Biology subjects

Smith, L.

Publications and source records attributed to Smith, L..

At least 19 recordsLinked to original sources

bioRxiv2026

KDM6A Haploinsufficiency Is Insufficient to Disrupt Cochlear Structure and Auditory Function in Mouse Models of Kabuki Syndrome Type 2

Objective: Kabuki syndrome type 2 (KS2) is a rare X-linked disorder caused by pathogenic variants in KDM6A and is frequently associated with hearing impairment. Because auditory phenotypes include sensorineural, conductive, and mixed hearing loss, we examined whether Kdm6a deficiency directly impairs cochlear morphology or auditory function in mice. Methods: We generated Nestin-Cre; Kdm6a conditional mutants and a germline-derived global Kdm6a deletion model using Sox2-Cre-mediated germline recombination. Auditory function and cochlear morphology were assessed by auditory brainstem responses (ABRs), distortion product otoacoustic emissions (DPOAEs), and histological analyses. Results: Whole-body hemizygous or homozygous Kdm6a deletion resulted in embryonic lethality. Analyses therefore focused on Nestin-Cre; Kdm6aflox/Y males and females carrying a germline-derived heterozygous Kdm6a deletion. In Nestin-Cre mutants, ABR thresholds, wave I amplitudes and latencies, and DPOAE measures at 8, 16, and 32 kHz were comparable with littermate controls at 4 and 8 weeks. In heterozygous deletion females, ABR thresholds, wave I amplitudes and latencies at 4-64 kHz and DPOAE measures at 8, 16, and 32 kHz were comparable with male and female wild-type controls. No overt cochlear pathology was observed in either model. Conclusion: Kdm6a deficiency in the viable mouse models examined did not produce overt cochlear pathology or baseline auditory dysfunction. These findings suggest that partial Kdm6a loss alone is insufficient to produce a robust primary cochlear phenotype in young mice and highlight the potential contributions of non-cochlear, developmental, central, and later-onset mechanisms to hearing impairment in KS2. Clinically, these findings support careful evaluation for potentially treatable middle-ear disease.

developmental biology↗

bioRxiv2026

RNF213 M1-ubiquitinates damaged mitochondria to activate pro-inflammatory NF-κB signaling

Through mitochondrial outer membrane permeabilization (MOMP), mitochondria are central to apoptosis. MOMP is pro-inflammatory, impacting diverse processes including anti-tumor immunity and cellular senescence. Despite this, how damaged mitochondria activate inflammation remains unclear. Recent studies have shown that following MOMP, mitochondria are extensively ubiquitinated activating pro-inflammatory NF-{kappa}B signaling. We identify the E3 ligase, RNF213, as essential for pro-inflammatory mitochondrial ubiquitination following MOMP. RNF213 has an established role in pro- inflammatory, cell-autonomous immunity to bacteria and other pathogens. We discover that RNF213 is required for mitochondrial M1-linked (linear) ubiquitination. Interestingly, this was found to be independent of the canonical M1-ubiquitin ligase complex LUBAC. RNF213 can directly catalyze M1-linked ubiquitination. By promoting mitochondrial M1-linked ubiquitination, RNF213 initiates the recruitment of the essential NF{kappa}B adaptor molecule, NEMO, and subsequently activates pro-inflammatory NF-{kappa}B signaling. Collectively, our findings highlight striking similarities between how cells detect damaged mitochondria and intracellular pathogens, leading to inflammation.

cell biology↗

bioRxiv2026

CFTR dysfunction in the intestinal epithelium is sufficient to promote pathogenic expansion of E. coli and enhanced barrier permeability in cystic fibrosis

Changes in the gut microbiome in cystic fibrosis (CF) are well characterized, yet their causes and downstream effects remain largely unknown. Well-documented alterations include reduced overall complexity (i.e. alpha diversity) of the gut microbiota and increased relative abundance of E. coli, which are associated with greater inflammation and shorter stature in infants. Previous results from our laboratory using a germ-free cystic fibrosis transmembrane conductance regulator (Cftr) mutant mouse model (CF mouse) demonstrated that the observed fecal microbiome dysbiosis is driven by mutated Cftr independent of factors such as diet or antibiotic treatment. We expand on these results in this report by using the defined 8-member community Altered Schaedler Flora (ASF) with and without E. coli, to show that E. coli is pathogenic in the context of the CF gut microbiome, resulting in increased intestinal permeability. We also show that Cftr deletion in intestinal epithelial cells alone, using a Villin-Cre targeted model, is sufficient to raise E. coli abundance in the fecal microbiome, increase intestinal permeability, and amplify the number of TH17 cells in the mesenteric lymph nodes. Together, our results demonstrate that the intestinal epithelium plays a dominant role in fecal microbiome alterations in CF and that the resultant dysbiosis contributes to CF pathogenesis.

