Biology subjects

Wade, M.

Publications and source records attributed to Wade, M..

14 recordsLinked to original sources

bioRxiv2026

Tailocin as an alternative weapon to type VI secretion system in bee gut symbionts

Antagonistic interactions often shape microbial communities, as co-residents compete for resources. One system of interbacterial antagonism involves tailocins: phage tail-like particles produced by some bacteria to kill close relatives. Their roles in natural communities are poorly studied. Here, we identified putative tailocin loci ubiquitously present in genomes of Snodgrassella species, core members of the bee gut microbiota. We purified tailocins from culture supernatants of different Snodgrassella strains and found that these inhibited growth of multiple Snodgrassella strains but not of strains of other species that cooccur in bee guts. Proteomic analyses corroborated the production of tailocins, and cryogenic electron microscopy imaging revealed their morphology and killing activity via membrane disruption. We generated single- and double-gene knockout mutants of a predator Snodgrassella strain that naturally possesses both tailocin and a type VI secretion system (T6SS) that was previously shown to function in intraspecies competition in bee guts. These mutants were used in tests for antagonism against a prey Snodgrassella strain in vivo. Co-inoculations within gnotobiotic honeybees including visualization within guts showed that both tailocin and T6SS are important for Snodgrassella in intraspecies competition. Each of these two antagonism mechanisms inhibits the establishment of susceptible strains within the ileum. Outcomes depend on the timing of colonization by competing strains, with both tailocin and T6SS giving a stronger advantage when the producing strain colonizes first. Thus, tailocin production can underlie priority effects that have been widely observed in the bee gut community and other host-associated bacterial communities.

microbiology↗

bioRxiv2026

Structure-function analysis of PI3K signalling cascade base editing screens in cancer cells

Knowledge of protein structure and function underpins rational drug discovery, yet many targets lack known selectively druggable sites. Furthermore, the identification of secondary druggable sites offers a strategy to overcome drug resistance. Fragment-based drug discovery (FBDD) can identify new ligandable binding pockets, though how to triage those with the ability to exert biologically relevant effects can be unclear. Systematic approaches to identify novel functionally-important protein sites for therapeutic intervention, such as allosteric pockets or protein-protein interaction (PPI) interfaces, has the potential to accelerate drug discovery, particularly when combined with structure-based hit-finding modalities. The phosphoinositide-3 kinase (PI3K) signalling pathway is frequently altered in human cancer and resistance to approved inhibitors is an ongoing challenge. Here, we performed large-scale CRISPR base editing mutagenesis screens across 30 PI3K pathway proteins in three disease-relevant cancer cell models to systematically map functional residues. Integration of base editing data with structural information identified residues corresponding to known catalytic sites, fragment-binding pockets and PPI interfaces, providing validation for the approach. Additionally, we identified putative allosteric pockets near regions of undefined function. Together, these findings establish high-throughput base editing mutagenesis combined with structural analysis as a scalable strategy to delineate structure-function relationships and inform drug development.

genomics↗

bioRxiv2026

Social hierarchy assays measure independent features of competitive ability

Social hierarchies are a nearly universal feature of animal groups, but whether dominance reflects a single generalized trait or a collection of context-specific competitive abilities remains unclear. Here, we assess social hierarchy in three strains of laboratory mice (BALB/c, C57BL/6, and Shank3B knockouts) of both sexes using three established paradigms: the tube test, the warm spot assay, and the void spot assay. Hierarchies emerged in all strains and both sexes across all three assays, but how animals established rank differed markedly by strain and sex. In the tube test, Shank3b-/- knockout females, but not males, lacked the winner effects seen in wild-type mice, indicating that the ability to build a winning streak depends on social recognition in a sex-specific manner. In the warm spot assay, females formed stronger hierarchies than males, particularly among mice on a C57BL/6 background, with high-ranking females actively displacing others from the warm platform. In the void spot assay, BALB/c mice of both sexes frequently displayed territory-marking behavior, a pattern that was less common in the other strains. Overall, individual rank rarely generalized across domains, despite high trial-to-trial repeatability for individuals within each assay. Together, these findings indicate that mice behave as dominance specialists rather than generalists, with strain- and sex-specific strategies for establishing rank in different competitive contexts, suggesting that distinct neural circuits likely underlie these separable components of competitive ability.

animal behavior and cognition↗

bioRxiv2026

Modifying integrated nursery management through the lens of mycorrhizal ecology improves radiata pine seedling performance and reshapes root mycobiome structure at operational industry scale

