Biology subjects

White, J. A.

Publications and source records attributed to White, J. A..

At least 19 recordsLinked to original sources

bioRxiv2026

Profiling the CFTR Variant Selectivity and Off-Target Interactions of VX-121

More than 1,200 variants of the cystic fibrosis transmembrane conductance regulator gene (CFTR) are associated with cystic fibrosis (CF), an autosomal recessive pulmonary disease affecting over 100,000 people. Most people with CF bear a common CFTR variant (F508del) that can be treated with therapeutics containing "correctors" that suppress the misfolding of the CFTR chloride channel. However, the pharmacological responsiveness of other rare CF variants can vary tremendously. The approval of VX-121, a VX-445 analog that serves as a key component of AlyftrekTM, potentially provides a new therapeutic option for those with rare CF variants. Nevertheless, it remains unclear whether VX-121 offers superior rescue across the entire spectrum of rare CF variants. In this work, we use deep mutational scanning (DMS) to survey the impact of VX-121 on the plasma membrane expression of 232 rare CF variants. Our results show that VX-121 generally enhances CF variant expression more than VX-445 and is most potent towards variants with mutations in the first membrane spanning domain (MSD1). However, we identify one variant (Y1032C) with diminished proteostatic and functional selectivity for VX-121 relative to VX-445. Computational docking suggests that the native Y1032 side chain forms favorable interactions with VX-121 that are disrupted by this mutation in a manner that alters its coordination. Finally, using photo-crosslinking, we show that VX-121 avoids a key off-target interaction of VX-445. Together, our findings provide new insights into the similarities and differences between current approved CF therapeutics.

pharmacology and toxicology↗

bioRxiv2026

Distinct cell-type contributions and network topography of theta-nested gamma oscillations in the medial entorhinal cortex

Theta-nested gamma oscillations in the medial entorhinal cortex (mEC) are essential for spatial coding and memory, but the underlying cellular mechanisms remain unclear. We combined optogenetics, whole-cell electrophysiology, intracellular voltage imaging, and local field potential (LFP) recordings in acute slices from CaMKII-ChR2 mice to investigate how excitation and inhibition shape theta-gamma coupling in layer II/III mEC. During theta-frequency stimulation, fast-spiking interneurons received strong gamma-frequency excitation and fired rhythmic bursts, whereas stellate and pyramidal neurons fired more sparsely and were dominated by gamma-frequency inhibition. This sparse firing could support the selective firing of grid cells. Excitatory post-synaptic currents in interneurons preceded inhibitory currents and LFP gamma by [~]3 ms, supporting a pyramidal-interneuron network gamma (PING) mechanism. Pyramidal neurons fired on the descending phase of the gamma cycle, whereas stellate cells and fast-spiking interneurons fired before and after the trough, respectively. Intracellular voltage imaging revealed network gamma synchronization among excitatory neurons at a population level, with topographic clustering of subthreshold membrane potentials, but not spike timing, while individual neurons often skipped gamma cycles. These findings identify the dominant role of reciprocal E-I interactions in generating theta-nested gamma oscillations and highlight distinct cell-type contributions to the temporal dynamics of the mEC. Further, a biophysically realistic computational model predicted gamma cycle skipping in stellate cells and burst firing in fast-spiking interneurons during PING. Our experimental and computational results provide mechanistic insight into how the intrinsic properties of mEC cell types generate oscillatory activity in a manner that could support grid cell function and spatial computation. Significance StatementTheta-nested gamma oscillations in the medial entorhinal cortex (mEC) are essential for spatial navigation and memory, yet the underlying circuit mechanisms remain incompletely understood. Using optogenetics, voltage imaging, electrophysiology, and biophysically realistic computational modeling, we show that reciprocal interactions between excitatory neurons and fast-spiking interneurons generate robust gamma oscillations through a pyramidal-interneuron network gamma (PING) mechanism. We reveal cell-type specific differences in gamma phase-locking and demonstrate that principal neurons synchronize at the population-level across large laminar distances (up to 800 {micro}m). Further, the voltage activity, but not spike timing, of principal neurons exhibited topographic clustering. These findings clarify how local circuits in mEC generate temporal dynamics critical for grid cell coding and further constrain computational models of spatial representation.

neuroscience↗

bioRxiv2025

Fast spiking interneurons autonomously generate fast gamma oscillations in the medial entorhinal cortex with excitation strength tuning ING-PING transitions