microbiology↗

bioRxiv2026

CAMSAP3 loss of function models suggest causative role in generalized genetic epilepsy

Advancements in next generation sequencing have led to the discovery of hundreds of human epilepsy gene associations. Newly associated genes require functional validation to establish causation and to inform patient treatment in the clinic. A recent exome trio analysis identified predicted pathogenic variants in two patients with generalized epilepsy in the gene CAMSAP3. CAMSAP3 regulates non-centrosomal microtubule dynamics, and the acetylation necessary for normal axonal differentiation and migration. We show that overexpression of patient variants leads to protein degradation and dysregulation of microtubule acetylation in cultured HEK cells. Camsap3 knockout zebrafish also exhibit increased axonal microtubule acetylation as well as epileptic features such as seizure-like swimming behaviors, aberrant inhibitory interneuron development and epileptiform via local field potential. Together these data suggest that CAMSAP3 plays an important role in generalized genetic epilepsy.

neuroscience↗

bioRxiv2026

Rapid phase resetting of Aedes aegypti circadian rhythms by transient alterations in light exposure

Circadian clocks enable mosquitoes to anticipate recurring environmental variations and coordinate behaviors critical for survival and disease transmission, such as locomotion, reproduction, host-seeking, and blood-feeding, with times of day when performance is maximal. In Aedes aegypti, locomotor activity follows a robust diurnal rhythm shaped by endogenous circadian clocks and environmental cues, among which light has been shown to be the primary source of temporal information. While early studies established the role of light in regulating locomotor activity, behavior, oviposition and pupation, it remains unclear which features of a light cycle drive changes in circadian rhythms. This question is increasingly relevant as Ae. aegypti is frequently exposed to artificial and dynamic lighting conditions in urban environments. Here, we investigated how transient changes in light schedules influence circadian rhythms in locomotor activity by systematically manipulating the timing, duration, and direction of light exposure. Using a high-throughput assay, we tested over 1900 individuals, including wild-type and timeless knockout mutants, and showed that a single day of al tered lighting is sufficient to induce robust phase shifts, with no evidence of masking effects. A 6-hour light pulse was sufficient to re-entrain mosquitoes regardless of the timing of the pulse, and phase shifts were primarily driven by the offset time of the light pulse, indicating that light-offset acts as a major zeitgeber. Together, these findings challenge conventional assumptions about the timescale of circadian synchronization and highlight the remarkable plasticity of mosquito behavior in response to anthropogenic light. Eventually, these effects could explain the rapid adaptation of the species to urban environments and have potential consequences for disease transmission dynamics.

animal behavior and cognition↗

bioRxiv2026

GenomeProt: User friendly proteogenomics for canonical and non-canonical proteoform characterisation

Quantifying the diversity of RNAs and proteins produced by cells is fundamental to the biological and clinical sciences. However, many RNAs and proteins remain uncharacterised, especially proteins translated from alternate RNA isoforms; untranslated regions of mRNAs and non-coding RNAs, as well as the effects of DNA variation on protein sequences. Proteogenomics aims to characterise the complete proteome by integrating genomics and/or transcriptomics with proteomics, but current tools have limitations in useability, analysis features and visualisation of resulting data. To address these gaps, we developed GenomeProt, a user-friendly GUI-based tool for integrative proteogenomic analysis. We demonstrate its utility by integrating long-read RNA sequencing with mass-spectrometry-based proteomics to pinpoint proteoform expression generated by alternative splicing; discover novel, unannotated proteins in human brain samples; and quantify variant-containing peptides associated with treatment resistance in a melanoma xenograft model. GenomeProt brings the discovery power of proteogenomics to biologists, illuminating the hidden proteome.

bioinformatics↗

bioRxiv2026

Seasonal Rebalancing of Assembly Processes and Cross-Domain Network Restructuring in Microbial Communities of a Large Eutrophic Lake