Early management decisions in operational forestry are critical for plantation success because it strongly influences seedling quality at planting. Beyond shaping seedling morphology, nursery inputs can also restructure root-associated fungal communities which has consequences for nutrient acquisition, stress tolerance and disease suppression after planting. In this study, we altered nutrient and fungicide inputs based on mycorrhizal ecological theory and quantified the effects of these treatments on key dimensions of the growth performance of radiata pine seedlings. In parallel, we profiled the root-associated mycobiome, assigning fungal taxa to functional guilds and summarizing their richness, diversity, relative abundance and community structure. Using a composite performance index that integrates the key morphological and health measures into a single response variable, together with conventional statistical models with machine learning approaches, we identified management practises that promote both plant performance and a favourable root fungal community and determined the consistent microbiome changes linked to overall quality of the seedlings. These results suggest that microbial feedback loops occur even in highly managed nursery conditions. More broadly, by combining a composite performance index with predictive modelling, we provide a practical way to test complex management combinations and identify microbiome features associated with high-quality planting stock.

ecology↗

bioRxiv2026

SMAD4 loss drives chromosomal instability during tumourigenesis via translational reprogramming

Chromosomal instability (CIN), arising from errors in chromosome segregation during cell division, is a hallmark of cancer. Whilst CIN can result from several mitotic defects, the mechanisms that initiate CIN to drive tumourigenesis remain incompletely understood. Here, we show that loss of SMAD4 reprograms translation to induce CIN, resulting in tumour formation. Multi-omics analysis of tumourigenesis models driven by loss of SMAD4 complemented by functional studies demonstrate that loss of SMAD4 in pre-neoplastic cells leads to dysfunctional mitosis and an altered global translation landscape. We show that CDK11B is translationally downregulated in SMAD4-\- cells, and re-expression of the mitosis-specific isoform of this protein (CDK11B-p58) rescues the mitotic defects. Analysis of patient tumours reveals a strong correlation between markers of CIN and SMAD4 status, indicating the clinical relevance of this phenotype. Collectively, we reveal a previously unrecognised role for SMAD4 as a gatekeeper for CIN-mediated tumourigenesis via regulation of translation.

cancer biology↗

bioRxiv2025

Amino acid biostimulant increases pine photosynthetic efficiency and growth through optimised mycobiome and nitrogen assimilation

BackgroundAmino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants. ResultsAmino-acid fertigation notably increased shoot biomass, plant height, and collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts correlated directly with elevated auxin concentrations observed in needle tissues, providing a plausible mechanism for the enhanced growth. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency. ConclusionsOur findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also promotes a beneficial root microbiome, thereby offering a sustainable pathway to nursery production of radiata pine.

plant biology↗

bioRxiv2024

CDK12 controls transcription at damaged genes and prevents MYC-induced transcription-replication conflicts

Oncogene-induced replicative stress is a potent tumor-suppressive mechanism that must be kept in check for cancer cells to thrive. Thus, the identification of genes and pathways involved in replicative stress is key to understand cancer evolution and to identify prospective therapeutic targets. Here, we investigated factors that modulate replicative stress upon deregulation of the MYC oncogene. We identified the cyclin-dependent kinase CDK12 as selectively required to prevent transcription-replication conflicts and the activation of a cytotoxic DNA-damage response (DDR). At the mechanistic level, CDK12 was recruited to damaged genes by PARP-dependent DDR-signaling and elongation-competent RNAPII. Once recruited, CDK12 repressed transcription by preventing the association of CDK9 with RNAPII. Either loss or chemical inhibition of CDK12 led to DDR-resistant transcription at damaged genes. Genome-wide profiling revealed that loss of CDK12 exacerbated transcription-replication conflicts in MYC-overexpressing cells and led to the accumulation of double-strand DNA breaks (DSBs), occurring preferentially between early- replicating regions and transcribed genes, organized in a co-directional head-to-tail orientation. Overall, our data demonstrate that CDK12 protects genome integrity by repressing transcription of damaged genes, which is required for proper resolution of DSBs at oncogene-induced transcription-replication conflicts. This provides a rationale that explains both how CDK12 deficiency can promote tandem duplications of early-replicated regions during tumor evolution, and how CDK12 targeting can exacerbate replicative-stress in tumors.

