapeutic strategies. Cationic lipidated oligomers (CLOs) have emerged as promising membrane-active antimicrobial agents; however, their mechanisms of action remain insufficiently understood. In this study, untargeted metabolomics was employed to systematically profile the temporal metabolic perturbations induced by two structurally distinct CLOs, C12-o-DMEN-10 and C12-o-BEDA-10, in MRSA across four defined time points (0.25, 0.5, 1, and 3 hours). These CLOs previously demonstrated differential antibacterial activity, as evidenced by dose-dependent propidium iodide (PI) uptake and growth inhibition assays. Metabolomic analysis revealed pronounced and sustained disruptions in bacterial membrane lipid metabolism, including significant depletion of phosphatidylglycerols ([≥] -2.5 log2FC, p < 0.05), alongside elevated levels of phosphatidylethanolamines, lysophospholipids, and fatty acid-derived metabolites indicative of membrane destabilization and lipid remodelling. Although both CLOs affected overlapping metabolic pathways, they differed in the extent and temporal dynamics of their effects. These findings provide mechanistic insights into CLO-mediated antibacterial activity and highlight the value of metabolomics in elucidating both direct and downstream cellular responses, which extend beyond the scope of conventional membrane integrity assays, such as PI fluorescence.

systems biology↗

bioRxiv2025

Is poor dose selection undermining the translational validity of antidepressant research involving animal models?

BackgroundBehavioural studies in animal models represent a critical component of psychiatric drug development. Positive results in animal studies have identified novel therapeutic targets for major depressive disorder (MDD) but efficacy in humans has largely not been borne out in clinical trials. A possible reason for this failed translation is inappropriate dose selection and the engagement of mechanisms not directly relevant to antidepressant effects in patients. MethodsWe first used PubMed to identify preclinical rodent studies in two assays used to assess antidepressants; the conventional forced swim test, (FST) and more recently developed affective bias test, (ABT). Dose ranges were extracted, as well as information about subjects, timing and route of administration, and justification and efficacy of dose(s). Dose ranges were compared against calculated animal equivalent doses. ResultsThe median FST dose across all antidepressants was 10mg/kg, with median doses for each drug exceeding the relevant animal equivalent dose by 1.5-25x. In contrast, effective doses in the ABT showed closer alignment to those used clinically. In the second study, 232 ketamine and 202 fluoxetine papers involving MDD-related research in rodents were reviewed. The median dose was 10mg/kg for both drugs, exceeding animal equivalent doses by 1.6-3.2x and 3.2-6.5x for ketamine and fluoxetine, respectively. ConclusionsThe results indicate pervasive use of antidepressant doses in conventional models of MDD that may not correspond with doses used in clinical practice. We discuss the implications of using doses which exceed therapeutic levels and the potential to engage receptors and underlying mechanisms which are not relevant to clinical effects.

neuroscience↗

bioRxiv2025

Oxidation of ΔFOSB at Cys172 Controls Hippocampal Gene Targets and Learning

Imbalance of reduction/oxidation (redox) in the brain is associated with numerous diseases including Alzheimers disease (AD), substance abuse disorders, and stroke. Moreover, cognitive decline can be caused by neuronal dysfunction that precedes cell death, and this dysfunction is in part produced by altered gene expression. However, the mechanisms by which redox state controls gene expression in neurons are not well understood. {Delta}FOSB is a neuronally enriched transcription factor critical for orchestrating gene expression underlying memory, mood, and motivated behaviors. It is dysregulated in many conditions including AD. We showed recently that {Delta}FOSB forms a redox-sensitive disulfide bond between cysteine 172 (C172) of {Delta}FOSB and C279 of its preferred binding partner JUND. This bond works as a redox switch to control DNA-binding, based on studies of recombinant proteins in vitro. Here, we show that this redox control of {Delta}FOSB function in vitro is conserved in vivo. We show that {Delta}FOSB C172 forms a redox-sensitive disulfide bond with JUND that regulates the stability of this AP1-transcription factor complex and its binding to DNA in cells. We also validate the formation of {Delta}FOSB-containing complexes held together via disulfide bonds in mouse brain in vivo. We show that exogenous oxidative stress reduces {Delta}FOSB binding to gene targets in mouse brain and that Fosb C172S knock-in mice, which lack a functional {Delta}FOSB redox switch, are insensitive to this oxidation-dependent reduction in target gene binding, demonstrating that {Delta}FOSB is regulated by a redox switch that modulates binding to target genes in the hippocampus. Finally, we demonstrate that FosB C172S knock-in mice are less sensitive to cognitive dysfunction induced by oxidative stress. This evidence supports {Delta}FOSB as an important mediator of oxidative stress-driven changes in gene expression and cognition and implicates {Delta}FOSB as a possible therapeutic target for diseases associated with oxidative stress in the brain, including AD.