Harmful algal bloom (HAB) succession in eutrophic lakes arises from seasonal rebalancing of selection, dispersal, and drift across interacting microbial domains, yet process attribution remains limited due to the scarcity of cross-domain analyses. Using multi-marker eDNA metabarcoding (16S rRNA, 18S rRNA, 23S rRNA), we show that bacterioplankton, cyanobacteria, phytoplankton, and zooplankton in Lake Taihu undergo coordinated spring-summer transitions, with inter-seasonal turnover far exceeding spatial heterogeneity. Assembly regimes shifted coherently across domains: spring communities were dominated by strong homogeneous selection--especially among cyanobacteria and microeukaryotes--whereas summer communities moved toward drift- or neutrality-like dynamics under bloom-stage mixing that enhanced dispersal. Null- and neutral-model diagnostics supported these trends. Cross-domain co-occurrence networks restructured seasonally, with summer networks becoming more connected and substantially more robust, indicating that bloom conditions foster cohesive, robust interaction structures rather than destabilization. These findings provide evidence that bloom progression restructures aquatic microbiomes through a seasonal rebalance of selection, drift, and dispersal coupled with adaptive strengthening of cross-domain connectivity, providing a process-explicit framework for understanding community stability and ecosystem resilience in eutrophic lakes.

ecology↗

bioRxiv2026

Widespread occurrence of bovine-like and new viruses in wild deer across the United States

Over the past several decades, deer populations in North America have grown considerably, resulting in frequent contact with humans and livestock, and increased potential for pathogen spillover. Despite the importance of pathogen spillover among humans, wildlife, and livestock, the diversity of viruses present in deer remains largely unknown. Using a metagenomic high-throughput sequencing approach, we characterized viral communities in the upper respiratory tracts of live mule deer (Odocoileus hemionus) and white-tailed deer (Odocoileus virginianus) captured at fourteen study sites in nine states across the United States. We identified vertebrate-infecting viruses in both deer species at all but two of the study sites, located in Illinois and Utah. Viral richness did not vary among species or study sites. However, viral community composition was different across study sites but not among deer species. Amongst the detected viral sequences, several originate from or were closely related to viruses previously described in humans (e.g., severe acute respiratory syndrome coronavirus 2) and livestock (e.g., bovine-like coronavirus). We also documented viruses recently discovered in deer, such as CHeRI orbivirus 1. Finally, we identified several new putative viruses in the Picornaviridae, Rhabdoviridae and Tobaniviridae families, including a novel Aphthovirus related to bovine rhinitis A virus in both deer species, across seven states and nine study sites. Our findings expand the understanding of viral diversity in two deer species across the United States, providing important insights for managing pathogens at the wildlife, livestock, and human interface.

microbiology↗

bioRxiv2026

Attenuated estrogen signaling disrupts placentation and drives trophoblast defects in Down syndrome

Proper establishment of the primitive placenta and subsequent tissue homeostasis in the mature placenta are critical for successful pregnancy in humans. Placental insufficiency is associated with adverse pregnancy outcomes, including fetal growth restriction, preeclampsia, and pregnancy loss. Moreover, emerging evidence suggests that placental defects are associated with long-term health challenges that manifest well into adulthood; yet the etiologies of such diseases are largely unknown. Defining the mechanistic basis for placental deficiencies, therefore, has important implications for improving both reproductive health and the lifelong well-being of affected children. Down syndrome is characterized by placental defects of unknown mechanistic origin, and notably, individuals with Down syndrome are at increased risk of developing diseases commonly associated with placental insufficiency later in life. Using induced pluripotent stem cells from Down syndrome patients, we found that stem cell-based embryo models (i.e., blastoids) and directed differentiation systems recapitulate trophoblast cell fate defects observed in placentas affected by Down syndrome. Furthermore, we demonstrate that attenuated estrogen signaling contributes to placental syncytialization defects and identify NRIP1, a transcriptional corepressor of estrogen receptor that is located on chromosome 21, as a key driver of trophoblast cell fate defects. Increased gene dosage of NRIP1 in an otherwise diploid cell line phenocopies cell fate defects observed in trophoblasts affected by Down syndrome. Our study suggests that estrogen signaling is a crucial regulator of trophoblast development and may serve as a potential target for therapeutic intervention. Highlights and eTOC blurbO_LIEstrogen signaling mediates syncytiotrophoblast fusion C_LIO_LIHuman iPS cells provide a tractable model for trophoblast defects in Down syndrome C_LIO_LITrophoblast differentiation and estrogen signaling are disrupted in Down syndrome C_LIO_LIIncreased NRIP1 expression is sufficient to induce trophoblast defects C_LI Logsdon and colleagues apply patient-derived induced pluripotent stem cells to recapitulate placentation defects observed in Down syndrome. The authors demonstrate that attenuated estrogen signaling disrupts trophoblast differentiation and identify NRIP1, a gene found on chromosome 21 that dampens estrogen signaling, as a regulator of trophoblast maturation. NRIP1 and estrogen signaling may represent important therapeutic targets for infertility and Down syndrome.

