Biology subjects

Moore, N.

Publications and source records attributed to Moore, N..

14 recordsLinked to original sources

bioRxiv2026

CountESS: a flexible, graphical pipeline tool for deep mutational scanning analysis

Deep Mutational Scanning (DMS) experiments generate large volumes of sequencing data that must be processed through multi-step computational pipelines to yield interpretable variant scores. At least twelve dedicated tools have been published for this purpose, yet the diversity of experimental designs, scoring strategies, and software implementations has produced a fragmented landscape in which no single tool accommodates the full range of workflows encountered in practice. Here we present CountESS (Count-based Experiment Scoring and Statistics), an open-source pipeline tool that provides a modular, graphical interface for constructing flexible DMS analysis workflows. CountESS supports a wide range of input formats, barcode translation, HGVS variant calling, and user-defined scoring functions, enabling it to accommodate diverse experimental designs including selection assays, time-series experiments, and bin-based assays such as VAMP-seq. Implemented in Python with DuckDB as a computational backend, the software provides high-performance, memory-efficient processing suitable for large datasets. CountESS is freely available at https://github.com/CountESS-Project/CountESS under the 3-Clause BSD Licence. Supplementary data, including demonstration pipelines and example datasets, are available at https://github.com/CountESS-Project/countess-demo.

bioinformatics↗

bioRxiv2026

Thermal performance in fishes varies systematically across latitude, habitat, and biological organization

Thermal performance curves are widely used to understand how ectotherms respond to anthropogenic climate change, yet comparable data remain fragmented for fishes despite their predicted sensitivity to warming. Here we introduce FishTherm, a compilation of 457 thermal responses from 107 wild fish species, spanning diverse performance metrics and temperatures. With this dataset, we estimated thermal optima, performance breadth, tolerance breadth, and activation energies, and tested how these thermal traits vary geographically, across latitude and habitat, and by type and functional context of performance. Thermal optima increase toward lower latitudes and warmer waters, consistent with established biogeographic patterns. We also found that responses measured at lower levels of biological organization exhibit higher thermal optima than population-level responses, supporting complexity constraints on thermal performance curves. Activation energies broadly matched predictions from the Metabolic Theory of Ecology, and we further found systematic variation of lower values in negatively-motivated responses, and associated with narrower thermal performance breadths, in line with theory. Our results provide supporting evidence for several unifying principles that advance our understanding of constraints and variation in thermal performance. FishTherm is a new resource for comparative thermal ecology and for improving our understanding of fish vulnerability under climate warming.

ecology↗

bioRxiv2026

Live triatomine bug, vector of Trypanosoma cruzi (Chagas disease), found engorged in Lisbon hotel room: A first for Portugal and for Europe

Triatomine bugs are blood feeding insects that transmit the parasite Trypanosoma cruzi, causative agent of Chagas disease. The bugs are found primarily in the Americas with a few species in Asia and Africa. Here we report the first case of a live triatomine bug in Europe, found in a Lisbon hotel room. In August, 2025, the hotel room occupants discovered a triatomine bug perched on the headboard of their bed. Upon capture, bright red blood emerged from the bug; the occupants suspected that it had bitten them during the night. The bug was identified morphologically as triatomine species Hospesneotomae protracta, which was confirmed molecularly. Hospesneotomae protracta is native to the southwestern United States where it is a competent T. cruzi vector. Trypanosoma cruzi was not detected in this specimen. Although this case likely represents an accidental importation, it illustrates the ease with which disease vectors can be unknowingly transported globally. Ergo it is crucial to document and share these findings to prevent introductions of non-native arthropods of medical importance.

ecology↗

bioRxiv2026

Biological Mechanisms of Strength Preservation During Calorie Restriction-Induced Weight Loss Among Young- to Middle-Aged Adults without Obesity