neuroscience↗

bioRxiv2025

Oxytocin neurons in the anterior and posterior paraventricular nucleus have distinct behavioral functions and electrophysiological profiles

Oxytocin is a neuropeptide that can promote or inhibit affiliative social behaviors. Recent evidence suggests that these diverse effects are mediated by distinct oxytocin receptor-expressing neurons. An outstanding question is whether these behavioral effects are also driven by distinct or overlapping populations of oxytocin-producing neurons. The paraventricular nucleus (PVN) of the hypothalamus is a major source of oxytocin and sends projections to the mesolimbic dopamine system and extended amygdala. Previous work found that social defeat increased oxytocin neuron activity in the anterior PVN (aPVN) but not posterior PVN (pPVN). We reduced oxytocin synthesis with antisense morpholino oligonucleotides in either anterior or posterior PVN in California mice (Peromyscus californicus), a strong model system for studying effects of social stress on brain function and behavior. Antisense morpholinos in aPVN had no effect on behavior in unstressed females but increased social approach and reduced social vigilance in females exposed to social defeat stress. In pPVN, antisense morpholinos reduced social approach in unstressed male and female California mice. We then used OxtCre mice to compare electrophysiological profiles of oxytocin in aPVN and pPVN with a population of oxytocin neurons in the bed nucleus of the stria terminalis (BNST). Oxytocin neurons in aPVN and BNST had higher post-synaptic events and responded more strongly to current injections than oxytocin neurons in pPVN, though they had similar excitatory and inhibitory input balance at the observed resting membrane potential. These findings shed light onto functional and physiological heterogeneity of PVN oxytocin neurons. Our results suggest that context dependent effects of oxytocin are mediated by different populations of oxytocin neurons.

neuroscience↗

bioRxiv2025

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads

Accurate detection of antimicrobial resistance (AMR) genes is essential for the surveillance, epidemiology and genotypic prediction of AMR. This is typically done by generating an assembly from the sequencing reads of a bacterial isolate and running AMR gene detection tools on the assembly. However, despite advances in long-read sequencing that have greatly improved the quality and completeness of bacterial genome assemblies, assembly tools remain prone to large-scale errors caused by repeats in the genome, leading to inaccurate detection of AMR gene content and consequent impact on resistance prediction. In this work we present Amira, a tool to detect AMR genes directly from unassembled long-read sequencing data. Amira leverages the fact that multiple consecutive genes lie within a single read to construct gene-space de Bruijn graphs where the k-mer alphabet is the set of genes in the pan-genome of the species under study. Through this approach, the reads corresponding to different copies of AMR genes can be effectively separated based on the genomic context of the AMR genes, and used to infer the nucleotide sequence of each copy. Amira achieves significant improvements in genomic copy number recall and nucleotide accuracy, demonstrated through objective simulations and comparison with alternative read and assembly-based methods on samples with manually curated truth assemblies. Applied to a dataset of 32 Escherichia coli samples with diverse AMR gene content, Amira achieves a mean genomic-copy-number recall of 98.4% with precision 97.9% and nucleotide accuracy 99.9%. Finally, we show that Amira consistently detects more true AMR genes across all E. coli, K. pneumoniae and E. faecium nanopore datasets from the ENA (n=8580, 2448 and 415 respectively) than an assembly-based approach.

bioinformatics↗

bioRxiv2025

Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus-MPro inhibitors with potent in vivo efficacy

