Biology subjects

Grady, C.

Publications and source records attributed to Grady, C..

7 recordsLinked to original sources

bioRxiv2025

Defining the Mycobacterium tuberculosis Pangenome and Suggestions for a New Composite Reference Sequence

Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB), a global disease with diverse clinical and microbiological manifestations. Studies into the biological causes of this phenotypic diversity have been largely limited to a few reference strains. A pangenome approach is likely to provide new insights. Pangenomic tuberculosis studies have been limited the availability of only fragmented genome sequences and error-prone reference genomes. We used a de novo assembly pipeline that generates extremely complete and accurate whole genome sequences to generate 50 closed Mtb genomes across all seven major lineages. We identified 3,377 core gene clusters and 379 accessory clusters. Analysis showed multi-copy core clusters were largely due to gene fragmentation (76%), paralogs (12%), nearly identical gene duplications (4%), or combinations (8%). Sixteen hypervariable regions (HVRs) were identified, including novel paralogs and variable PE/PPE genes. We consolidated these findings into a Pangenome Gene Reference Resource (PGRR) for precision alignment. Our study demonstrates the closed nature of the Mtb pangenome, with most variation in accessory genes and HVRs. The PGRR provides a foundation for improved drug/vaccine target discovery and highlights the need to move beyond the commonly used H37Rv strain to study Mtb genetic and phenotypic diversity. IMPORTANCETuberculosis (TB), caused by Mycobacterium tuberculosis, affects millions globally. Genetic differences among Mtb strains have been difficult to resolve due to incomplete genome references. We sequenced and analyzed complete genomes of 50 Mtb strains from all lineages, identifying 16 hypervariable regions and 3,498 core gene clusters whose diversity mostly stemmed from gene fragmentation, paralog duplication and deletion events and differences in the PE/PPE gene family representation. These differences may explain many of the varied clinical manifestations of TB. We created Pangenome Gene Reference Resource to unify genetic data for precise comparison studies to aid in developing new drugs vaccines and other interventions against this disease.

microbiology↗

bioRxiv2025

ALE Meta-Analysis Reveals Neural Substrates for the Impact of Prematurity on Executive Functioning in Children and Adults

Premature birth has known impacts on brain development, leading to sustained differences in cognitive function throughout the lifespan. Despite known deficits in executive functioning (EF) within individuals born premature, the extent to which neural engagement during executive functioning tasks differs between those born preterm and full-term is not fully understood. Additionally, it is unknown whether regions of differential engagement are the same in children and adults. This meta-analysis synthesizes fMRI results of activation differences between preterm and full-term subjects during executive functioning tasks in adult and child groups separately. Our results indicate that differences in neural engagement during EF tasks differ between pre-term (PT) and full term (FT) individuals in both age groups. Moreover, the regions affected contribute to well-known brain networks, including the fronto-striatal circuitry, the default mode network (DMN), and the salience network, all of which subserve broad EF capabilities. We found no differences between child and adult maps in a direct contrast, suggesting that effects of prematurity on executive functioning may persist from childhood into adulthood, although these findings should be interpreted in context of methodological limitations and potential confounding factors. This meta-analysis provides greater insight into the neural mechanisms behind EF disruption following premature birth. HighlightsO_LIDifferences in neural activation during executive function tasks exist in both children and adults with a history of premature birth. C_LIO_LIPT children show hyperactivity in fronto-striatal regions while PT adults show differential engagement of default mode network regions. C_LI

neuroscience↗

bioRxiv2022

Development of amidase-dependent pyrazinoic acid prodrugs with activity against pyrazinamide resistant Mycobacterium tuberculosis

Rapid emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is one of the most significant healthcare challenges of our time. The cause of drug resistance is multifactorial, with the long course anti-tubercular therapy required to treat tuberculosis (TB) constituting a major contributing factor. Introduction of pyrazinamide (PZA) resulted in shortening of TB treatment from twelve to six months and consequently played a critical role in curbing drug resistance that developed over long course therapy. Nevertheless, because PZA is a prodrug activated by a nonessential amidase, PncA, resistance to PZA develops and frequently results in treatment failure. Here, we leveraged a whole cell drug screening approach to identify anti-tuberculars with unconventional mechanisms of action or activation that could be further developed into compounds effective at killing Mtb resistant to PZA. We discovered an amide containing prodrug, DG160, that was activated by the amidase, Rv2888c (AmiC). This amidase was capable of metabolizing a variety of amide containing compounds including a novel pyrazinoic acid-isoquinolin-1-amine prodrug, JSF-4302, which we developed as a potential PncA-independent replacement for PZA. As predicted, AmiC activation of JSF-4302 led to the generation of POA in Mtb including in a PZA resistant clinical isolate, thereby successfully delivering the active component of PZA while bypassing the need for activation by PncA. This work provides a framework for a new approach to drug development and prodrug activation in Mtb. SIGNIFICANCEPyrazinamide (PZA) is a vital component of Mycobacterium tuberculosis (Mtb) treatment since its inclusion shortened tuberculosis therapy by six months. However, PZA is a prodrug and resistance develops at a high frequency due to mutations in its activator PncA. Here, we present the discovery of amide-containing anti-tubercular prodrugs that are activated intracellularly by the Mtb amidase, AmiC. Taking advantage of this finding, we successfully designed and synthesized pyrazinoic acid (POA) prodrugs that were activated by AmiC and found that these compounds delivered intracellular POA to PZA- resistant Mtb isolates that contained a nonfunctional PncA. This new approach to prodrug development provides a method for delivering conjugated drugs into Mtb with the potential to overcome clinical drug resistance.