developmental biology↗

bioRxiv2026

Rapid vaccine induction of macaque HIV-1 V2 Apex broadly neutralizing antibodies with immunogenetic signatures that are potentially translatable to humans

Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

immunology↗

bioRxiv2026

Global adaptation to climate change in the twilight zone revealed by shared signals of selection in mesopelagic lanternfishes

Rapid accumulation of greenhouse gases threatens humanity and global diversity. The oceans absorb 30% of anthropogenic carbon emissions annually, but adaptation to climate change by the biotic components of this sink are poorly understood. Lanternfishes (Myctophiformes) are the most abundant vertebrates on the planet by biomass and the dominant mesopelagic vertebrate consumers, thus crucial components of the global carbon cycle. However, it is unknown whether lanternfishes are adapting to global warming and ocean acidification (OA). We hypothesized that warming and OA would act as major shared selective forces across diverse oceanic environments and that disparate taxa would respond in parallel through shared genetic pathways. We used whole-genome sequencing to test this hypothesis by identifying shared signals of selection across lanternfishes from multiple sites in the Atlantic and Pacific spanning three genera (Benthosema glaciale, Triphoturus mexicanus, and Diaphus theta). Across all species we found evidence of expansion from a population bottleneck possibly corresponding to the last glacial maximum and effective population sizes of only 5 million, suggesting substantial reproductive skew and spatially restricted populations. We successfully identified 34 candidate genes experiencing strong shared selection pressure across all taxa in both oceans. 81% of these candidate genes were consistent with adaptations to warming and OA, including a heat-shock protein (HSP70) and genes related to skeletal development, calcium homeostasis, and biomineralization. 14 out of 34 candidate genes are also known from experimental climate change studies to be involved in the response to hypoxia, altered pH, and thermal stress. We found significant gene ontology enrichment within these candidates for otolith morphogenesis, a major component of OA adaptation in fishes. This study provides a new approach for studying climate change adaptation at a global scale and our results imply widespread shared adaptive responses of marine species to climate change.

evolutionary biology↗

bioRxiv2026

A novel antiviral strategy targeting human metapneumovirus through pH modulation in human airway epithelial cells

Human metapneumovirus (hMPV) is a major cause of respiratory infections, particularly among infants, older adults, and immunocompromised individuals, yet no approved vaccines or targeted antiviral therapies are currently available. pH-regulated processes, including airway epithelial physiology, endosomal acidification, and viral fusion mediated by the fusion (F) protein, are critical for hMPV infection. This study evaluates PHOH-001, an inhaled alkaline buffer, as a potential therapeutic strategy to modulate airway epithelial pH and inhibit hMPV infection. Using a recombinant hMPV expressing green fluorescent protein (rhMPV-GFP), viral replication was assessed in primary human airway epithelial cells (HAECs). PHOH-001 significantly reduced GFP expression at 72 hours post-infection in both submerged and air-liquid interface (ALI) cultures, with effects comparable to those of the endosomal acidification inhibitor bafilomycin A1. In Vero E6 cells, used as a mechanistic in vitro model, PHOH-001 increased extracellular and intracellular pH in a concentration-dependent manner and correspondingly reduced hMPV infection. In HAECs, PHOH-001 reduced viral replication, as measured by TCID50 assays of infectious virus, and inhibited syncytium formation, a key step in viral spread. Furthermore, PHOH-001 altered F protein localization and was associated with changes in actin organization, consistent with impaired viral spread. Collectively, these findings demonstrate that PHOH-001 alters multiple pH-dependent steps in hMPV infection in vitro and support airway pH modulation as a potential antiviral strategy against hMPV.

molecular biology↗

bioRxiv2026

A novel dual-chimeric surrogate virus to select, test and characterize mutants of protease and glycoprotein inhibitors.