The main protease (MPro) of SARS-CoV-2 is crucial for viral replication and is the target of nirmatrelvir (the active ingredient of Paxlovid) and ensitrelvir. The identification of new agents with differentiated pharmacokinetic and drug resistance profiles will increase therapeutic options for COVID-19 patients and bolster pandemic preparedness generally. Starting with a lead-like dihydrouracil chemotype from a large-library docking campaign, we improved MPro inhibition >1,000-fold by engaging additional sub-sites in the MPro active site, most notably by employing a latent propargyl electrophile to engage the catalytic Cys145. Advanced leads from this series, including AVI-4516 and AVI-4773 show pan-coronavirus antiviral activity in cells, very low clearance in mice, and for AVI-4773 a rapid reduction in viral titers more than a million-fold after just three doses, more rapidly and effectively than the approved drugs, nirmatrelvir and ensitrelvir. Both AVI-4516 and AVI-4773 are well distributed in mouse tissues, including brain, where concentrations ten or fifteen-thousand times the EC90, respectively, are observed eight hours after an oral dose. As exemplar of the series, AVI-4516 shows minimal inhibition of major CYP isoforms and human cysteine and serine proteases, likely due to its latent-electrophilic warhead. AVI-4516 also exhibits synergy in cellular infection models in combination with the RdRp inhibitor molnupiravir, while related analogs strongly inhibit nirmatrelvir-resistant MPro mutant virus in cells. The in vivo and antiviral properties of this new chemotype are differentiated from existing clinical and pre-clinical MPro inhibitors, and will advance new therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses. One sentence summaryThis manuscript describes the discovery of a new class of potent inhibitors of the SARS-CoV-2 major proteases (MPro) with a unique mechanism of inhibition, pan coronaviral activity in cellulo, exquisite selectivity vs. the human proteome, and exceptional in vivo efficacy in SARS-CoV-2 infection models that surpasses that of currently approved agents.

biochemistry↗

bioRxiv2024

Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins

Proteolysis of hydrophobic helices is required for complete breakdown of every transmembrane protein trafficked to the lysosome and sustains high rates of endocytosis. However, the lysosomal mechanisms for degrading hydrophobic domains remain unknown. Combining lysosomal proteomics with functional genomic data mining, we identify Lysosomal Leucine Aminopeptidase (LyLAP; formerly Phospholipase B Domain-Containing 1) as the hydrolase most tightly associated with elevated endocytic activity. Untargeted metabolomics and biochemical reconstitution demonstrate that LyLAP is not a phospholipase, but a processive monoaminopeptidase with strong preference for N-terminal leucine - an activity necessary and sufficient for breakdown of hydrophobic transmembrane domains. LyLAP is upregulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake, and its ablation led to buildup of undigested hydrophobic peptides, which compromised lysosomal membrane integrity and inhibited PDA cell growth. Thus, LyLAP enables lysosomal degradation of membrane proteins, and may represent a vulnerability in highly endocytic cancer cells. One sentence summaryLyLAP degrades transmembrane proteins to sustain high endocytosis and lysosomal membrane stability in pancreatic cancer.

biochemistry↗

bioRxiv2024

Human stem cell-derived GABAergic interneuron development reveals early emergence of subtype diversity followed by gradual electrochemical maturation

Medial ganglionic eminence-derived inhibitory GABAergic pallial interneurons (MGE-pINs) are essential regulators of cortical circuits; their dysfunction is associated with numerous neurological disorders. We developed human (h) MGE-pINs from pluripotent stem cells for the treatment of drug-resistant epilepsy. Here, we analyzed xenografted hMGE-pINs over the lifespan of host mice using single nuclei RNA sequencing. Comparative transcriptomics against endogenous human brain datasets revealed that 97% of grafted cells developed into somatostatin (SST) and parvalbumin (PVALB) subtypes, including populations that exhibit selective vulnerability in Alzheimers disease. Transplanted hMGE-pINs demonstrated rapid emergence of subclass features, progressing through distinct transcriptional states sequentially involving neuronal migration, synapse organization, and membrane maturation. We present molecular, electrophysiological, and morphological data that collectively confirm the derivation of diverse bona-fide human SST and PVALB subtypes, providing a high-fidelity model to study human MGE-pIN development and functional maturation as well as a compositional atlas for regenerative cell therapy applications.

neuroscience↗

bioRxiv2024

A randomized controlled trial of the effectiveness of a community-based rabies vaccination strategy

