Biology subjects

Porter, M.

Publications and source records attributed to Porter, M..

9 recordsLinked to original sources

bioRxiv2026

vep-rs: high-throughput Rust variant annotation with population-scale concordance to Ensembl VEP

Summary: Ensembl VEP is the de facto reference for variant consequence annotation, but its Perl implementation limits throughput, and the open reimplementation benchmarked here is validated on a set too small to bound its disagreement with it. We present vep-rs, a Rust reimplementation of Ensembl VEP release 115.2, audited over 260,638,766 VEP consequence tuples, each a (location, allele, feature) key carrying a Sequence Ontology term set, from six variant datasets (ClinVar, gnomAD chr21, and 1000 Genomes chr21 across GRCh37 and GRCh38). On SNPs and indels vep-rs emits exactly VEP's tuple count on all six and attains F1 [≥] 0.999974, differing from VEP on 3,169 tuples, at most one in 38,000 per dataset; with two documented VEP defect shapes set aside, F1 rounds to 1.000000 on all six. Per consequence class, 29 of the 30 Sequence Ontology terms carrying at least 1,000 tuples exceed F1 0.99, and the lowest, 0.540 on start_retained_variant, is entirely a VEP defect. On structural variants, F1 is 0.975395 (GRCh37) and 0.909998 (GRCh38). Timed on 20 independent machines per engine and architecture, vep-rs is faster than VEP by 101x-284x on ARM (geometric mean 176x) and 78.3x-192x on x86 (geometric mean 135x). Five divergence classes are documented, four of them defects in VEP release 115 that vep-rs does not reproduce: a consequence call that contradicts itself, a splice-region term dropped from a variant that lies in a splice region, annotation against a chromosome the variant does not lie on, and output that depends on input batch composition. A pipeline keyed on VEP consequence terms can therefore adopt vep-rs against a measured, per-term bound, shed VEP's contradictory and batch-dependent calls, and annotate population-scale inputs at 78.3 to 284 times VEP's throughput, and per-file structural-variant sets at 22.5 to 52.9 times. Availability and implementation: vep-rs, its harness, both comparators, and every per-machine wall time are released under Apache-2.0 at https://github.com/natera-open-source/vep-rs (release v0.1.0, archived at https://doi.org/10.5281/zenodo.22837897). Supplementary information: Supplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2026

Quantifying Exposure of Pacific Salmon and Steelhead to Climate Change in the Fraser River basin

Climate change can affect salmon and steelhead (Oncorhynchus spp.) throughout their anadromous life cycles, yet there have been no assessments of which Canadian populations face the greatest exposure. We developed a framework to quantify relative climate change exposure of salmon and steelhead populations based on the spatial and temporal distribution of different life stages. Exposure was calculated from climate model projections for freshwater and marine climate variables considering unique impact thresholds for each population and life stage. We applied this framework to 60 Conservation Units of Pacific salmon and steelhead in the Fraser River basin, British Columbia. Lake-type sockeye had the highest exposure, driven by elevated stream temperatures during adult freshwater migration and spawning stages and relatively low thermal tolerance of marine stages. Chinook salmon were the next most exposed, while coho, pink, and chum salmon had relatively low exposure. Uniquely, steelhead exposure was driven by high stream temperatures during incubation. Our framework is broadly applicable, and our findings provide critical input for climate change vulnerability assessments and forward-looking resilience planning for Pacific salmon.

ecology↗

bioRxiv2025

Spectral tuning and signaling of diverse and most red sensitive visual rhodopsins that drive high colour discrimination in Mantis Shrimp eyes

Stomatopod crustaceans (mantis shrimps) possess extraordinary eyes with unmatched visual opsin diversity, but their potential for broad colour detection remains unclear. Here, we report that seventeen opsins, mostly from the midband eye region, are involved in colour sensing and signaling via Gq/Gi-coupling and describe the underlying mechanisms of spectral tuning. Two mid-wavelength opsins preferentially absorb blue light and a majority of long-wavelength opsins absorb in the green range, but three absorb light beyond 600 nm, representing exquisite far-red-sensitive animal opsins. Several blue and red opsins exhibit photoreversibility with opposite spectral shifts explained by retinal binding interactions, revealing unrecognised photochemical flexibility in stomatopod photoreception. Row-specific spectral sensitivity results from combining carotenoid filters with multiple individually-tuned rhodopsins, altogether extending broad vision to the far-red spectrum.

