Biology subjects

Fisher, H.

Publications and source records attributed to Fisher, H..

12 recordsLinked to original sources

bioRxiv2026

Protein architectures of the bacterial spore envelope - common principles of assembly

Bacterial spores are among the most durable of cell forms, protected by robust envelopes of layered protein assemblies. Remarkably, these envelopes often share similar architectures across distantly related bacteria despite extensive divergence in their molecular components. How evolution has converged on such similar highly ordered and resilient cellular structures is relatively unexplored. Here, we combine targeted mutagenesis, cryo-electron microscopy, atomic force microscopy and structure prediction to determine the organisation and assembly of the outer spore envelope of Clostridium sporogenes, a genetically tractable surrogate for Group I Clostridium botulinum. We reveal a hierarchy of protein structures, including a semi-permeable two-dimensional crystalline exosporium; CsxA forms the exosporium scaffold with an outer "hairy nap" partially composed of BclA. We observe a previously uncharacterised multilayered three-dimensional crystalline parasporal assembly within the interspace between exosporium and coat (CsxC). These distinct structures are built from related cysteine-rich SPOCS (SpoVID-CotE-SipL)-domain proteins that self-assemble into highly ordered lattices. Such crystalline organisation, combined with high symmetry, can provide a template for local enhancement of cysteine concentration, favouring cooperative disulphide cross-linking and the formation of exceptionally stable supramolecular structures. Unexpectedly, the three-dimensional CsxC structure grows through screw dislocations, a mechanism familiar from inorganic and synthetic crystal growth but rarely demonstrated in native biological assemblies, with the exception of some biomineralisation processes. Our observations now suggest that this classical crystal-growth mechanism can be exploited in both mineralised and proteinaceous biological materials. Related SPOCS-domain proteins are implicated in spore-envelope assembly across diverse Clostridia, where they have diversified to act as both structural components and morphogenetic organisers. Remarkably, distantly related Bacilli construct similarly highly symmetric crystalline, cysteine-rich and disulphide-stabilised spore layers using proteins with very different protein folds. Thus, crystallisation and cooperative disulphide formation appear to represent a convergent physicochemical strategy for building diverse self-assembling proteins into exceptionally robust cellular assemblies. Together these findings provide the first molecular framework for understanding the organisation and assembly of the Clostridium spore envelope and reveal previously unrecognised principles governing the evolution of protective proteinaceous structures across the Bacillota (Firmicutes).

microbiology↗

bioRxiv2026

Carbonara: a SAXS-guided seeding framework for exploring protein solution-state dynamics

Proteins in solution often populate conformational ensembles that differ from the static states captured by crystallography or AI-based structure prediction. Conventional molecular dynamics (MD) simulations often fail to cross the energy barriers separating these states on accessible timescales, and statistical reweighting cannot recover conformations never sampled. Here we present Carbonara, a framework that uses experimental small-angle X-ray scattering (SAXS) data to predict alternative physically plausible protein conformations. Carbonara builds on Wiggle, a standalone C-based SAXS forward model validated against explicit-solvent calculations and experimental benchmarks. Using two case studies, an AI-predicted multi-domain helicase (SMAR-CAL1) and a crystallographic antibody fragment (ChiLob7/4 IgG2), we show how seeding MD simulations from Carbonara conformations enables efficient exploration of solution-state conformational landscapes. In both cases, MD ensembles initiated from available models either fail to match the SAXS data or do so only after discarding nearly all sampled conformations, whereas Carbonara-seeded ensembles reach agreement while retaining the majority of conformations. Our modelling framework provides a route from static structural models of flexible multi-domain proteins and multimeric assemblies to solution-state ensembles.

biophysics↗

bioRxiv2026

Molecular basis of mitogen-activated protein kinase ERK2 activation by its upstream kinase MEK1

The RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) pathway relays extracellular signals into a cellular response and its dysregulation leads to many pathologies, particularly cancer. Here, we determined cryo-EM structures of the MAP2K MEK1 activating its substrate MAPK ERK2, the final event in the cascade. We define the molecular details of specificity and phosphoryl transfer to the tyrosine of the ERK2 activation loop and examine the mechanism of substrate recognition using solution techniques and molecular dynamics. Binding of the substrate MAPK leads to release of the MAP2K catalytic machinery, a mechanism enhanced in many gain of function disease mutations. Further, we observe that ERK2 release is not required for nucleotide exchange, suggesting how a processive mechanism could proceed. Our data advance the understanding of MAPK signalling and provide a starting point for drug development. One-Sentence SummaryCryo-EM structures of the MEK1-ERK2 complex reveal details of cellular signal transmission.