Gamma oscillations (40-140 Hz) play a fundamental role in neural coordination, facilitating communication and cognitive functions in the medial entorhinal cortex (mEC). While previous studies suggest that pyramidal-interneuron network gamma (PING) and interneuron network gamma (ING) mechanisms contribute to these oscillations, the precise role of inhibitory circuits remains unclear. Using optogenetic stimulation and whole-cell electrophysiology in acute mouse brain slices, we examined synaptic input and spike timing in neurons across layer II/III mEC. We found that fast-spiking interneurons exhibited robust gamma-frequency firing, while excitatory neurons engaged in gamma cycle skipping. Stellate and pyramidal cells received minimal recurrent excitation, whereas fast-spiking interneurons received strong excitatory input. Both excitatory neurons and fast-spiking interneurons received gamma frequency inhibition, emphasizing the role of recurrent inhibition in gamma rhythm generation. Notably, gamma activity was reduced, but persisted after AMPA/kainate receptor blockade, indicating that interneurons can sustain gamma oscillations independently through an ING mechanism. Selective activation of PV+ interneurons confirmed their ability to sustain fast gamma inhibition autonomously. To further assess the interplay of excitation and inhibition, we developed computational network models constrained by our experimental data. Simulations revealed that weak excitatory input to interneurons supports fast ING-dominated rhythms ([~]100-140 Hz), while strengthening excitatory drive induces a transition to slower PING-dominated oscillations (60-100 Hz). These findings highlight the dominant role of inhibitory circuits in sustaining gamma rhythms, demonstrate how excitation strength tunes the oscillatory regime, and refine models of entorhinal gamma oscillations critical for spatial memory processing. Significance StatementGamma oscillations in the medial entorhinal cortex (mEC) are essential for spatial navigation and memory, yet the mechanisms underlying their generation remain unresolved. Combining optogenetics, whole-cell electrophysiology, and computational modeling, we show that fast-spiking interneurons can autonomously sustain gamma rhythms via interneuron network gamma (ING). Blocking excitatory input reduced, but did not abolish gamma-frequency inhibition, and selective activation of PV+ interneurons confirmed their capacity to generate fast gamma independently. Modeling revealed that excitatory strength tunes the oscillatory regime, with weak excitation favoring fast ING and stronger excitation inducing slower pyramidal-interneuron network gamma (PING). These findings refine entorhinal gamma models and suggest a hybrid mechanism for switching between faster and slower gamma critical for spatial computation.

neuroscience↗

bioRxiv2025

CaNetiCs - An Open-Source Toolbox for Standardized Dimensionality Reduction of Neuronal Calcium Activity

The widespread use of calcium imaging has produced large-scale datasets capturing neuronal population activity across diverse experimental contexts, posing challenges for analyzing complex, high-dimensional data. Dimensionality reduction (DR) methods have been pivotal in addressing these challenges by simplifying data into interpretable, low-dimensional structures, while capturing essential network dynamics. Among DR methods, Nonnegative Matrix Factorization (NMF) can produce biologically meaningful representations through its nonnegativity constraint and parts-based decomposition, making it especially suited for analyzing neuronal calcium signals. To enhance accessibility and standardization in the analysis of state-dependent neuronal dynamics, we introduce Calcium Network dynamiCs (CaNetiCs), an open-source toolbox centered on NMF, integrating standardized DR methods (PCA, ICA, UMAP), geometric low-dimensional component space analyses, and neuronal network simulation modules. We validate our toolbox by applying it to two diverse experimental datasets that describe responses to graded anesthesia: whole-ganglion cellular calcium imaging of C. elegans and two-photon imaging of murine somatosensory cortex. Our analyses recapitulate previously observed trends, such as network suppression and decorrelation with anesthesia, while uncovering novel insights into neuronal activity under differing contexts. CaNetiCs provides an accessible, modular, and interpretable framework, facilitating broader adoption of standardized dimensionality reduction methodologies for deeper exploration of neuronal network dynamics across experimental paradigms. The open-source code, along with documentation, is available at https://github.com/dannycarbonero/CaNetiCs.

neuroscience↗

bioRxiv2025

Untangling overlapping barcodes in spatial genomics data

Difficulty in resolving spatially overlapping barcodes is a major bottleneck for imaging-based spatial genomics methods. Here, we present an approach for untangling spatially overlapping barcodes by using strong encoding and global optimization to reduce spurious solutions resulting from recombinations of barcode signals. We demonstrate experimentally that cellular regions with average local densities of 127 barcodes per {micro}m2 can be decoded with an estimated FDR of less than 4%, enabling a new type of super-resolution microscopy by coding.