PurposeWeight loss is often pursued to improve cardiometabolic health and quality of life. However, rapid weight loss can lead to reductions in lean soft tissue mass and strength to compromise body composition and functional ability. Thus, identifying molecular predictors of muscular strength preservation during weight loss is critical to mitigating these effects. MethodsWe conducted a secondary analysis of the CALERIETM (Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy) trial, a two-year randomized controlled study of caloric restriction (CR) or ad-libitum intake in healthy adults without obesity. Among 198 participants, changes in whole-body mass and knee extensor strength were assessed over the first 12 months of the study which was primarily characterized by weight loss. Transcriptomic profiling was conducted in a subset of 42 participants who provided skeletal muscle samples. Linear regression was used to model the relationship between strength change and gene expression change, while controlling for changes in whole-body mass. Gene set enrichment analysis (GSEA) was performed using Hallmark pathways. Individual-level pathway analysis was performed via gene set variation analysis (GSVA). ResultsWe identified 96 out of 198 individuals (48.5%) who maintained or improved strength relative to body mass during weight loss (i.e. individuals with residuals > 0). Transcriptomics analysis on a subset of 42 individuals revealed 151 genes significantly associated with change in strength after accounting for change in whole-body mass (p < 0.01). Hub genes were identified as HSP90AA1 ({beta} = 34.45, SE = 7.32, p <0.001), EIF3A ({beta} = 36.14, SE = 10.27, p < 0.001), EIF5B ({beta} = 49.94, SE = 11.28, p < 0.001), and H3C1 ({beta} = -15.87, SE = 4.85, p < 0.001). GSEA revealed significant involvement of pathways related to cellular proliferation, immune regulation, protein secretion, and checkpoint control processes. GSVA identified a similar set of pathways. ConclusionsThese findings highlight molecular pathways supporting strength retention during CR-induced weight loss. Heat-shock protein, HSP90AA1, warrants further investigation as a candidate target for preserving muscle strength during interventions aimed at weight reduction.

molecular biology↗

bioRxiv2025

The Effects of DMSO Cryopreservation on the Biomechanics and Histology of Human Cerebrovascular Tissue

IntroductionTissue preservation techniques, chiefly cryopreservation, have been demonstrated to alter vascular histology and tissue biomechanics via rapid osmotic change--resulting in collagen fiber rearrangement and internal elastic laminae (IEL) microfractures; however, this has not yet been evaluated in cerebrovascular tissue. As such, we sought to measure the effectiveness of a canonical cryopreservation strategy on the thickness and continuity of human cerebrovascular tissue. With the recent rise in biomechanical analyses of cerebrovascular tissue for the design of novel treatments and optimization of surgical strategies, the importance of designing models with accurate tissue proxies is paramount. MethodsFresh, human cerebrovascular tissue was obtained through the Cleveland Clinic institutional cadaver donation program. Donors with prior craniotomy, intracranial malignancy, or history of cerebrovascular disease were excluded. Cadaveric tissue dissections were completed within fourteen days of patient expiration and sectioned into four specimens. The 164 tissue samples obtained from three donors were then randomized into one of the following experimental conditions: 10% formalin (control), distilled water (dH2O), dimethyl sulfoxide (DMSO), or -80 {degrees}C DMSO cryopreservation. Specimens were then processed into paraffin-embedded sections and treated with Movat pentachrome staining. Vessel layers were measured by two blinded evaluators and discontinuities in internal elastin lamina were tallied. ResultsWe found that DMSO cryopreservation failed to consistently provide a protective effect to cerebrovascular specimens. Tissue stored via this method was reported to occasionally swell in specific vessel tunics of select vessel territories compared to formalin controls. We also observed an increase in the number of transverse elastin breaks with DMSO cryopreservation. ConclusionsThis data demonstrates that conventional tissue preservation methods may fail to preserve layer thicknesses between some vessels and alter biomechanical properties for future testing. Further, with more frequent elastin fractures in the cryopreservation group, recoilability of preserved vessels may vary from in vivo counterparts. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/679363v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@1d8cc51org.highwire.dtl.DTLVardef@4ddcd6org.highwire.dtl.DTLVardef@1dd94f1org.highwire.dtl.DTLVardef@5d99bf_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

Functional evidence for G6PD variant classification from mutational scanning

G6PD deficiency is one of the most common enzyme deficiencies worldwide, and increases the likelihood of adverse reactions to certain drugs and foods. Identifying people at risk is challenging, since most are asymptomatic until they encounter a trigger. This is further complicated since over 60% of 1,559 known genetic variants in G6PD are variants of uncertain significance and thus cannot guide drug prescribing and dosing. To resolve which variants are clinically meaningful and avoid harm from adverse drug reactions, we conducted two high-throughput functional assays: one for G6PD activity, and one for abundance. We measured the function of 9,527 missense, nonsense, and synonymous G6PD variants. The patterns of variant effect on activity and abundance confirmed the importance of structural NADP+ for G6PD activity and abundance, and G6PD dimerization for G6PD activity. Based on the ability of our functional assay scores to accurately classify G6PD variants of known clinical effect, we generated evidence that 4,870 missense variants contribute to G6PD deficiency and 2,245 are unlikely to contribute to G6PD deficiency. Our data can be used to deepen our understanding of G6PD as a protein, and to close the gap in classification for variants of uncertain significance to improve implementation of genetic medicine for G6PD deficiency.

