Biology subjects

Horton, J.

Publications and source records attributed to Horton, J..

8 recordsLinked to original sources

bioRxiv2026

The modular evolution of chitinases is governed by coevolution of auxiliary and catalytic domains

The modular architecture of multi-domain enzymes is a key source of functional diversity. GH18 chitinases exemplify this, possessing a variety of auxiliary domains that have been postulated to underpin their role as essential global nutrient cyclers. However, there is no evolutionary framework that accounts for vast the assortment of domain compositions observed across the protein family. Here, we map the sequence space of nearly 40,000 bacterial chitinases, integrating phylogenetics with a quantitative analysis of domain promiscuity to decode their evolutionary history. We reveal that diversification follows distinct trajectories: enzymes necessary for environmental chitin scavenging evolve via high modular plasticity and structural elaboration of the catalytic core, whereas sequences required for specialized, essential developmental roles fix their domain architecture to fulfill lineage-specific physiological roles. By resolving how domain accretion co-evolves with catalytic scaffolds, this work provides a framework for understanding how multi-domain enzymes adapt to complex environments.

evolutionary biology↗

bioRxiv2025

3D osteocyte networks under Pulsatile Unidirectional Fluid Flow Stimuli (PUFFS)

Although osteocytes are known to play a key role in skeletal mechano-adaptation, few in vitro models have investigated how pulsatile mechanical stimuli influence the properties of 3D osteocyte networks. Here we design and develop a microfluidic based in vitro model to study 3D osteocyte networks cultured under Pulsatile Unidirectional Fluid Flow Stimuli (PUFFS). Digital light projection stereolithography was used to design and fabricate a three-chambered PDMS microfluidic chip. Model osteocytes (murine MLO-Y4) were encapsulated in collagen matrix within the chip to form self-assembled three-dimensional (3D) cell networks. Daily stimulus in the form of PUFFS was then applied for upto 21 days. A combination of experiments, computational simulation and analytical modeling was used to characterize the mechanical environment experienced by embedded cells during PUFFS. Viability, morphology, cell-connectivity, expression of key proteins, and gene expression, and real-time calcium signaling within 3D osteocyte networks were characterized at select time-points and compared to static conditions. Results show that PUFFS stimulation at 0.33 and 1.66 Hz can initiate mechanotransduction via calcium signals that are propagated across the network of collagen encapsulated osteocytes via Cx43 junctions. Furthermore, osteocytes cultured in these devices maintain expression of several key osteocyte genes for up to 21d. Taken together, this model can potentially serve as a testbed to study how 3D osteocyte networks respond to dynamic mechanical stimulation relevant to skeletal tissues.

bioengineering↗

bioRxiv2025

Comparative susceptibility of Old World and New World bat cell lines to Zika virus: Insights into viral replication and inflammatory responses

BackgroundFrom the first isolation of Zika virus (ZIKV) in Uganda in 1947, ZIKV had primarily been associated with sporadic human cases in Africa and Asia until ZIKV emerged as an epidemic in the Americas in 2015. As ZIKV spread into new geographic regions, it now has the potential to interact with many novel potential host species whose susceptibility to the virus has yet to be determined. Bats, with their ability to fly and live in or near human structures, are plausible ZIKV reservoirs. However, their competence as hosts for ZIKV remains unresolved. In this study, we investigate the immune response of Old World and New World bats to ZIKV infection in vitro. ResultsWe demonstrate that Egyptian Rousette bat (Rousettus aegyptiacus; Old World) cells are susceptible to ZIKV, while we observed little to no ZIKV replication in Jamaican fruit bat (Artibeus jamaicensis) cells. Notably, both the Asian and African ZIKV lineages elicited a strong proinflammatory response in the R. aegyptiacus cell line including upregulation of IL6, CXCL8, and CCL5. These data contrast with the dampened inflammatory response detected in these bats to other viruses. ConclusionsThe findings reveal that R06E cells derived from Egyptian Rousette bats exhibit robust proinflammatory and antiviral responses upon Zika virus (ZIKV) infection, characterized by significant upregulation of proinflammatory cytokines. This suggests that while these cells support productive ZIKV replication, they also mount a strong immune response, challenging the notion of these bats as immune-tolerant reservoirs and indicating a more complex interaction with the virus.