biophysics↗

bioRxiv2025

Regulatory Rewiring Drives Intraspecies Competition in Bacillus subtilis

Intraspecies interactions shapes microbial community structure and evolution, yet the mechanisms determining competitive outcomes among closely related strains remain unclear. The soil bacterium Bacillus subtilis is a model for microbial social interactions, where quorum-sensing systems regulate cooperation and antagonism. Here, we take a multifaceted approach to dissect the role of quorum-sensing regulation in competitive fitness. Isolate NCIB 3610 carries a signal unresponsive RapP-PhrP module that alters quorum-sensing control and promotes faster growth. Modelling and mutant analysis demonstrate that the small differences in growth rate conferred by RapP-PhrP3610 are sufficient to drive competitive exclusion. The importance of quorum sensing control is further exemplified by experimental evolution of distinct wild isolates, which revealed recurrent mutations in the sensor kinase comP, which phenocopy complete comP or comA deletions and confer a growth-linked competitive advantage. Key quorum sensing mechanisms are abandoned even in structured microbial communities, where it might be expected that communal traits are favoured. Furthermore, a phylogenomic survey of 370 B. subtilis genomes identified disruptive comP mutations in [~]16% of isolates. However, growth rate alone does not explain all interaction outcomes as even isogenic strains with equivalent doubling times differ in competitiveness. Transcriptomic profiling and validation experiments implicated a type VII secretion system toxin as an additional effector. These findings reveal that disruption of quorum-sensing pathways, whether naturally or through selection, provides a rapid route to competitive advantage, highlighting a fundamental trade-off between communal signalling and individual fitness in microbial populations. ImportanceMicrobial competition and cooperation are key in shaping the structure and evolution of microbial communities. Our study on Bacillus subtilis, a model for microbial social interactions, reveals how alterations in cell-cell communication can enhance competitive fitness. We show, through a combination of modelling, mutational analysis, and experimental evolution, that certain strains of B. subtilis gain competitive advantage by disrupting their quorum sensing pathways, which leads to faster growth and enhanced competitiveness. Such mutations are prevalent in [~]16% of analysed genomes, underscoring their widespread evolutionary benefit under competitive conditions. Our research highlights the delicate balance between individual success and community cooperation in microbes, providing insights into microbial behaviour and potential applications in modifying microbial ecosystems.

microbiology↗

bioRxiv2025

The highly conserved aphid effector pair Mp1-Mp58 associates to form an effector complex that targets host trafficking protein VPS52

Pathogen and pest effectors play a crucial role in manipulating plant biological processes, facilitating infection and infestation. While pathogens and pests secrete repertoires of effectors into their host plants, most effector function studies focus on characterising individual proteins. We previously identified a genetically linked and co-regulated gene pair in the aphid Myzus persicae encoding effectors Mp1 and Mp58. Here, we explored the functional link between these effectors. We used ectopic expression assays in Nicotiana benthamiana followed by co-immunoprecipitation assays and confocal microscopy to explore effector-effector and effector-target interactions and their subcellular localisation. We produced recombinant proteins to validate effector interactions and used computational modelling to predict effector complex 3D structures. We revealed that effectors Mp1 and Mp58 interact in planta and in vitro and likely form an oligomeric complex. Both effectors associate with the host target Vacuolar Protein Sorting associated Protein 52 (VPS52) to form an Mp1-Mp58-VPS52 complex which localises at vesicle-like structures. Our findings point to effector complex formation in plant-insect interactions and highlight a further layer of complexity in the molecular dialogue between plants and insects. Our work also shows the importance of considering the context in which effectors may function within a larger effector repertoire.

plant biology↗

bioRxiv2022

Systematic microscopical analysis reveals obligate synergy between extracellular matrix components during Bacillus subtilis colony biofilm development

