Biology subjects

Connor, C.

Publications and source records attributed to Connor, C..

9 recordsLinked to original sources

bioRxiv2026

Neuronal Dynamics During Isoflurane Induction in Caenorhabditis elegans

BackgroundHow does neuronal activity change as an animal transitions from being awake to a state of general anesthesia? Previous studies used C. elegans to investigate awake and anesthetized states, emergence from anesthesia, and to establish metrics characterizing how system-wide neuronal dynamics differ under these conditions. This study employs a new technique to image pan-neuronal activity in C. elegans continuously during induction of anesthesia with isoflurane. MethodsC. elegans worms expressing pan-neuronal nuclear RFP and cytosolic GCaMP6s were imaged with light sheet microscopy to measure single cell activity in the majority of neurons in the animals head during induction via isoflurane exposure. Stable concentrations of isoflurane were maintained throughout the experiment by measured flow vaporization of isoflurane into a specially designed gas enclosure compatible with the imaging system. Building on our previous work investigating emergence from anesthesia, we analyzed ensemble neuronal activity, spectrograms of frequency over time, and metrics of information flow between neurons. ResultsInduction of isoflurane anesthesia caused a progressive reduction in neuronal activity over the course of 40 minutes. Spectrograms indicated a loss of bulk signal power across all frequencies, notably in low frequencies too. State Decoupling and Internal Predictability were among the most useful metrics for discriminating the anesthetized state, demonstrating induction kinetics that are the inverse of emergence. However, each animal does not arrive at the anesthetized state at the same time; response times are highly individualized. ConclusionsInformation metrics of neurodynamic activity demonstrate that isoflurane induction results in a gradual increase in neuronal disconnection and disorganization. Thus, at the level of individual neuron connectivity and system dynamics, the induction of anesthesia in C. elegans nematodes is in essence the reverse of emergence. Induction however occurs more rapidly and shows marked variability between individuals. Future genetic studies will show which molecular targets define sensitivity to volatile anesthetics like isoflurane. Summary StatementIsoflurane-induced unconsciousness is a common phenomenon across species. Does the induction of anesthesia arise by distinct state transitions, or through gradual changes in system dynamics when activity is measured at the level of individual neurons?

neuroscience↗

bioRxiv2024

The RND efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection.

Tripartite resistance-nodulation-division (RND) efflux pumps confer multidrug resistance (MDR) in Gram-negative bacteria and are critical for many physiological functions including virulence and biofilm formation. The common laboratory strain of E. coli, K-12 MG1655 has six recognised RND transporters participating in tripartite pump formation (AcrB, AcrD, AcrF, CusA, MdtBC, and MdtF). However, by studying >20,000 E. coli genomes we show that E. coli belonging to phylogroups B2, D, E, F and G, which are commonly associated with infection, possess an additional, seventh RND transporter, EefB. It is found in a five gene operon, eefRABCD, which also encodes a TetR family transcription factor, a periplasmic adapter protein, an outer membrane factor and major facilitator superfamily pump. In contrast, E. coli from phylogroups A, B1 and C, generally containing environmental and commensal strains, do not encode the operon and instead encode an uncharacterised ORF, ycjD. In phylogroups where the eefRABCD operon is present it was very highly conserved. In fact, conservation levels were comparable to that of the major E. coli RND efflux system AcrAB-TolC, suggesting a critical biological function. Protein modelling shows that this pump is highly divergent from endogenous E. coli RND systems with unique structural features, while showing similarities to efflux systems found in Pseudomonas aeruginosa. However, unlike other major RND efflux systems, EefABC does not appear to transport antimicrobials and instead may be important for infection or survival in the host environment. ImportanceEfflux pumps are molecular machines that export molecules out of bacterial cells. The efflux pumps belonging to the RND family are particularly important as they export antibiotics out of Gram-negative bacterial cells, contributing to antibiotic resistance. The important human pathogen, E. coli, has been previously reported to have six RND pumps. However, we show that phylogroups of E. coli commonly associated with infection encode a seventh RND pump, EefABC which is highly conserved, suggesting an important biological function. While the function of EefABC in E. coli remains to be resolved, it does not seem to transport antimicrobial compounds. These findings are important because they reveal a new RND pump, potentially involved in virulence and survival in the host, that could represent a new therapeutic target. Additionally, it again shows that laboratory type strains of common bacterial pathogens are not representative of those that are infection causing.

microbiology↗

bioRxiv2024

An inferotemporal coding strategy robust to partial object occlusion

Object coding in primate ventral pathway cortex progresses in sparseness/compression/efficiency, from many orientation signals in V1, to fewer 2D/3D part signals in V4, to still fewer multi-part configuration signals in AIT (anterior inferotemporal cortex).1-11 This progression could lead to individual neurons exclusively selective for unique objects, the sparsest code for identity, especially for highly familiar, important objects.12-18 To test this, we trained macaque monkeys to discriminate 8 simple letter-like shapes in a match-to-sample task, a design in which one-to-one coding of letters by neurons could streamline behavior. Performance increased from chance to >80% correct over a period of weeks, after which AIT neurons showed clear learning effects, with increased selectivity for multi-part configurations within the trained alphabet shapes. But these neurons were not exclusively tuned for unique letters based on training, since their responsiveness generalized to different, non-trained shapes containing the same configurations. This multi-part configuration coding limit in AIT is not maximally sparse, but it could explain the robustness of primate vision to partial object occlusion, which is common in the natural world and problematic for computer vision. Multi-part configurations are highly diagnostic of identity, and neural signals for various partial object structures can provide different but equally sufficient evidence for whole object identity across most occlusion conditions.