molecular biology↗

bioRxiv2024

Enterococcal cell wall remodelling underpins pathogenesis via the release of the Enteroccocal Polysaccharide Antigen (EPA)

Enterococci are opportunistic pathogens displaying a characteristic ovoid shape, typically forming pairs of cells (diplococci) and short chains. Control of cell chain length in Enterococcus faecalis relies on the activity of the major N-acetylglucosaminidase AtlA. The formation of short chains and diplococci is critical during pathogenesis for dissemination in the host and to limit recognition by innate immune effectors such as complement molecules and phagocytes. Here, we identify AtlE, an N-acetylmuramidase that contributes to septum cleavage during stationary phase in the absence of AtlA. AtlE is encoded by the locus required to produce the decoration subunits of the Enterococcal Polysaccharide Antigen (EPA), which mediate evasion of phagocytosis. We show that peptidoglycan hydrolysis by AtlE is essential for pathogenesis and demonstrate that soluble cell wall fragments containing EPA decorations increase the virulence of E. faecalis, suggesting that EPA plays a role as a decoy molecule to evade host defences. This research sheds light on the complex interplay between bacterial cell division, cell wall remodelling, and the host immune system, providing valuable insights into a novel mechanism underlying the virulence of E. faecalis. Author summaryThe major component of the bacterial cell envelope (peptidoglycan) undergoes partial hydrolysis during growth. This process, referred to as remodelling, is required for the incorporation of novel peptidoglycan building blocks, and cell separation at the end of division. In Enterococcus faecalis, only one ubiquitous peptidoglycan hydrolase, named AtlA, has been described so far. AtlA plays a prominent role in septum cleavage and is responsible for the characteristic formation of diplococci and short cell chains. The minimization of cell chain length by AtlA is critical for innate immune evasion and underpins pathogenesis. Here, we identify another ubiquitous peptidoglycan hydrolase named AtlE encoded by the Enterococcal Polysaccharide Antigen (EPA) biosynthetic locus. We show that AtlE displays N-acetylmuramidase activity and requires strain-specific EPA decorations to be active. Whilst AtlE only plays a marginal role in septum cleavage during growth, AtlE is essential for virulence in the zebrafish model of infection. We demonstrate that AtlE activity contributes to release cell wall fragments and promotes phagocyte evasion, indicating that EPA plays a role as a decoy molecule produced by enterococci to counteract host immune defenses.

microbiology↗

bioRxiv2023

An interactive web application for exploring human plasma and fibroblast metabolomics data from patients with inborn errors of metabolism

Metabolomic profiling is instrumental in understanding the systemic and cellular impact of inborn errors of metabolism (IEMs), monogenic disorders caused by pathogenic genomic variants in genes involved in metabolism. This study encompasses untargeted metabolomics analysis of plasma from 474 individuals and fibroblasts from 67 subjects, incorporating healthy controls, patients with 65 different monogenic diseases, and numerous undiagnosed cases. We introduce a web application designed for the in-depth exploration of this extensive metabolomics database. The application offers a user-friendly interface for data review, download, and detailed analysis of metabolic deviations linked to IEMs at the level of individual patients or groups of patients with the same diagnosis. It also provides interactive tools for investigating metabolic relationships and offers comparative analyses of plasma and fibroblast profiles. This tool emphasizes the metabolic interplay within and across biological matrices, enriching our understanding of metabolic regulation in health and disease. As a resource, the application provides broad utility in research, offering novel insights into metabolic pathways and their alterations in various disorders.

bioinformatics↗

bioRxiv2022

Examination of Onset Trajectories and Persistence of Binge-Like Eating Behavior in Mice after Intermittent Palatable Food Exposure

Binge eating (BE) is a persistent behavior associated with a chronic course of illness and poor treatment outcomes. While clinical research is unable to capture the full course of BE, pre-clinical approaches offer the opportunity to examine binge-like eating from onset through chronic durations, allowing identification of factors contributing to BE persistence. The current study quantified the trajectories of binge-like eating onset and modeled cycles of abstinence/relapse to develop a translational model for BE persistence. Adult male and female C57Bl6/J mice were randomized to a binge-like palatable food (PF) access schedule (daily 2-hour, 3x/week) or continuous, non-binge like PF access for 12 days (Experiment 1). Persistence of PF consumption in both binge-like PF access groups was then examined across three cycles of forced abstinence and re-exposure to PF (incubation) to model the persistence of BE in clinical populations. Mice with daily 2 hour PF access escalated their intake more than mice in the 3x/week or continuous groups (Experiment 1).This pattern was more pronounced in females. In addition, this pattern of PF intake re-emerged across multiple cycles of behavioral incubation (Experiment 2). These findings provide a model of binge-like eating in mice that can be used in future studies examining both environmental factors and neural mechanisms contributing to BE persistence.