BackgroundApproximately 60,000 people die from dog-mediated rabies annually. Low and heterogeneous coverage reduces the effectiveness of dog vaccination campaigns that can eliminate rabies. Campaigns typically involve teams travelling annually to villages to deliver cold chain stored vaccines from centralized headquarters. Thermotolerant vaccines enable novel decentralized delivery of locally-stored vaccines by communities throughout the year. We compared the effectiveness of annual team-based versus continuous community-based dog vaccination strategies. MethodsWe conducted a cluster randomized controlled trial across Mara region, Tanzania. Trial clusters were administrative wards (112, on average four villages each). For the team-based arm vaccinators hosted annual static-point clinics, whilst for the community-based arm, a ward-based animal health officer with a village community leader managed vaccinations using vaccines stored within the ward. We measured vaccination coverage, the primary outcome, twice annually per cluster (month 1 and 11) through household surveys over three years (November 2020 to October 2023) and examined spatial and temporal coverage variations as secondary outcomes. FindingsCommunity-based delivery achieved significantly higher coverage (49-62%) than team-based delivery (22-46%), and consistently exceeded the critical threshold for herd immunity (40%), Odds ratio (OR): 1.48-3.49. The lower less uniform coverage achieved through team-based delivery had a higher monthly probability of falling below the critical threshold (0.6, 95% CI: 0.38-0.81) vs 0.18 (95% CI: 0.04-0.40). Greater declines in coverage over the year were recorded in the team-based arm compared to the community-based ConclusionCommunity-based mass dog vaccination achieves higher more consistent coverage than team-based delivery across settings typical of many sub-Saharan African countries. This approach could play an important role in national rabies elimination programmes aiming to end human rabies deaths by 2030 as part of the global zero by 30 strategy. FundingDepartment of Health and Human Services of the National Institutes of Health (R01AI141712), Wellcome Trust (207569/Z/17/Z, 224520/Z/21/Z) and MSD Animal Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

immunology↗

bioRxiv2024

Reducing spatial heterogeneity in coverage improves the effectiveness of dog vaccination against rabies

Vaccination programs are the mainstay of control for many infectious diseases. Heterogeneous coverage is hypothesised to reduce vaccination programme effectiveness, but this impact has not been quantified in real systems. We address this gap using fine-scale data from two decades of rabies contact tracing and dog vaccination campaigns in Serengeti district, Tanzania. We also aimed to identify drivers of continued circulation of rabies in the district despite annual vaccination campaigns. Using generalised linear mixed models, we find that current focal (village-level) dog rabies incidence decreases with increasing recent focal vaccination coverage. However, current focal incidence depends most on recent incidence, both focally and in the wider district, consistent with high population connectivity. Removing the masking effects of prior non-focal incidence shows that, for the same average prior non-focal (wider-district) vaccination coverage, increased heterogeneity in coverage among the non-focal villages leads to increased focal incidence. These effects led to outbreaks following years when vaccination campaigns missed many villages, whereas when heterogeneity in coverage was reduced, incidence declined to low levels (<0.4 cases/1,000 dogs annually and no human deaths) and short vaccination lapses thereafter did not lead to resurgence. Through transmission-tree reconstruction, we inferred frequent incursions into the district each year (mean of 7). Inferred incursions substantially increased as a percentage of all cases in recent years, reaching 50% in 2022, suggesting regional connectivity is driving residual transmission. Overall, we empirically demonstrate how population connectivity and spatial heterogeneity in vaccination can impact disease outcomes, highlighting the importance of fine-scale monitoring in managing vaccination programs.

ecology↗

bioRxiv2024

Effect of cyclic loading on the ultimate tensile strength of small metallic suture anchors used for attaching artificial tendons in rabbits

BackgroundSuture anchor failures can lead to revision surgeries which are costly and burdensome for patients. The durability of musculoskeletal reconstructions is therefore partly affected by the design of the suture anchors. PurposeThe purpose of the study was to quantify the strength of different suture anchors whose sizes are suitable for attaching artificial Achilles and tibialis cranialis tendons in a rabbit model, as well as determine the effect of cyclic loading on the anchoring strength. MethodFour anchors (two with embedded eyelet and two with raised eyelet, n=5 per group) were tested with cyclical loading (1000 cycles and 4.5 mm/sec) and without cycling, to inform the failure loads and mode of failure of the suture anchors. An eyebolt screw with smooth eyelet was used as a control for the test groups. ResultsAll samples in all groups completed 1000 cycles and failed via suture breakage in both test conditions. All anchors had failure loads exceeding the peak Achilles tendon force in rabbits during hopping gait. The data analysis showed an effect of anchor type on the maximum tensile force at failure (Fmax) in all suture categories but not an effect of loading condition. Also, the Anika anchor had a significantly less adverse effect on suture strength compared to Arthrex anchor (p=0.015), IMEX anchor (p=0.004) and Jorvet anchor (p<0.001). We observed a greater percentage of failure at the mid-section for the anchors with the raised eyelets compared to the anchors with embedded eyelets, which all failed at the knot. ConclusionAnchors with embedded eyelets had clinically preferred mode of failure with less adverse effects on suture and, may be more reliable than anchors with raised eyelets for attaching artificial Achilles and tibialis cranialis tendons in rabbits.

bioengineering↗

bioRxiv2024

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 4,471,579 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of June 2024, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

bioinformatics↗