neuroscience↗

bioRxiv2023

Loss of type VI secretion systems in multi-drug resistant Escherichia coli clones

The repeated emergence of multi-drug resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonisation observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug resistant E. coli clones. We employed large scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20,000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterised the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones. Data SummaryThe genome sequence data generated in this study is publicly available from NCBI under BioProject PRJNA943186, alongside a complete assembly in GenBank under accessions CP120633-CP120634. All other sequence data used in this paper has been taken from ENA with the appropriate accession numbers listed within the methods section. The E. coli genome data sets used in this work are from a previous publication, the details of which can be found in the corresponding supplementary data files 10.6084/m9.figshare.21360108 [1]. Impact StatementEscherichia coli is a globally significant pathogen that causes the majority of urinary tract infections. Treatment of these infections is exacerbated by increasing levels of drug resistance. Pandemic multi-drug resistant (MDR) clones, such as ST131-C2/H30Rx, contribute significantly to global disease burden. MDR E. coli clones are able to colonise the human gut and displace the resident commensal E. coli. It is important to understand how this process occurs to better understand why these pathogens are so successful. Type VI secretion systems may be one of the antagonistic systems employed by E. coli in this process. Our findings provide the first detailed characterisation of the T6SS loci in ST410 and ST131 and shed light on events in the evolutionary pathways of the prominent MDR pathogens ST410-B4/H42RxC and ST131-C2/H30Rx.

microbiology↗

bioRxiv2022

Multi-drug resistant E. coli displace commensal E. coli from the intestinal tract, a trait associated with elevated levels of genetic diversity in carbohydrate metabolism genes.

Extra-intestinal pathogenic E. coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multi-drug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model we demonstrate that an MDR E. coli ST131 is capable out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonized mice results in displacement and dominant intestinal colonization by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonization ability by MDR E. coli, we used a functional pangenomic analysis of 19,571 E. coli genomes revealing that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.

microbiology↗

bioRxiv2022

Pangenome evolution in Escherichia coli is sequence type, not phylogroup, specific

The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that pangenome evolution is independent of phylogenetic signal at the phylogroup level, which may be a consequence of distinct sequence type-specific driving factors relating to ecology and pathogenic phenotype. Data SummarySupporting data and code have been provided within the article or through Supplementary Data files available at https://doi.org/10.6084/m9.figshare.19793758. Custom Python scripts used to perform analyses are available at github.com/lillycummins/InterPangenome unless otherwise stated in the text.

microbiology↗

bioRxiv2021

Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene, suggesting that cooperation is more common than conflict in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships. Data summaryAll Supplementary Data files and the Python scripts used in the analyses are available at doi.org/10.17639/nott.7103. Impact statementThe pangenome of a species encompasses the core genes encoded by all genomes, as well as the accessory genes found in only a subset. Much remains to be understood about the relationships and interactions between accessory genes; in particular, what drives pairs of genes to appear together in the same genome, or what prevents them from being in the same genome together, more often than expected by chance. How these co-occurrence and avoidance relationships develop, and what effect they have on the dynamics and evolution of the pangenome as a whole, is largely unknown. Here, we present a springboard for understanding prokaryote pangenome evolution by uncovering significant gene relationships in a model Escherichia coli pangenome. We identify mobile genetic elements and the sharing of common function as possible driving forces behind the co-occurrence of accessory genes. Furthermore, this work offers an extensive dataset from which gene relationships could be identified for any gene of interest in this E. coli accessory genome, providing a rich resource for the community.

evolutionary biology↗

bioRxiv2018

Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition

Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. Through direct-to-patient outreach, we developed genomically faithful patient-derived models of RMC. Using whole genome sequencing, we identified intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele, confirming that SMARCB1 loss occurs in RMC. Biochemical and functional characterization of these RMC models revealed that RMC depends on the loss of SMARCB1 for survival and functionally resemble other cancers that harbor loss of SMARCB1, such as malignant rhabdoid tumors or atypical teratoid rhabdoid tumors. We performed RNAi and CRISPR-Cas9 loss of function genetic screens and a small-molecule screen and identified UBE2C as an essential gene in SMARCB1 deficient cancers. We found that the ubiquitin-proteasome pathway was essential for the survival of SMARCB1 deficient cancers in vitro and in vivo. Genetic or pharmacologic inhibition of this pathway leads to G2/M arrest due to constitutive accumulation of cyclin B1. These observations identify a synthetic lethal relationship that may serve as a therapeutic approach for patients with SMARCB1 deficient cancers.

cancer biology↗

bioRxiv2018

Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

Escherichia coli is a major cause of bloodstream and urinary tract infections globally. The wide dissemination of multi-drug resistant (MDR) strains of extra-intestinal pathogenic E. coli (ExPEC) poses a rapidly increasing public health burden due to narrowed treatment options and increased risk of failure to clear an infection. Here, we present a detailed population genomic analysis of the ExPEC ST131 clone, in which we seek explanations for its success as an emerging pathogenic strain beyond the acquisition of antimicrobial resistance (AMR) genes. We show evidence for evolution towards separate ecological niches for the main clades of ST131 and differential evolution of anaerobic metabolism, key colonisation and virulence factors. We further demonstrate that negative frequency-dependent selection acting across accessory loci is a major mechanism that has shaped the population evolution of this pathogen.

microbiology↗