Biology subjects

Braithwaite, J.

Publications and source records attributed to Braithwaite, J..

4 recordsLinked to original sources

bioRxiv2026

Cas1 epistasis tunes conformational coupling to enhance CRISPR adaptation

CRISPR adaptation requires Cas1-Cas2 to capture prespacers, undergo conformational rearrangement and catalyse integration, but how these steps are coupled remains unclear. Using nine hyperactive Escherichia coli Cas1 substitutions as perturbational probes, we identified a prespacer-coupling module intersecting an interior conformational-coupling module. Single substitutions increased adaptation up to sixfold, whereas combinatorial reassortment generated a genotype with 103-fold greater activity than wild type. Genotype-network analysis and quantitative reconstruction revealed strong background-dependent epistasis: the same substitution could enhance activity in one genotype but impair it in another, and high activity emerged only from compatible combinations spanning both modules. These findings indicate that Cas1-Cas2 activity is constrained by compatibility among changes distributed across the Cas1 dimer, rather than by optimization of individual catalytic or DNA-binding interactions. We propose that coordinated tuning of prespacer engagement and conformational coupling governs Cas1-Cas2 activity during CRISPR adaptation.

biochemistry↗

bioRxiv2026

RecA status determines SOS- and RecBCD-dependent outcomes in CRISPR-Cas adaptation

CRISPR-Cas immunity depends on integrating DNA fragments from invading elements, yet how this process is tuned by host physiology remains poorly understood. Here, we investigate the relationship between CRISPR adaptation and the bacterial SOS DNA damage response in Escherichia coli using a highly sensitive colony-based adaptation assay. Blocking SOS with a lexA3 allele suppresses adaptation, while paradoxically, deleting recA enhances it. These findings indicate that RecA contributes positively to adaptation indirectly, through LexA cleavage and induction of SOS-regulated functions, while complete loss of RecA is associated with a RecBCD-dependent DNA-processing state that favours successful adaptation. The RecA inhibitors RecX and PsiB did not phenocopy {triangleup}recA, indicating that inhibitor-mediated perturbation of RecA in RecA-proficient cells and complete loss of RecA have different consequences for adaptation. Genome-wide maps of recovered spacers show that RecA and LexA reshape the relative distribution of chromosomal and plasmid-derived spacers, linking CRISPR adaptation to replication and DNA repair dynamics. Although Cas1-Cas2 catalyses spacer integration autonomously in vitro, our findings suggest that successful adaptation in vivo emerges from interactions between spacer acquisition, DNA repair, and bacterial stress physiology, embedding CRISPR adaptation within cellular networks that balance immune protection with the risk of autoimmunity.

microbiology↗

bioRxiv2021

An Experimental Test of the Effects of Redacting Grant Applicant Identifiers on Peer Review Outcomes

Blinding reviewers to applicant identity has been proposed to reduce bias in peer review. This experimental test used 1200 NIH grant applications, 400 from Black investigators, 400 matched applications from White investigators, and 400 randomly selected applications from White investigators. Applications were reviewed by mail in standard and redacted formats. Redaction reduced, but did not eliminate, reviewers ability to correctly guess features of identity. The primary, pre-registered analysis hypothesized a differential effect of redaction according to investigator race in the matched applications. A set of secondary analyses (not pre-registered) used the randomly selected applications from White scientists and tested the same interaction. Both analyses revealed similar effects: Standard format applications from White investigators scored better than those from Black investigators; redaction reduced the size of the difference by about half (e.g. from a Cohens d of 0.20 to 0.10 in matched applications); redaction caused applications from White scientists to score worse but had no effect on scores for Black applications. The primary statistical test of the study hypothesis was not significant; the secondary analysis was significant. The findings support further evaluation of peer review models that diminish the influence of applicant identity.

scientific communication and education↗

bioRxiv2019

Differences in Early and Late Pattern-Onset Visual-Evoked Potentials between Self-Reported Migraineurs and Controls

Striped patterns have been shown to induce strong visual illusions and discomforts to migraineurs in the literature. Previous research has suggested that those unusual visual symptoms be linked with the hyperactivity on the visual cortex of migraine sufferers. The present study searched for evidence supporting this hypothesis by comparing the visual evoked potentials (VEPs) elicited by striped patterns of specific spatial frequencies (0.5, 3, and 13 cycles) between a group of 29 migraineurs (17 with aura/12 without) and 31 non-migraineurs. In addition, VEPs to the same stripped patterns were compared between non-migraineurs who were classified as hyperexcitable versus non-hyperexcitable using a previously established behavioural pattern glare task. We found that the migraineurs had a significantly increased N2 amplitude for stimuli with 13 cpd gratings but an attenuated late negativity (LN: 400 - 500 ms after the stimuli onset) for all the spatial frequencies. Interestingly, non-migraineurs who scored as hyperexcitable appeared to have similar response patterns. We proposed that the enhanced N2 could reflect disruption of the balance between parvocellular and magnocellular pathway, which is in support of a grating-induced cortical hyperexcitation mechanism on migraineurs. On the other hand, the attenuation of the late negativity could reflect a top-down feedback mechanism to suppress visual processing of an aversive stimulus.

neuroscience↗