microbiology↗

bioRxiv2023

DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite, Plasmodium falciparum

Development of the human malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is still largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized PfAP2-G and PfAP2-EXP which bind unique DNA motifs (GTAC and TGCATGCA). We interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We determined that DNA sequence context minimally impacts binding site selection for CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization contribute to differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we find that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions in vivo due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms. Key PointsO_LISequence and chromatin context determine differential DNA-binding specificity of P. falciparum TFs C_LIO_LITFs with paralogous DNA-binding domains in P. falciparum are not functionally redundant C_LIO_LITFs with differing sequence-specificity can co-occupy sites through low-affinity DNA interactions C_LI

genomics↗

bioRxiv2021

The chemical synthesis of knob domain antibody fragments

Cysteine-rich knob domains found in the ultralong complementarity determining regions of a subset of bovine antibodies, are capable of functioning autonomously as 3-6 kDa peptides. While they can be expressed recombinantly in cellular systems, in this paper we show that knob domains are also readily amenable to chemical synthesis, with a co-crystal structure of a chemically synthesised knob domain in complex with antigen showing structural equivalence to the biological product. For drug discovery, following immunisation of cattle, knob domain peptides can be synthesised directly from antibody sequence data, combining the power and diversity of the bovine immune repertoire with the ability to rapidly incorporate non-biological modifications. We demonstrate that, through rational design with non-natural amino acids, paratope diversity can be massively expanded, in this case improving the efficacy of an allosteric peptide. As a potential route to further improve stability, we also performed head-to-tail cyclisation, exploiting the unusual proximity of the N- and C-termini to synthesise functional, fully cyclic antibody fragments. Lastly, we highlight the stability of knob domains in plasma and, through pharmacokinetic studies, use palmitoylation as a route to extend the plasma half-life of knob domains in vivo. This study presents an antibody-derived medicinal chemistry platform, with protocols for solid-phase synthesis of knob domains; together with characterisation of their molecular structures, in vitro pharmacology and pharmacokinetics.

biochemistry↗

bioRxiv2019

Cohort Profile: HealthWise Wales. A research register and data collection and analysis platform with linkage to NHS datasets in Wales

PurposeRecruitment and follow-up in epidemiological studies is challenging, time-consuming and expensive. Combining online data collection with a register of individuals who agree to be contacted with information on research opportunities provides an efficient, cost-effective platform for population-based research. HealthWise Wales (HWW) aims to support researchers by recruiting a cohort of \"research-ready\" individuals; advertising relevant studies to these participants; providing access to cohort data for secondary analyses; and supporting data collection on specific topics that can be linked with healthcare data.\n\nParticipantsAdults (aged 16 and above) living or receiving their healthcare in Wales are eligible for inclusion. Participants consent to be followed-up every 6 months; for their details to be used to access their routinely-collected NHS records for research purposes; to be contacted about research projects in which they could participate; and to be informed about involvement or engagement opportunities. Data are collected using a web-based application, with new questionnaires added every six months. Data collection on socio-demographic and lifestyle factors is repeated at two-to-three year intervals. Recruitment is ongoing, with 21,779 active participants (alive and currently registered).\n\nFindings to date99% of participants have complete information on age and sex, and 64% have completed questionnaires on socio-demographic and lifestyle factors. These data can be linked with national health databases within the Secure Anonymised Information Linkage (SAIL) databank, with 93% of participants matching a record in SAIL. HWW has facilitated recruitment of 43,826 participants to 15 different studies.\n\nFuture plansThe medium-term goal for the project is to enrol at least 50,000 adults. Recruitment strategies are being devised to achieve a study sample that closely models the population of Wales, with sufficient numbers in socio-demographic subgroups to allow for the selection of populations for research from those groups. Potential bio-sampling methods are also currently being explored.

epidemiology↗

bioRxiv2018

DNA sequence context controls the binding and processivity of T7 DNA primase

Primases are key enzymes involved in DNA replication. They act on single-stranded DNA, and catalyze the synthesis of short RNA primers used by DNA polymerases. Here, we investigate the DNA-binding and activity of the bacteriophage T7 primase using a new workflow called High-Throughput Primase Profiling (HTPP). Using a unique combination of high-throughput binding assays and biochemical analyses, HTPP reveals a complex landscape of binding specificity and functional activity for the T7 primase, determined by sequences flanking the primase recognition site. We identified specific features, such as G/T-rich flanks, which increase primase-DNA binding up to 10-fold and, surprisingly, also increase the length of newly formed RNA (up to 3-fold). To our knowledge, variability in primer length has not been reported for this primase. We expect that applying HTPP to additional enzymes will reveal new insights into the effects of DNA sequence composition on the DNA recognition and functional activity of primases.

biophysics↗

bioRxiv2017

Intrinsic specificity differences between transcription factor paralogs partly explain their differential in vivo binding

Members of transcription factor (TF) families, i.e. paralogous TFs, are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions in the cell. Differential genomic targeting by paralogous TFs is generally assumed to be due to interactions with protein cofactors or the chromatin environment. Contrary to previous assumptions, we find that paralogous TFs have different intrinsic preferences for DNA, not captured by current motif models, and these differences partly explain differential genomic binding and functional specificity. Our finding was possible due to a unique combination of carefully designed high-throughput assays and rigorous computation modeling, integrated into a unified framework called iMADS. We used iMADS to quantify, model, and analyze specificity differences between 11 paralogous TFs from 4 distinct human TF families. Our finding of differential specificity between closely related TFs has important implications for the interpretation of the regulatory effects of non-coding genetic variants.

genomics↗