Biology subjects

Hammond, L.

Publications and source records attributed to Hammond, L..

5 recordsLinked to original sources

bioRxiv2025

From Morphology to Computation: How Synaptic Organization Shapes Place Fields in CA1 Pyramidal Neurons

How spatial organization of synaptic inputs along the dendritic tree of neurons influence their feature selectivity is a central question in neuroscience. Here, we mapped the three-dimensional distribution of all excitatory and inhibitory synapses across the entire dendritic arbor of individual mouse CA1 pyramidal neurons in vivo and built biophysically detailed computational models to probe their functional impact on their ability to emerge as place cells. We found that excitatory, but not inhibitory, synapses are non-uniformly distributed, forming structural clusters preferentially on terminal dendrites. These excitatory synaptic clusters generate high-quality place fields more efficiently than randomized synaptic distributions, requiring fewer active synapses to achieve equivalent somatic output. Crucially, even when firing rates are matched, clustered inputs sustain significantly higher voltage-gated calcium influx and NMDA receptor activation, key substrates for synaptic plasticity. Further analysis reveals that clustering enables domain-specific computational strategies: oblique dendrites rely on cluster location, basal dendrites on cumulative synaptic strength, and the trunk on local input dispersion. Disrupting clustering collapses this compartmentalized processing into uniform summation. Our results establish synaptic clustering as a key mechanism that maximizes computational efficiency and enables sophisticated dendritic processing underlying hippocampal spatial representation.

neuroscience↗

bioRxiv2025

Two-timepoint assays of neural responses increase the sensitivity and specificity of single-cell whole-brain activity screens

Current approaches for surveying whole brains for neurons activated during a particular state typically rely on immediate early gene (IEG) expression. However, IEG expression is variable across subjects and brain areas, demanding large sample sizes. Further, it cannot determine if the same or different neurons respond to two events. To overcome these issues, we present a whole-brain screening method utilizing transgenic mice to label neurons activated at two timepoints. An imaging and analysis pipeline surveys activity in ~500 brain areas in different conditions. Compared to IEG methods, this approach reduces required sample sizes and enhances sensitivity and specificity. Finally, graph theoretical analyses are utilized to identify key circuit nodes - brain areas whose activity correlates with activity in other areas in a state-dependent manner. We validate this method by surveying whole-brain activity during hunger and satiety, and by investigating neural circuits activated by the GLP1 agonist semaglutide used to treat obesity.

neuroscience↗

bioRxiv2024

RESPAN: an accurate, unbiased and automated pipeline for analysis of dendritic morphology and dendritic spine mapping

Quantification of dendritic spines is essential for studying synaptic connectivity, yet most current approaches require manual adjustments or the combination of multiple software tools for optimal results. Here, we present Restoration Enhanced SPine And Neuron Analysis (RESPAN), an open-source pipeline integrating state-of-the-art deep learning for image restoration, segmentation, and analysis in an easily deployable, user-friendly interface. Leveraging content-aware restoration to enhance signal, contrast, and isotropic resolution further enhances RESPANs robust detection of spines, dendritic branches, and soma across a wide variety of samples, including challenging datasets such as those from live imaging and in vivo 2-photon microscopy with limited signal. Extensive validation against expert annotations and comparison with other software demonstrates RESPANs superior accuracy and reproducibility across multiple imaging modalities. RESPAN offers significant improvements in usability over currently available approaches, streamlining and democratizing access to a combination of advanced capabilities through an accessible resource for the neuroscience community. MOTIVATIONAccurate and unbiased reconstructions of neuronal morphology and quantification of dendritic spines are widely used in neuroscience but remain a significant challenge for efficient large-scale analysis. Current methods rely heavily on parameter optimization between images and manual annotation, introducing bias and creating bottlenecks that limit large-scale studies. Additionally, existing automated tools often require complex workflows across multiple software platforms and lack integrated validation capabilities. We developed RESPAN to address these limitations by providing a comprehensive, automated pipeline that combines state-of-the-art deep learning approaches for image restoration, model training, image segmentation and analysis within one user-friendly graphic interface. This enables rapid, unbiased analysis of dendritic spine morphology across diverse imaging modalities while maintaining high accuracy and reproducibility.

neuroscience↗

bioRxiv2022

Bacterial threat assessment of bacteriophage infection is mediated by intracellular polyamine accumulation and Gac/Rsm signaling

When eukaryotic cells are killed by pathogenic microorganisms, damage-associated and pathogen-associated signals are generated that alert other cells of nearby danger. Bacteria can detect the death of their kin; however, how bacteria make threat assessments of cellular injury is largely unexplored. Here we show that polyamines released by lysed bacteria serve as damage-associated molecules in Pseudomonas aeruginosa. In response to exogenous polyamines, Gac/Rsm and cyclic-di-GMP signaling is activated and intracellular polyamine levels increase. In the absence of a threat, polyamines are catabolized, and intracellular polyamines return to basal levels, but cells infected by bacteriophage increase and maintain intracellular polyamine levels, which inhibits phage replication. Phage species not inhibited by polyamines did not trigger polyamine accumulation by P. aeruginosa, suggesting polyamine accumulation and metabolism are targets in the phage-host arms-race. Our results suggest that like eukaryotic cells, bacteria can differentiate damage-associated and pathogen-associated signals to make threat assessments of cellular injury. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/486733v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1f69334org.highwire.dtl.DTLVardef@13a4422org.highwire.dtl.DTLVardef@4f3edeorg.highwire.dtl.DTLVardef@a86c43_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Phenogenomic characterization of a newly domesticated and novel species from the genus Verrucosispora

The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental hole in our knowledge of microbial diversity. Herein we present the domestication of such an organism: a previously uncultured, novel species from the rare-Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media, but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic decay through the pseudogenization of amino acids metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread SNP, indel and pseudogene mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability.

microbiology↗