Antivirals are life-saving medications. However, pathogens develop resistances, mitigating their effect. Resistance studies (gain-of-function, GOF) are therefore paramount before and while antivirals are used clinically to characterize resistances and ideally study how to counteract them with other antivirals. The ability to switch from one antiviral, against which the virus is resistant, to another, depends on the availability of alternative drugs. Furthermore, targeting different parts of the virus synergistically with multiple drugs decreases the odds of simultaneous resistance. However, studying resistance, cross-resistance and remaining susceptibility requires working with the actual pathogen. Especially when introducing resistances into dangerous viruses, performing GOF studies would raise safety concerns and require firm biological containment. In this study we developed a novel dual-chimeric virus encoding both SARS-CoV-2 spike glycoprotein and main protease (Mpro) based on the model virus, vesicular stomatitis virus (VSV). We applied selection pressure with spike and Mpro inhibitors, generated mutants of these viruses and determined their resistance and cross-resistance profiles by performing dose-response experiments with live and pseudotyped viruses. Additionally, we conducted in silico calculations to determine the impact of spike substitutions to the observed resistance phenotype. With the new technology presented here, we demonstrate that it is possible to carry out GOF studies more safely and highlight their importance in the future challenges of virological research.

microbiology↗

bioRxiv2025

River pollution threatens preferred macroinvertebrate prey of endemic fishes in Aotearoa, New Zealand

O_LIMacroinvertebrates are a critical source of food for riverine fishes. Anthropogenic stressors can transform riverine macroinvertebrate communities, yet the consequences of such transformations to the fishes that feed on them are poorly understood. Changes in any combination of food abundance, accessibility or quality may be referred to as changes in the foodscape of fishes. Stressor-driven increases of inaccessible prey that are difficult for fish to detect, capture or ingest, may render foodscapes less profitable to fishes. C_LIO_LIWe examined how nutrient enrichment, fine sediment, acid mine drainage (AMD), flooding and drying reshape fish foodscapes by altering the accessibility of macroinvertebrate prey for two New Zealand river fishes, Galaxias vulgaris and Gobiomorphus breviceps. We determined relative accessibility of macroinvertebrate taxa and traits to these fishes by comparing the abundance of prey taxa and traits in the environment with their corresponding abundances in fish diets. To make these comparisons, invertebrate and fish gut samples were collected from the same river reaches, at the same times, over three years. Environmental DNA (eDNA) metabarcoding of fish gut contents facilitated efficient diet characterisation of over 700 fish guts. Finally, to determine how multiple stressors might affect fish foodscapes, we related invertebrate trait-specific accessibilities to published data defining how the composition of those macroinvertebrate traits varies along stressor gradients. C_LIO_LIMacroinvertebrate traits that were most accessible to fishes were those promoting detection (e.g., active foraging behaviours exhibited by crawlers and scrapers) and ingestion (e.g., moderate size, morphologies lacking defensive structures), typical of mayfly and free-living caddisfly larvae. In contrast, prey with traits inhibiting detection (e.g., small size and burrowing behaviour) and ingestion by gape-limited fishes (e.g., large size), were less accessible to the fishes we studied. C_LIO_LITrait abundance-stressor relationships revealed that that increasing fine sediment, nutrients, AMD and drying, and decreased flooding frequency, favoured macroinvertebrates with traits that erode accessibility to fishes. These results show that multiple stressors may decrease the profitability of fish foodscapes by filtering out macroinvertebrate prey with traits promoting accessibility to fishes. C_LIO_LIFood web approaches to understanding multi-stressor impacts are rare, but are necessary to understand how the effects of multiple stressors on primary consumers then go on to affect predators of higher trophic position. A major barrier to fish foodscape research is the difficulty and cost of estimating trophic networks. We discuss how eDNA metabarcoding, coupled with trait-based approaches may help overcome these barriers, enabling generalisable assessments of foodscape changes caused by multiple stressors. C_LI

ecology↗

bioRxiv2025

Exome Sequencing and Allele Dosage Analysis of Coast Redwood, a Hexaploid Conifer, Identifies a Major Population Break South of San Francisco Bay