neuroscience↗

bioRxiv2022

Female reproductive fluid composition differs based on mating system in Peromyscus mice

Post-copulatory sexual selection is theorized to favor female traits that allow them to control sperm use and fertilization, leading to the prediction that female reproductive traits that influence sperm migration should differ between polyandrous and monogamous species. Here we exploit natural variation in the female mating strategies of closely related Peromyscus mice to compare female traits that influence sperm motility - the viscosity, pH, and calcium concentration of fluids in the reproductive tract - between polyandrous and monogamous species. We find that the viscosity and pH, but not calcium concentration, of fluids collected from both the uterus and the oviduct significantly differ between species based on mating system. Our results demonstrate the existence of a viscosity gradient within the female reproductive tract that increases in monogamous species but decreases in polyandrous species. Both species have a more alkaline environment in the uterus than oviduct, but only in the polyandrous species did we observe a decrease in calcium in the distal end of the tract. These results suggest that fluid viscosity and pH in the female reproductive tracts of these mice may be influenced by post-copulatory sexual selection and provide a promising potential mechanism for female sperm control given their importance in modulating sperm behavior.

evolutionary biology↗

bioRxiv2021

Transcriptional expression changes during compensatory plasticity in the prothoracic ganglion of the adult cricket Gryllus bimaculatus

Most adult organisms are limited in their capacity to recover from neurological damage. The auditory system of the Mediterranean field cricket, Gryllus bimaculatus, presents a compelling model for investigating neuroplasticity due to its unusual capabilities for structural reorganization into adulthood. Specifically, the dendrites of the central auditory neurons of the prothoracic ganglion sprout in response to the loss of auditory afferents. Deafferented auditory dendrites grow across the midline, a boundary they normally respect, and form functional synapses with the contralateral auditory afferents, restoring tuning-curve specificity. The molecular pathways underlying these changes are entirely unknown. Here, we used a multiple k-mer approach to re-assemble a previously reported prothoracic ganglion transcriptome that included ganglia collected one, three, and seven days after unilateral deafferentation in adult, male animals. We used EdgeR and DESeq2 to perform differential expression analysis and we examined Gene Ontologies to further understand the potential molecular basis of this compensatory anatomical plasticity. Enriched GO terms included those related to protein translation and degradation, enzymatic activity, and Toll signaling. Extracellular space GO terms were also enriched and included the upregulation of several protein yellow family members one day after deafferentation. Investigation of these regulated GO terms help to provide a broader understanding of the types of pathways that might be involved in this compensatory growth and can be used to design hypotheses around identified molecular mechanisms that may be involved in this unique example of adult structural plasticity.

neuroscience↗

bioRxiv2021

Corticostriatal dynamics underlying components of binge-like eating in mice

Binge eating (BE) is a maladaptive repetitive feeding behavior present across nearly all eating disorder diagnoses. Despite the substantial negative impact of BE on psychological and physiological health, its underlying neural mechanisms are largely unknown. Other repetitive behavior disorders (e.g., obsessive compulsive disorder) show dysfunction within corticostriatal circuitry. Additionally, previous pre-clinical and clinical work has highlighted an imbalance between goal-directed and habitual responding in BE. The aim of the current study was to longitudinally examine in vivo neural activity within corticostriatal regions associated with habitual behavior- the infralimbic cortex (IL) and dorsolateral striatum (DLS)- in a robust pre-clinical model for BE. Female C57BL/6 mice (N=32) were randomized to receive: 1) intermittent (daily, 2-hour) binge-like access to palatable food (BE mice), or 2) continuous, non-intermittent (24-hour) access to palatable food (non-BE mice). In vivo calcium imaging was performed via fiber photometry at baseline and after chronic (4 weeks) engagement in the model for BE. Feeding behaviors (feeding bout onset/offset) during the recordings were captured using lickometers which generated TTL outputs for precise alignment of behavior to neural data. IL showed no specific changes in neural activity related to BE. However, BE animals showed decreased DLS activity at feeding onset and offset at the chronic timepoint when compared to baseline. Additionally, BE mice had significantly lower DLS activity at feeding onset and offset at the chronic timepoint compared to non-BE mice. These results point to a role for DLS hypofunction in chronic BE, highlighting a potential target for future treatment intervention. Significance StatementBinge eating is a chronic and repetitive eating behavior that is associated with poor physiological and psychosocial outcomes. Despite the negative impact of binge eating, little is known about the neurobiological mechanisms contributing to the chronic course and persistence of the behavior. To investigate potential neural mechanisms underlying binge eating, we are using approaches developed to monitor neural activity in rodents. This study is the first to identify longitudinal changes in neural activity within regions of the prefrontal cortex and dorsal striatum during binge-like eating behavior in mice. Findings from this work could inform targeted biological treatments for binge eating.