cancer biology↗

bioRxiv2024

Particulate Contamination of Human Placenta: Plastic and Non-Plastic

Recent evidence indicates that the human womb is contaminated with a variety of particulate contaminants. Microplastics (MPs, tiny plastic particles (<5 mm) generated by the breakdown of larger plastic products in the environment) accumulation in human placenta has recently been described. In addition, recent evidence has correlated the number of air pollution particulates in term placentas to the loading of these particles in dust from the gestational parent home. The current study sought to characterize the accumulation of plastic and non-plastic particles (NPP) within the term human placenta. Placenta tissues were collected from healthy, singleton pregnancies following vaginal (n=5) and caesarean section (n=5) deliveries at a tertiary care centre located in an urban Canadian city (Ottawa, ON), with particles detected and characterized by Raman micro-spectroscopy. Both plastic and non-plastic particles were identified in all placentas examined, with an average of 1 {+/-} 1.2 MPs /g and 4 {+/-} 2.9 NPP /g of tissue. Similar tissue concentrations of MPs and NNP were identified in all regions of the placenta (basal plate, chorionic villous, chorionic plate), and did not differ according to mode of delivery. MPs ranged in size (2 - 60 m), with the most abundant MPs being polyethylene (PE), polypropylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). The most abundantly identified NPP were carbon, graphite, and lead oxide. Collectively, these results demonstrate the accumulation of foreign particles, including MPs, throughout the human placenta. Given the vital functions of the placenta in supporting fetal growth and development, and a potential for MPs to induce toxicity, further investigations into the potential harmful effects of these environmental toxicants on maternal and fetal health is warranted. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=193 HEIGHT=200 SRC="FIGDIR/small/583005v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@9f5b0org.highwire.dtl.DTLVardef@1e13468org.highwire.dtl.DTLVardef@37aa3forg.highwire.dtl.DTLVardef@8a197e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBoth plastic and non-plastic foreign particles were observed in term placentas from Canadian women C_LIO_LIPlacenta contamination with most of the non-plastic particle types observed has not previously been reported. C_LIO_LIParticles were observed in similar frequency in placenta regions corresponding to maternal or fetal circulation suggesting that particles pass unhindered through the placenta. C_LI

physiology↗

bioRxiv2023

Generating and testing reagents for CRISPR/Cas9 based homologous recombination and gene drive in Tribolium

CRISPR/Cas9 gene drive systems are possible in a few insects and ever expanding. Nonetheless, success in one species and techniques developed for it are not necessarily applicable to other species. As such, the development and expansion of gene drive systems is dependent upon direct experimentation. A critical aspect and potentially limiting factor of gene drive is the ability to induce Cas9-dependent homologous recombination. Here we report our attempts to induce Cas9-dependent homologous recombination and subsequent gene drive in Tribolium castaneum. Utilizing constructs containing one or two target gRNAs in combination with Cas9 under two different promoters and corresponding homology arms, we found a high incidence of CRISPR/Cas9 induced mutations but a complete lack of evidence of homologous recombination and genetic drive. Even though the generated constructs provide new resources for CRISPR/Cas9 modification of the Tribolium genome, our results suggest that Tribolium genome may be refractory towards Cas9-induced homologous recombination and additional modifications will be necessary to increase the potential for homologous recombination.

genetics↗

bioRxiv2023

Novel determinants of NOTCH1 trafficking and signaling in breast epithelial cells

The evolutionarily conserved Notch pathway controls cell-cell communication during development and in adult metazoans. It influences cell fate decisions, cell proliferation and cell differentiation, and contributes to the maintenance of normal tissue homeostasis. Consequently, misregulation of the Notch pathway is associated with a wide range of diseases, including congenital disorders and cancers with little to no cure. Signaling by Notch receptors is regulated by a complex set of cellular processes that include maturation and trafficking to the plasma membrane, endocytic uptake and sorting, lysosomal and proteasomal degradation, and ligand-dependent and independent proteolytic cleavages. We devised assays to follow quantitively the lifetime of endogenous human NOTCH1 receptor in breast epithelial cells in culture. Based on such analysis, we executed a high-content screen of 2749 human genes for which modulatory compounds exist, to identify new regulators of Notch signaling activation that might be amenable to pharmacologic intervention. We uncovered 39 new NOTCH1 genetic modulators that affect different steps of NOTCH1 cellular dynamics. In particular, we find that PTPN23 and HCN2 act as positive NOTCH1 regulators by promoting endocytic trafficking and NOTCH1 maturation in the Golgi apparatus, respectively, while SGK3 serves as a negative regulator that can be modulated by pharmacologic inhibition. Our findings might be relevant in the search of new strategies to counteract pathologic Notch signaling.

cell biology↗

bioRxiv2020

Quantifying Color Vision Changes Associated with Cataracts Using Cone Contrast Thresholds