microbiology↗

bioRxiv2020

Disulfiram inhibits M. tuberculosis growth by altering methionine pool, redox status and host-immune response

Methionine biosynthetic pathway, essential for the growth of Mycobacterium tuberculosis (Mtb) in the host, represents an attractive target for the development of novel anti-tuberculars. Here, we have biochemically characterized homoserine acetyl transferase (HSAT viz. MetA) of Mtb, which catalyses the first committed step of methionine and S-adenosylmethionine (SAM) biosynthesis. High-throughput screening of a 2300 compound library resulted in identification of thiram, an anti-fungal organosulfur compound, as the most potent MetA inhibitor. Further analysis of thiram analogs led to the identification of orally bioavailable disulfiram (DIS, an anti-alcoholism FDA approved drug) as a novel inhibitor of MetA. Both thiram and DIS restricted the growth of drug-sensitive and drug-resistant Mtb strains in a bactericidal manner. ThermoFlour assay demonstrated direct binding of DIS with MetA. Metabolomic and transcriptomic studies showed DIS mediated perturbation of methionine and redox homeostasis, respectively, in Mtb. In concordance, the effect of DIS on Mtb growth was partially rescued by supplementation with either L-methionine as well as N-acetyl cysteine, suggesting a multi-target killing mechanism. In Mtb-infected mice, DIS administration restricted bacterial growth, increased efficacy of isoniazid, ameliorated lung pathology, modulated lung immune cell landscape and protective immune response. Taken together, our results demonstrate that DIS can be repurposed for designing an effective anti-tubercular therapy.

microbiology↗

bioRxiv2019

Recollection and prior knowledge recruit the left angular gyrus during recognition

The human angular gyrus (AG) is implicated in recollection, or our ability to retrieve detailed memory content from a specific study episode. Parallel work also highlights a key role of the AG in the representation of general knowledge and semantics. How these two lines of research converge remains unclear. The present fMRI experiment used a remember-know paradigm with famous and non-famous faces to test whether activity in the AG could be modulated by both task-specific recollection and general prior knowledge in the same participants. Increased BOLD activity in the left AG was observed during both recollection in the absence of prior knowledge (i.e., recollected > non-recollected or correctly rejected non-famous faces) and when prior knowledge was accessed in the absence of recollection (i.e., famous > non-famous correct rejections). This pattern was unique to the left AG, and was not present in any other regions of the lateral inferior parietal lobe. Furthermore, the response profile of the left AG was consistent with accounts of recollection strength. Recollection-related activity was greater for faces with longer exposures at encoding than those with shorter exposures and was greater for stimuli with prior knowledge than those without, despite prior knowledge being incidental to the recognition decision. Therefore, the left AG is recruited during the access of both task-specific recollection and general prior knowledge, with greater activity as the amount of retrieved information increases, irrespective of its episodic or semantic nature. Significance StatementThe human angular gyrus (AG) is often implicated in our ability to remember past events. A separate line of research examining our ability to represent general knowledge has also highlighted the AG as a core region of interest. To reconcile these separate views of AG function, we used fMRI to test whether the human left AG was sensitive to remembering details from a specific study episode (i.e., recollection) or more general prior knowledge, within the same participants. Overall, activity in the left AG was sensitive to both recollection and prior knowledge, suggesting any complete functional account of the left AG during retrieval must consider its sensitivity to both kinds of mnemonic representations.

neuroscience↗

bioRxiv2017

Differential spatiotemporal representations along the hippocampal long axis in humans

Increased place field size and signal autocorrelation along the dorsoventral hippocampal axis in rodents are considered a fundamental aspect of hippocampal organization, yet such evidence is lacking in humans. Using fMRI, we report corresponding evidence of increasing neural similarity from posterior to anterior hippocampus (dorsoventral homologues) in humans. These findings help account for observed shifting in representational granularity, from global context (anterior) to local details (posterior), along the hippocampal axis.

neuroscience↗

bioRxiv2017

Long-term consolidation switches goal proximity coding from hippocampus to retrosplenial cortex

Recent research indicates the hippocampus may code the distance to the goal during navigation of newly learned environments. It is unclear however, whether this also pertains to highly familiar environments where extensive systems-level consolidation is thought to have transformed mnemonic representations. Here we recorded fMRI while University College London and Imperial College London students navigated virtual simulations of their own familiar campus (> 2 years of exposure) and the other campus learned days before scanning. Posterior hippocampal activity tracked the proximity to the goal in the newly learned campus, but not in the familiar campus. By contrast retrosplenial cortex tracked the distance to the goal in the familiar campus, but not in the recently learned campus. These responses were abolished when participants were guided to their goal by external cues. These results open new avenues of research on navigation and consolidation of spatial information and help advance models of how neural circuits support navigation in novel and highly familiar environments.\n\nSignificance StatementHistorically, research on the hippocampal formation has focused on its role in long-term memory and navigation - often in isolation. No study to date has directly compared realistic navigation within familiar with recently learned environments, nor has it been explored how the neural substrates, along with computational codes, may change. In this study, we show for the first time, a shift from hippocampal to cortical coding of distance to a goal during active navigation. This study bridges the gap between memory consolidation and navigation, and paves the way for more functional and realistic understanding of the hippocampus.

neuroscience↗