1The coast redwood (Sequoia sempervirens) is a long-lived, hexaploid conifer of high ecological, cultural, and economic value whose range has been greatly reduced by historical logging [1]. Effective restoration and conservation depend on understanding patterns of genetic differentiation across the redwood range to delineate populations for management prioritization. Yet, past range-wide studies provided only a partial picture of population structure in coast redwood as they relied on a limited set of genetic markers [2, 3] or limited sampling, as sequencing was done on the same range-wide provenance collection [4, 5]. Here, we analyze 334,029 SNPs from a new range-wide set of 224 individuals using a dosage-based approach that accounts for polyploidy. Principal coordinates and clustering analyses reveal clear latitudinal structure, with a steeper break south of San Francisco Bay. Outlier SNP analysis identified new candidate loci involved in salinity tolerance, climate stress response, and nutrient uptake, suggesting potential local adaptation. These results point to the central role of geography in shaping genetic variation in coast redwood and give scientific basis for designing new conservation and management strategies aimed at preserving the species genetic diversity into the future.

ecology↗

bioRxiv2025

Retrosplenial cortex enables context-dependent goal-directed sensorimotor transformation

The ability to dynamically adjust a behavioral response to a stimulus depending on context is of critical importance for animals. To investigate the neural basis supporting context-dependent sensory processing we developed a behavioral task in which mice changed their response to a single whisker deflection according to a continuously present contextual cue. Through unbiased optogenetic inactivation mapping, we found that neuronal activity in sensory and motor cortices contributed to task execution and, interestingly, we uncovered an unexpected role of retrosplenial cortex for contextual integration. Widefield calcium imaging revealed that retrosplenial cortex was the first dorsal cortical area to show context discrimination in response to whisker stimulation, followed by whisker motor cortex. Finally, we combined optogenetic inactivation with calcium imaging to define causal context-dependent changes in sensorimotor processing. Our cortex-wide mapping experiments thus begin to define key cortical nodes for context-dependent sensorimotor transformation and highlight an important contribution of retrosplenial cortex.

neuroscience↗

bioRxiv2025

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century

Citizen science plays an increasingly important role in generating scientific knowledge and supporting environmental and social action. However, its potential to address complex global challenges remains underutilised. This study explores how to improve citizen science by involving the public in all stages of scientific research. Using participatory research methods, we conducted online surveys and group discussions with researchers, citizen scientists, and Indigenous people. Thematic coding was used to identify key challenges, opportunities, and best practices to enhance citizen science initiatives. Additionally, nine case studies were reported using the Standardised Data on Initiatives (STARDIT) reporting tool. The study identifies key strategies for enhancing participant engagement and retention in citizen science initiatives. Findings underscore the importance of inclusive, evidence-informed approaches such as targeted outreach, fair compensation, tailored support, and co-creation practices. Ensuring data quality and fostering trust require adherence to FAIR data principles, transparent validation and sharing processes, and the establishment of ethical research partnerships. Persistent challenges include short-term funding, which undermines long-term project sustainability, and the lack of centralized support for ethics and project management. Formal recognition of citizen scientists through co-authorship, standardized training, and professional development opportunities can further strengthen involvement and build capacity. Finally, emerging technologies--including AI and open data platforms--present opportunities to scale and improve efficiency, provided they are implemented with appropriate ethical safeguards and investment. Drawing together these insights, we provide 10 actionable recommendations for citizen science in the 21st century. These highlight the importance of embedding citizen science in national research infrastructure, education, and policy, alongside consistent evaluation and reporting, to improve its inclusivity, longevity, and impact. We conclude by arguing that as the world confronts climate change, public health crises, and biodiversity loss, broader public involvement in science is key for equitable, efficient and evidence-informed responses.

scientific communication and education↗

bioRxiv2025

A novel approach to Caudoviricetes taxonomy utilising whole proteome structure-structure comparison

Viral proteins often evolve so rapidly that sequence similarity is lost even among conserved functional genes, complicating phylogenetic analysis and classification. This challenge is acute for Caudoviricetes, a highly diverse class of dsDNA tailed bacteriophages recently redefined by the International Committee on Taxonomy of Viruses (ICTV). To address the limitations of sequence-based taxonomy, we present a structure-based classification framework using whole-proteome structural clustering. From 4,082 exemplar genomes, we predicted 445,098 protein structures with ESMFold and clustered them using Foldseek. Genomes were encoded as binary profiles of structural fold presence, and phylogenetic distances were inferred and normalized using Relative Evolutionary Divergence (RED). This yielded a revised structural taxonomy comprising 159 orders, 267 families, 502 subfamilies, and 1,189 genera. We also introduce PhagePleats, a Python tool for classifying novel phage genomes based on structural similarity. Our approach highlights the utility of protein structure for resolving distant viral relationships.

microbiology↗