Single-species bacterial colony biofilms often present recurring morphologies that are thought to be of benefit to the population of cells within and known to be dependent on the self-produced extracellular matrix. However, much remains unknown in terms of the developmental process at the single cell level. Here, we design and implement systematic time-lapse imaging and quantitative analyses of the growth of Bacillus subtilis colony biofilms. We follow development from the initial deposition of founding cells through to the formation of large-scale complex structures. Using the model biofilm strain NCIB 3610, we examine the movement dynamics of the growing biomass and compare with those displayed by a suite of otherwise isogenic matrix-mutant strains. Correspondingly, we assess the impact of an incomplete matrix on biofilm morphologies and sessile growth rate. Our results indicate that radial expansion of colony biofilms results from division of bacteria at the biofilm periphery rather than being driven by swelling due to fluid intake. Moreover, we show that lack of exopolysaccharide production has a negative impact on cell division rate, and the extracellular matrix components act synergistically to give the biomass the structural strength to produce aerial protrusions and agar substrate-deforming ability.

microbiology↗

bioRxiv2022

Northward Expansion of Amblyomma americanum (Acari: Ixodidae) into Southern Michigan

Amblyomma americanum (Linnaeus) (Acari: Ixodidae) (lone star tick) is an aggressive, generalist parasite that vectors numerous important human and animal pathogens. In recent decades its geographic range has expanded northwards from endemic regions in the southeastern and southcentral US. In 2019 five questing A. americanum comprising two life stages were detected at one site in Berrien County, in southwestern Michigan, satisfying one CDC criterium for an established population for the first time in the state. To better characterize the northern extent of emerging A. americanum, we conducted active surveillance (i.e., drag sampling) in summer 2020 throughout Michigans southern counties and detected one adult A. americanum from each of six widespread sites, including where they had been detected in 2019. A larger established population was identified at another site in Berrien County, which yielded 691 A. americanum comprising three life stages. Questing tick phenologies at this site were similar to that reported for other regions. Statewide surveillance in 2021 revealed no A. americanum outside of Berrien County, but establishment criteria were met again at the two sites where established populations were first detected respectively in 2019 and 2020. These observations may represent the initial successful invasion of A. americanum into Michigan. Data from passive (1999-2020) and active surveillance (2004-2021) efforts, including a domestic animal sentinel program (2015-2018), are reported to provide context for this nascent invasion. Continued active surveillance is needed to help inform the public, medical professionals, and public health officials of the health risks associated with this vector.

ecology↗

bioRxiv2019

Phenotypic plasticity as an important mechanism of cave colonization and adaptation in Astyanax cavefish

A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus.

evolutionary biology↗

bioRxiv2019

Pulcherrimin formation controls growth arrest of the Bacillus subtilis biofilm

Biofilm formation by Bacillus subtilis is a communal process that culminates in the formation of architecturally complex multicellular communities. Here we reveal that the transition of the biofilm into a non-expanding phase constitutes a distinct step in the process of biofilm development. Using genetic analysis we show that B. subtilis strains lacking the ability to synthesize pulcherriminic acid form biofilms that sustain the expansion phase, thereby linking pulcherriminic acid to growth arrest. However, production of pulcherriminic acid is not sufficient to block expansion of the biofilm. It needs to be secreted into the extracellular environment where it chelates Fe3+ from the growth medium in a non-enzymatic reaction. Utilizing mathematical modelling and a series of experimental methodologies we show that when the level of freely available iron in the environment drops below a critical threshold, expansion of the biofilm stops. Bioinformatics analysis allows us to identify the genes required for pulcherriminic acid synthesis in other Firmicutes but the patchwork presence both within and across closely related species suggests loss of these genes through multiple independent recombination events. The seemingly counterintuitive self-restriction of growth led us to explore if there were any benefits associated pulcherriminic acid production. We identified that pulcherriminic acid producers can prevent invasion from neighbouring communities through the generation of an \"iron free\" zone thereby addressing the paradox of pulcherriminic acid production by B. subtilis.\n\nSignificanceUnderstanding the processes that underpin the mechanism of biofilm formation, dispersal, and inhibition are critical to allow exploitation and to understand how microbes thrive in the environment. Here, we reveal that the formation of an extracellular iron chelate restricts the expansion of a biofilm. The countering benefit to self-restriction of growth is protection of an environmental niche. These findings highlight the complex options and outcomes that bacteria need to balance in order to modulate their local environment to maximise colonisation, and therefore survival.

microbiology↗