genetics↗

bioRxiv2025

Age-dependent alterations in the head-direction signal in a rat model of Fragile X Syndrome

Fragile X Syndrome (FXS) is a common inherited monogenic cause of autism spectrum disorder and intellectual disability (ASD/ID), but the neural mechanisms underlying its symptoms remain unclear. Here, we investigate the development of the head-direction (HD) system in a rat model of FXS (Fmr1-/y rats) and its role in spatial cognition. Using high-density silicon probes, we recorded neuronal activity in the postsubiculum (PoSub), a cortical hub of the HD system, during exploration and sleep in juvenile and adult Fmr1-/y and wild-type (WT) rats. Surprisingly, juvenile Fmr1-/y rats exhibited enhanced HD tuning characterized by sharper directional tuning curves and improved stability of the HD signal in relation to the external environment. This enhancement was intrinsic to the HD circuit and persisted across behavioral and sleep states. However, by adulthood, HD tuning in Fmr1-/y rats became unstable, with increased drift in the allocentric reference frame despite intact intrinsic HD dynamics. These findings reveal a transient enhancement of spatial coding in the HD system of juvenile Fmr1-/y rats, followed by a degradation in adulthood, mirroring the developmental regression often observed in autism. Overall, our work reveals network-level dysfunctions in FXS and their developmental trajectories.

neuroscience↗

bioRxiv2023

A Computational Framework for the Administration of 5-Aminovulinic Acid before Glioblastoma Surgery

5-Aminolevulinic Acid (5-ALA) is the only fluorophore approved by the FDA as an intraoperative optical imaging agent for fluorescence-guided surgery in patients with glioblastoma. The dosing regimen is based on rodent tests where a maximum signal occurs around 6 hours after drug administration. Here, we construct a computational framework to simulate the transport of 5-ALA through the stomach, blood, and brain, and the subsequent conversion to the florescent agent protoporphyrin IX at the tumor site. The framework combines compartmental models with spatially-resolved partial differential equations, enabling one to address questions regarding quantity and timing of 5-ALA administration before surgery. Numerical tests in two spatial dimensions indicate that, for tumors exceeding the detectable threshold, the time to peak flouresent concentration is 2-7 hours, broadly consistent with the current surgical guidelines. Moreover, the framework enables one to examine the specific effects of tumor size and location on the required dose and timing of 5-ALA administration before glioblastoma surgery.

pharmacology and toxicology↗

bioRxiv2023

Neuropathy target esterase activity predicts retinopathy among PNPLA6 disorders

Biallelic pathogenic variants in the PNPLA6 gene cause a broad spectrum of disorders leading to gait disturbance, visual impairment, anterior hypopituitarism, and hair anomalies. PNPLA6 encodes Neuropathy target esterase (NTE), yet the role of NTE dysfunction on affected tissues in the large spectrum of associated disease remains unclear. We present a clinical meta-analysis of a novel cohort of 23 new patients along with 95 reported individuals with PNPLA6 variants that implicate missense variants as a driver of disease pathogenesis. Measuring esterase activity of 46 disease-associated and 20 common variants observed across PNPLA6-associated clinical diagnoses unambiguously reclassified 10 variants as likely pathogenic and 36 variants as pathogenic, establishing a robust functional assay for classifying PNPLA6 variants of unknown significance. Estimating the overall NTE activity of affected individuals revealed a striking inverse relationship between NTE activity and the presence of retinopathy and endocrinopathy. This phenomenon was recaptured in vivo in an allelic mouse series, where a similar NTE threshold for retinopathy exists. Thus, PNPLA6 disorders, previously considered allelic, are a continuous spectrum of pleiotropic phenotypes defined by an NTE genotype:activity:phenotype relationship. This relationship and the generation of a preclinical animal model pave the way for therapeutic trials, using NTE as a biomarker.

neuroscience↗

bioRxiv2023

ATOMDANCE: interpretable kernel-based learning for denoising functional and evolutionary comparisons of protein dynamics

