Biology subjects

Brennan, A.

Publications and source records attributed to Brennan, A..

8 recordsLinked to original sources

bioRxiv2026

Intracellular Bismuth Coordination of Peptides and Miniproteins

Cyclisation of peptides has emerged as a powerful methodology to enhance molecular stability and functional efficacy. Bismuth(III) coordination represents a particularly compact and chemoselective cyclisation modality, yet to date has remained confined to in vitro or phage-based systems. Here we report the first example of bismuth-mediated peptide and minprotein cyclisation occurring within living cells, achieved directly during recombinant expression in E. coli. Supplementation of growth media with bismuth salts enables efficient intracellular coordination of either three or six cysteine residues, yielding bicyclic and tetracyclic architectures with minimal cellular toxicity. Bis-bismuth coordination generated a tetra-cyclic minprotein with exceptional thermal and serum stability, representing a level of intracellular structural reinforcement not previously accessible. This chemistry enables the intracellular constraint of peptides and proteins and is directly compatible with genetically encoded peptide and miniprotein libraries, establishing bismuth coordination as a compact and robust modality for live-cell molecular screening.

synthetic biology↗

bioRxiv2025

Evaluating transboundary connectivity to support cross-border conservation between Canada and the United States

Landscape connectivity is considered critical for maintaining biodiversity. Many jurisdictions have identified the importance of considering connectivity in land use plans, and connectivity has recently been included as a metric in international conservation agreements. Consequently, there is a need for measures of connectivity that can be applied at national and international scales; however, evaluating connectivity across international boundaries remains a challenge due to inconsistencies in mapping data, and differences in sociopolitical systems. Canada and the United States of America (USA) share a long international border, and thus, there is a need and opportunity to develop transboundary connectivity plans for this international region. We extended a previously published pan-Canadian multi-species connectivity model into the USA to produce a seamless and high-resolution omnidirectional connectivity map for the two countries. We identify several significant animal movement corridors across the transboundary region and show that about 20% of connectivity hotspots in the region are covered by protected areas. We also demonstrate the potential of the map for identifying important areas for wildlife movement and the spread of zoonotic diseases. Our map will be useful for supporting transboundary connectivity conservation between Canada and the USA and our modelling approach can easily be applied to other countries to support their own connectivity initiatives.

ecology↗

bioRxiv2025

Enhancing the efficacy, utility and throughput of the Transcription Block Survival peptide library screening platform

Genetically encoded peptide library screening is a powerful strategy for discovering inhibitors of protein-protein and protein-DNA interactions. The Transcription Block Survival (TBS) assay enables the in vivo selection of peptides that antagonise transcription factor (TF) binding by linking inhibition of DNA-binding to E.coli survival. However, previous TBS implementations required laborious re-engineering of the mDHFR coding region for each new target, limiting utility. Here, we present an enhanced and streamlined TBS platform that increases throughput, simplifies target switching and improves selection stringency. By relocating TF-DNA binding sites from within the mDHFR coding sequence into the mDHFR 5-promoter/untranslated region, we preserve mDHFR folding and function, enabling rapid interchange of TF targets without the need for extensive construct redesign. We validated this system using three distinct TF targets, CREB1, ATF2 and DLX5, and two distinct consensus sites, demonstrating robust transcriptional block upon TF binding and efficient growth rescue upon peptide-mediated antagonism. Importantly, we expand the platform to accommodate full-length TFs, as exemplified by DLX5, allowing selection against biologically relevant multi-domain proteins. TBS continues to function exclusively by selecting for disruption of protein-DNA binding, ensuring mechanistic precision. Using this optimised TBS system, we successfully screened an 11.3-million-member peptide library to identify a potent antagonist of ATF2-CRE DNA binding within three months. This next generation TBS-platform dramatically improves screening efficiency and selection pressure while maintaining high biological relevance, providing a versatile and scalable tool for discovering functional peptide inhibitors of protein-DNA interactions with therapeutic potential.

synthetic biology↗

bioRxiv2024

Spatiotemporal dynamics of non-ecological speciation in rubyspot damselflies (Hetaerina spp.)