neuroscience↗

bioRxiv2021

Prefrontal cortex neural compensation during an operant devaluation task

Deficits in goal-directed action are reported in multiple neuropsychiatric conditions, including schizophrenia. However, dysfunction is not always apparent in early stages of schizophrenia, possibly due to neural compensation. We designed a novel devaluation task in which goal-directed action could be guided by stimulus-outcome (S-O) [presumably orbitofrontal cortex (OFC)-mediated] or response-outcome (R-O) associations [presumably prelimbic cortex (PL)-mediated]. We previously found suggestive evidence that OFC and PL could compensate for each other in this task, and we more directly assessed this potential compensation here. In Experiment 1, rats received OFC, PL, combined OFC+PL, or sham lesions and then completed our devaluation task. The OFC+PL lesion group exhibited impaired devaluation. In Experiment 2, rats received cholera-toxin-b (CTb) into OFC and either neurotoxic or sham PL lesions. Rats were then sacrificed on the last training day to double-label for Arc and CTb. We found increased Arc+CTb in mediodorsal thalamus (MD) and increased Arc+ neurons in OFC when PL was lesioned, suggesting that PL lesions lead to a compensatory increased activation of the MD[->]OFC circuit. Our results suggest that our devaluation task can model neural compensation between OFC and PL and this compensation may be regulated by MD. Significance StatementTo detect compensatory responses, behavioral models that use different strategies must be developed to determine if the strategies shift when a brain area or circuit is incapacitated. Neural compensation is commonly observed in human research but only a few models of neural compensation exist, and few identify compensation within the prefrontal cortex. This research is among the first to show neural compensation between prefrontal cortex regions and implicate a thalamocortical circuit in modulating this compensation. Not only will this model provide a way to behaviorally identify subtle neurological shifts, it can also elucidate basic neurological mechanisms that mediate how circuits interact with each other and how dysfunction in one circuit can affect connectivity in other brain areas.

neuroscience↗

bioRxiv2021

Chromosome size affects sequence divergence between species through the interplay of recombination and selection

The structure of the genome shapes the distribution of genetic diversity and sequence divergence. To investigate how the relationship between chromosome size and recombination rate affects sequence divergence between species, we combined empirical analyses and evolutionary simulations. We estimated pairwise sequence divergence among 15 species from three different Mammalian clades - Peromyscus rodents, Mus mice, and great apes - from chromosome-level genome assemblies. We found a strong significant negative correlation between chromosome size and sequence divergence in all species comparisons within the Peromyscus and great apes clades, but not the Mus clade, suggesting that the dramatic chromosomal rearrangements among Mus species may have masked the ancestral genomic landscape of divergence in many comparisons. Our evolutionary simulations showed that the main factor determining differences in divergence among chromosomes of different size is the interplay of recombination rate and selection, with greater variation in larger populations than in smaller ones. In ancestral populations, shorter chromosomes harbor greater nucleotide diversity. As ancestral populations diverge, diversity present at the onset of the split contributes to greater sequence divergence in shorter chromosomes among daughter species. The combination of empirical data and evolutionary simulations revealed that chromosomal rearrangements, demography, and divergence times may also affect the relationship between chromosome size and divergence, and deepen our understanding of the role of genome structure on the evolution of species divergence.

evolutionary biology↗

bioRxiv2019

An inexpensive wireless video recording system for continuous behavioral observations

Video recording technology is an important tool for studies of animal behavior because it reduces observer effects and produces a record of experiments, interactions among subjects, and contextual information, however it remains cost prohibitive for many researchers. Here we present an inexpensive method for building a remotely-operated video recording system to continuously monitor behavioral or other biological experiments. Our system employs Raspberry Pi computers and cameras, open-source software, and allows for wireless networking, live-streaming, and the capacity to simultaneously record from several cameras in an array. To validate this system, we continuously monitored home-cage behavior of California mice (Peromyscus californicus) in a laboratory setting. We captured video in both low- and bright-light environments to record behaviors of this nocturnal species, and then quantified mating interactions of California mouse pairs by analyzing the videos with an open-source event logging software. This video recording platform offers users the flexibility to modify the specifications for a range of tasks and the scalability to make research more efficient and reliable to a larger population of scientists.

animal behavior and cognition↗