Comparative methods in molecular biology and molecular evolution rely exclusively upon the analysis of DNA sequence and protein structure, both static forms of information. However, it is widely accepted that protein function results from changes in dynamic machine-like motions induced by molecular interactions, a type of data for which comparative methods of analysis are challenged by the large fraction of protein motion created by random thermal noise in the surrounding solvent. Here, we introduce ATOMDANCE, a suite of statistical and kernel-based machine learning tools designed for comparing and denoising functional states of protein motion captured in time-series from molecular dynamics simulations. ATOMDANCE employs interpretable Gaussian kernel functions to compute site-wise maximum mean discrepancy (MMD) between learned features of motion representing two functional, malfunctional or evolutionary protein states (e.g. bound vs. unbound, wild-type vs. mutant). ATOMDANCE derives empirical p-values identifying functional similarity/difference in dynamics at each amino acid site on the protein. ATOMDANCE also employs MMD to contextually analyze potential random amino-acid replacements thus allowing for a site-wise test of neutral vs. non-neutral evolution in the divergence of dynamic function in protein homologs. Lastly, ATOMDANCE also employs mixed-model ANOVA combined with graph network community detection to identify functional shifts in protein regions that exhibit time-coordinated dynamics or resonance of motion across sites. Here, we demonstrate the utility of the software for identifying key sites involved in dynamic responses during functional binding interactions involving DNA, small molecule drugs, and virus-host recognition. We also demonstrate its utility in understanding dynamic resonance changes occurring during the allosteric activation of a pathogenic protease. ATOMDANCE offers a user-friendly interface and only requires an input structure, topology and trajectory files for each of the two proteins being compared (i.e .pdb, .prmtop, and .nc). A separate interface for generating molecular dynamics simulations via open-source tools is also offered. Lay Audience Summary - ATOMDANCE is a suite of software pipelines controlled by a single user interface and designed to comprehensively simulate, calculate and compare protein motions between two functional or evolutionary states while controlling for random noise. It is useful for finding amino acid sites on a given protein that are important in binding other proteins, DNA, or drugs/toxins. It can also be used to assess the effect of genetic mutation on protein motion, and identifies regions of sites on proteins that tend to move together or resonate as a whole unit or community.

biophysics↗

bioRxiv2021

The C. albicans virulence factor Candidalysin polymerizes in solution to form membrane pores and damage epithelial cells.

The pathogenic fungus Candida albicans causes severe invasive candidiasis. C. albicans infection requires the action of the virulence factor Candidalysin (CL), which damages the plasma membrane of the target human cells. However, the molecular mechanism that CL uses to permeabilize membranes is poorly understood. We employed complementary biophysical, modeling, microscopy, and cell biology methods to reveal that CL forms membrane pores using a unique molecular mechanism. Unexpectedly, it was observed that CL readily assembles into linear polymers in solution. The basic structural unit in polymer formation is a CL 8-mer, which is sequentially added into a string configuration. Finally, the linear polymers can close into a loop. Our data indicate that CL loops spontaneously insert into the membrane to become membrane pores. We identified a CL mutation (G4W) that inhibited the formation of polymers in solution and prevented formation of pores in different synthetic lipid membranes systems. Studies in epithelial cells showed that G4W CL failed to activate the danger response signaling pathway, a hallmark of the pathogenic effect of CL. These results indicate that CL polymerization in solution is a necessary step for the damage of cellular membranes. Analysis of thousands of CL pores by atomic force microscopy revealed the co-existence of simple depressions and complex pores decorated with protrusions. Imaging and modeling indicate that the two types of pores are formed by CL molecules assembled into alternate orientations. We propose that this structural rearrangement represents a maturation mechanism that might stabilize pore formation to achieve more robust cellular damage. Taken together, the data show that CL uses a previously unknown mechanism to damage membranes, whereby pre-assembly of CL loops in solution directly leads to formation of membrane pores. Our investigation not only unravels a new paradigm for the formation of membrane pores, but additionally identifies CL polymerization as a novel therapeutic target to treat candidiasis.

biophysics↗

bioRxiv2020

Clinical interpretation of integrative molecular profiles to guide precision cancer medicine