Non-ecological speciation is a common mode of speciation which occurs when allopatric lineages diverge in the absence of pronounced ecological differences. Yet, relative to other speciation mechanisms, non-ecological speciation remains understudied. Numerous damselfly clades are characterized as non-adaptive radiations (the result of several rounds of non-ecological speciation), but there are few damselfly lineages for which we have a detailed understanding of the spatiotemporal dynamics of divergence. Recent phylogeographic analyses demonstrate that American rubyspot damselflies (Hetaerina americana sensu lato) actually comprise at least two cryptic lineages that coexist sympatrically across most of Mexico. To broaden our understanding of the dynamics of diversification to other rubyspot lineages, we investigated the phylogeographic history of smoky rubyspot damselflies (Hetaerina titia) using genomic data collected across Central and North America. Unexpectedly, we found evidence of reproductive isolation between the highly genetically differentiated Pacific and Atlantic lineages of H. titia in a narrow secondary contact zone on the Isthmus of Tehuantepec, Mexico. We then fit models of historical demography to both H. americana sensu lato and H. titia to place these comparisons in a temporal context. Our findings indicate that Pacific and Atlantic lineages of H. titia split more recently than the broadly sympatric lineages within H. americana sensu lato, supporting key assumptions of the non-ecological speciation model and demonstrating that these two pairs of sister lineages are at different stages of the speciation cycle.

evolutionary biology↗

bioRxiv2022

Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Supergenes govern balanced polymorphisms in a wide range of systems. The reciprocal placement of stigmas and anthers in pin and thrum floral morphs of distylous species constitutes an iconic example of a balanced polymorphism governed by a supergene, the distyly S-locus. Recent studies have shown that the Primula and Turnera distyly supergenes are both hemizygous in thrums, but it remains unknown if hemizygosity is pervasive among distyly S-loci. Here we have characterized the genetic architecture and evolution of the distyly supergene in Linum by generating a chromosome-level genome assembly of Linum tenue, followed by the identification of the S-locus using population genomic data. We show that hemizygosity and thrum-specific expression of S-linked genes, including a pistil-expressed candidate gene for style length, are major features of the Linum S-locus. Structural variation is likely instrumental for recombination suppression, and although the non-recombining dominant haplotype has accumulated transposable elements, S-linked genes are not under relaxed purifying selection. Our findings reveal remarkable convergence in the genetic architecture and evolution of independently derived distyly supergenes. The chromosome-level genome assembly and detailed characterization of the distyly S-locus in L. tenue will facilitate elucidation of molecular mechanisms underlying the different forms of flowers described by Darwin.

evolutionary biology↗

bioRxiv2021

Areas Important for Ecological Connectivity Throughout Canada

Governments around the world have acknowledged the importance of conserving ecological connectivity to help reverse the decline of biodiversity. In this study we employed recent methodological developments in circuit theory to conduct the first pan-Canadian analysis of multi-species connectivity for all terrestrial regions of the country, at a spatial grain sufficient to support local land-management decisions. We developed a movement cost surface with a limited number of thematic categories using the most recently updated land cover data available for the country. We divided the country into 17 tiles and used a wall-to-wall, omnidirectional mode of Circuitscape on each tile in order to assess ecological connectivity throughout entire landscapes as opposed to strictly among protected areas. The resulting raw current density map of Canada revealed heterogenous patterns of current density across the country, strongly influenced by geography, natural barriers, and human development. We included a validation analysis of the output current density map with independent wildlife data from across the country and found that mammal and herpetofauna locations were predicted by areas of high current density. We believe our current density map can be used to identify areas important for connectivity throughout Canada and thereby contribute to efforts to conserve biodiversity.