PurposeThe cone contrast threshold (CCT) test quantified color vision changes in subjects of all ages and those undergoing cataract surgery. MethodsTwenty-four healthy volunteers from two cohort studies performed CCT using best corrected visual acuity, filters, mydriasis, and pinhole correction. Retrospective cross-sectional study of patients seen in eye clinics evaluated the relationship between age and color vision, and age and lens status in 355 eyes. Lastly, 25 subjects performed CCT before and after cataract surgery. ResultsCCT scores were most reliable in the non-mydriatic condition without pinhole correction. Progressively dense brown filters produced small but significant reductions in S-cone sensitivity. Linear regression analysis of phakic subjects showed a decline for all cone classes with age. Rate of decline was greater for S-cones (slope (95% CI) = -1.09 (-1.23, 0.94)) than M-cones (slope (95% CI) = -0.80 (-0.95, -0.66)) and L-cones (slope (95% CI) = -0.66 (-0.81, - 0.52)). CCT scores increased for S-cones but reduced for L- and M-cones in pseudophakic subjects compared to phakic patients. CCT scores after cataract surgery increased for S-cones, M-cones, and L-cones by 33.0 (p<0.001), 24.9 (p=0.001), and 22.0 (p=0.008). ConclusionsCCT assessment allows for clinically practical quantitation of color and contrast vision improvement after cataract surgery and aging patients who note poor vision despite good visual acuity. Translational RelevanceCCT testing, historically used in research, is now a clinically practical tool to evaluate age and cataract related changes in color and contrast vision and routinely quantify vision beyond black and white visual acuity testing.

pathology↗

bioRxiv2019

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis.

Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions, is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics accounting explicitly for metabolic activities of composing microbes, system pH, and chemical exchanges. We calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing experimental population dynamics of these synthetic communities that feature relevant species utilising low-energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis and elaborates on previous estimates of lactate fermentation by sulfate reducers. The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.

microbiology↗

bioRxiv2018

Child Growth Predicts Brain Functional Connectivity and Future Cognitive Outcomes in Urban Bangladeshi Children Exposed to Early Adversities

BackgroundFaltered growth has been shown to affect 161 million children worldwide and derail cognitive development from early childhood. The neural pathways by which growth faltering in early childhood affects future cognitive outcomes remain unclear, which is partially due to the scarcity of research using both neuroimaging and sensitive behavioral techniques in low-income settings. We employed EEG to examine the association between growth faltering and brain functional connectivity and whether brain functional connectivity mediates the effect of early adversity on cognitive development.\n\nMethodsWe recruited participants from an urban impoverished neighborhood in Dhaka, Bangladesh. One sample consisted of 85 children whose EEG and growth measures (height for age, weight for age, and weight to height) were collected at 6 months and cognitive outcomes were assessed at 27 months. Another sample consisted of 115 children whose EEG and growth measures were collected at 36 months and IQ scores were assessed at 48 months. Path analysis was used to test the effect of growth measures on cognitive outcomes through brain functional connectivity.\n\nFindingsFaltered growth was found to be accompanied by overall increased functional connectivity in the theta and low-beta frequency bands for the 36-month-old cohort. For both cohorts, brain functional connectivity was negatively predictive of later cognitive outcomes at 27 and 48 months, respectively. Faltered growth was found to have a negative impact on childrens IQ scores in the older cohort, and this effect was found to be mediated by brain functional connectivity in the low-beta band.\n\nInterpretationThe association found between growth measures and brain functional connectivity may reflect a broad deleterious effect of malnutrition on childrens brain development. The mediation effect of functional connectivity on the relation between physical growth and later IQ scores provides the first experimental evidence that brain functional connectivity may mediate the effect of biological adversity on cognitive development.\n\nFundingBill and Melinda Gates Foundation (OPP1111625)

neuroscience↗

bioRxiv2018

Synthetic methanogenic communities reveal differential impact of ecological perturbations on aceto- and hydrogeno-trophic methanogens

Synthetic microbial communities provide reduced microbial ecologies that can be studied under defined conditions. Here, we use this approach to study the interactions underpinning anaerobic digestion communities and involving the key microbial populations of a sulfate reducer (Desulfovibrio vulgaris), and aceto-(Methanosarcina barkeri) and hydrogenotrophic (Methanococcus maripaludis) methanogens. We create all possible mixed culture combinations of these species and analyse the stability and productivity of each system over multiple sub-culturings and under different sulfate levels, mimicking ecological perturbation in the form of strong electron acceptor availability. We find that all three species can co-exist in the absence of sulfate, and that system productivity (in form of methane production from lactate) increases by almost two-fold compared to co-cultures. With increasing sulfate availability, co-existence is perturbed and both methanogenic populations display a diminishing trend. Interestingly, we find that, despite the continued presence of acetate in the system, the acetotrophic methanogens are more readily disrupted by sulfate perturbation. We show that this is due to a shift in M. barkeri metabolism towards increased co-utilisation of hydrogen with acetate, which we verified through experiments on mono cultures and mass balance calculations in co-cultures. We conclude that hydrogen is a key factor for both hydrogeno- and aceto-trophic methanogenesis and can influence these populations differentially under the common ecological perturbation of strong electron acceptor availability. These findings will help engineering of larger synthetic communities for specific applications in biodegradation and understanding complex anaerobic digestion communities found in animal guts, sediments, and bioreactors.

synthetic biology↗