Individual tumor molecular profiling is routinely used to detect single gene-variant ("first-order") genomic alterations that may inform therapeutic actions -- for instance, a tumor with a BRAF p.V600E variant might be considered for RAF/MEK inhibitor therapy. Interactions between such first-order events (e.g., somatic-germline) and global molecular features (e.g. mutational signatures) are increasingly associated with clinical outcomes, but these "second order" alterations are not yet generally accounted for in clinical interpretation algorithms and knowledge bases. Here, we introduce the Molecular Oncology Almanac (MOAlmanac), a clinical interpretation algorithm paired with a novel underlying knowledge base to enable integrative interpretation of genomic and transcriptional cancer data for point-of-care treatment decision-making and translational hypothesis generation. We compared MOAlmanac to first-order interpretation methodology in multiple retrospective patient cohorts and observed that the inclusion of preclinical and inferential evidence as well as second-order molecular features increased the number of nominated clinical hypotheses. MOAlmanac also performed matchmaking between patient molecular profiles and cancer cell lines to further expand individualized clinical actionability. When applied to a prospective precision oncology trial cohort, MOAlmanac nominated a median of two therapies per patient and identified therapeutic strategies administered in 46% of patient profiles. Overall, we present a novel computational method to perform integrative clinical interpretation of individualized molecular profiles. MOAlmanc increases clinical actionability over conventional approaches by considering second-order molecular features and additional evidence sources, and is available as an open-source framework.

cancer biology↗

bioRxiv2020

SARS-CoV-2 genomics beyond the consensus sequence: evidence for circulating mixed viral populations

Extensive global sampling and whole genome sequencing of the pandemic virus SARS-CoV-2 have enabled researchers to characterise its spread, and to identify mutations that may increase transmission or enable the virus to escape therapies or vaccines. Two important components of viral spread are how frequently variants arise within individuals, and how likely they are to be transmitted. Here, we characterise the within-host diversity of SARS-CoV-2, and the extent to which genetic diversity is transmitted, by quantifying variant frequencies in 1390 clinical samples from the UK, many from individuals in known epidemiological clusters. We show that SARS-CoV-2 infections are characterised by low levels of within-host diversity across the entire viral genome, with evidence of strong evolutionary constraint in Spike, a key target of vaccines and antibody-based therapies. Although within-host variants can be observed in multiple individuals in the same phylogenetic or epidemiological cluster, highly infectious individuals with high viral load carry only a limited repertoire of viral diversity. Most viral variants are either lost, or occasionally fixed, at the point of transmission, consistent with a narrow transmission bottleneck. These results suggest potential vaccine-escape mutations are likely to be rare in infectious individuals. Nonetheless, we identified Spike variants present in multiple individuals that may affect receptor binding or neutralisation by antibodies. Since the fitness advantage of escape mutations in highly-vaccinated populations is likely to be substantial, resulting in rapid spread if and when they do emerge, these findings underline the need for continued vigilance and monitoring.

genomics↗

bioRxiv2018

Inherited DNA Repair Defects in Colorectal Cancer

Colorectal cancer (CRC) heritability has been estimated to be around 30%. However, mutations in the known CRC susceptibility genes explain CRC risk in under 10% of the cases. Germline mutations in DNA-repair genes (DRGs) have recently been reported in CRC but their contribution to CRC risk is largely unknown. We evaluated the gene-level germline mutation enrichment of 40 DRGs in 680 unselected CRC individuals compared to 27728 ancestry-matched cancer-free adults. Significant findings were then examined in independent cohorts of 1661 unselected CRC cases and 1456 early-onset CRC cases. Of 680 individuals in the discovery set, 31 (4.56%) individuals harbored germline pathogenic mutations in known CRC susceptibility genes while another 33 (4.85%) individuals had DRG mutations that have not been previously associated with CRC risk. Germline pathogenic mutations in ATM and PALB2 were enriched in both the discovery (OR= 2.81; P= 0.035 and OR= 4.91; P= 0.024, respectively) and validation sets (OR= 2.97; Adjusted P= 0.0013 and OR= 3.42; Adjusted P= 0.034, for ATM and PALB2 respectively). Biallelic loss of ATM was evident in all cases with matched tumor profiling. CRC cases also had higher rates of actionable mutations in the HR pathway that can substantially increase the risk of developing cancers other than CRC. Our analysis provides evidence for ATM and PALB2 as CRC risk genes, underscoring the importance of the homologous recombination pathway in CRC. In addition, we identified frequent complete homologous recombination deficiency in CRC tumors, representing a unique opportunity to explore targeted therapeutic interventions such as PARPi.

genetics↗