ecology↗

bioRxiv2021

Functional Connectivity of the World's Protected Areas

Rapid environmental change threatens to isolate the worlds wildlife populations and intensify biodiversity loss. Global policies have called for expanding and connecting the worlds protected areas (PAs) to curtail the crisis, yet how well PA networks currently support wildlife movement, and where connectivity conservation or restoration is most critical, have never been mapped globally. Here, we map the functional connectivity (how animals move through landscapes) of the worlds terrestrial PAs for the first time. Also, going beyond existing global connectivity indices, we quantify national PA-connectedness using an approach that meaningfully represents animal movement through anthropogenic landscapes. We find that reducing the human footprint may improve national PA-connectivity more than adding new PAs; however, both strategies are critical for improving and preserving connectivity in places where the predicted flow of animal movement is highly concentrated. We show that the majority of critical connectivity areas (CCAs) (defined as globally important areas of concentrated animal movements) remain unprotected. Of these, 72% overlap with previously-identified global conservation priority areas, while 3% of CCAs occur within moderate to heavily modified lands. Conservation and restoration of CCAs could safeguard connectivity of the worlds PAs, and dovetail with previously identified global conservation priorities.

ecology↗

bioRxiv2018

Building a National HIV Cohort from Routine Laboratory Data: Probabilistic Record-Linkage with Graphs

BackgroundChronic disease management requires the ability to link patient records across multiple interactions with the health sector. South Africas National Health Laboratory Service (NHLS) conducts all routine laboratory monitoring for the countrys national public sector HIV program. However, the absence of a validated patient identifier has limited the potential of the NHLS database for epidemiological research, policy evaluation, and longitudinal patient care. We developed and validated a record linkage algorithm, creating a unique patient identifier and enabling analysis of the NHLS database as a national HIV cohort. To our knowledge, this is the first national HIV cohort in any low-or middle-income country.\n\nMethods.We linked data on all CD4 counts, HIV viral loads (VL), and ART workup laboratory tests from 2004-2016. Each NHLS laboratory test result is associated with a name, sex, date of birth (DOB), gender, and facility. However, due to typographical and other errors and patient mobility between facilities, different patient specimens may be associated with different sets of identifying information. We developed a graph-based probabilistic record linkage algorithm and used it to construct a unique identifier for all patients with laboratory results in the national HIV program. We used standard probabilistic linkage methods with Jaro-Winkler string comparisons and weights informed by response frequency. We also used graph concepts to guide the linkage in determining whether a cluster of patient specimens could plausibly reflect a single patient. This approach allows matching thresholds to vary with the density of the network and limits over-matching.\n\nTo train and validate our approach, we constructed a quasi-gold standard based on manual review of 59,000 candidate matches associated with 1000 randomly sampled specimens. These data were divided into training and validation sets. Domain weights and graph parameters were optimized using the manually matched training data.\n\nTo evaluate performance, we calculated the probability that a true match was correctly identified by our algorithm (sensitivity, Sen) and the probability that a match identified by our algorithm was truly a match (positive predictive value, PPV) in the manually-matched data. We also assessed validity in the full cohort using proxies for under-and over-matching and assessed sensitivity vis-a-vis national identification numbers and patient folder numbers, which were available for a sub-set of records. We compared the performance of our algorithm for exact matching and a prior identifier that had been developed by the NHLS Corporate Data Warehouse.\n\nResults.As of December 2016, the NHLS database contained 117 million patient specimens with a CD4, VL, or other laboratory test used in HIV care. These specimens had 63 million unique combinations of patient identifying information. From these data, our matching algorithm identified 11.6 million unique HIV patients who had at least one CD4 count or VL result. These patients 70.9 million total specimens, with a median of 3 specimens per patient (IQR 1 to 8). Sensitivity and PPV of the algorithm were estimated to be 93.7% and 98.6% in manually-matched data, compared to 64.1% and 100.0% for the existing NHLS identifier. We estimated that in 2016 there were 3.35 million patients on ART and virologically monitored, similar to the National Department of Health estimate of 3.50 million.\n\nConclusion.We constructed a South African National HIV Cohort by applying novel graph-based probabilistic record linkage techniques to routinely collected laboratory data, with high sensitivity and positive predictive value. Information on graph structure can guide record linkage in large populations when identifying data are limited.

epidemiology↗