bioengineering↗

bioRxiv2025

Comparative phenotypic, genomic and transcriptomic characterisation of two Salmonella Typhimurium strains for a first-in-human challenge model

BackgroundInvasive non-typhoidal Salmonella (iNTS) disease remains a major public health challenge in sub-Saharan Africa. Salmonella Typhimurium is responsible for the majority of cases, with specific lineages being associated with increased risk of bloodstream infection. We have recently developed a Salmonella Typhimurium controlled human infection model (CHIM) to better understand disease pathogenesis and to provide a platform to test candidate vaccines. Selecting appropriate challenge strainsis a central design consideration in developing challenge model protocols. We describe the rationale, manufacture, and detailed characterisation of the two Salmonella Typhimurium strains used in the first-in-human NTS CHIM. MethodsTwo Salmonella Typhimurium strains, 4/74 (ST19) and D23580 (ST313), were selected from the UK Health Security Agency National Collection of Type Cultures and manufactured under Good Manufacturing Practice (GMP) conditions. Challenge agent stocks underwent microbial limits testing, viability and stability assessments, and phenotypic characterisation including growth kinetics, motility, acid sensitivity, and antibiotic susceptibility. Whole-genome sequencing was performed to confirm genetic stability post-manufacture. The effect of pre-challenge handling conditions was assessed in saline and sodium bicarbonate buffers, and bacterial survival was evaluated under simulated gastric and intestinal conditions using a modified Rossett-Rice model. Transcriptomic profiling was undertaken to determine whether sodium bicarbonate exposure altered expression of key virulence genes. ResultsBoth strains retained their expected phenotypic characteristics, including reduced motility and melibiose utilisation in D23580. GMP stocks remained pure, viable, and stable post-manufacture, with no unexpected genomic mutations detected. Both strains were susceptible to clinically relevant antibiotics used in the study. Survival was maintained in neutral and mildly acidic conditions, with significant reduction below pH 3.5. Stability was preserved for up to one hour in saline buffer and during simulated gastric transit in the Rossett-Rice model. Transcriptomic analysis showed no significant changes in Salmonella pathogenicity island-1 or 2, or flagellar gene expression following sodium bicarbonate exposure ConclusionsThese findings confirm that the Salmonella Typhimurium 4/74 and D23580 strains retained genomic and phenotypic integrity post-manufacture. The resulting challenge stocks provide the foundation for an ongoing NTS CHIM that aims to advance understanding of NTS and iNTS pathogenesis and support candidate vaccine testing.

microbiology↗

bioRxiv2025

Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1

During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. Recently, engineered versions of these defective interfering particles (DIPs) have been proposed as an HIV-1 therapeutic. However, DIPs have yet to be reported in people with HIV-1 (PWH). Here, we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viremia (NSV). While antiretroviral therapy (ART) rapidly reduces viremia to undetectable levels, some individuals experience sustained viremia due to virus production from cell clones harboring intact or defective proviruses. We characterized the source of NSV in two PWH who never reached undetectable viral load despite ART adherence. Remarkably, in each participant, we found a diverse set of defective viral genomes all sharing the same fatal deletions. We found that this paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. We show that these defective proviruses interfere with WT virus replication, conditionally replicate, and, in one case, have an R0 > 1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs.

microbiology↗

bioRxiv2025

Long-term editing of brain circuits in mice using an engineered electrical synapse

Electrical signaling across distinct populations of brain cells underpins cognitive and emotional function; however, approaches that selectively regulate electrical signaling between two cellular components of a mammalian neural circuit remain sparse. Here, we engineered an electrical synapse composed of two connexin proteins found in Morone americana (white perch fish) - connexin34.7 and connexin35 - to accomplish mammalian circuit modulation. By exploiting protein mutagenesis, devising a new in vitro system for assaying connexin hemichannel docking, and performing computational modeling of hemichannel interactions, we uncovered a structural motif that contributes to electrical synapse formation. Targeting these motifs, we designed connexin34.7 and connexin35 hemichannels that dock with each other to form an electrical synapse, but not with other major connexins expressed in the mammalian central nervous system. We validated this electrical synapse in vivo using C. elegans and mice, demonstrating that it can strengthen communication across neural circuits composed of pairs of distinct cell types and modify behavior accordingly. Thus, we establish Long-term integration of Circuits using connexins (LinCx) for precision circuit-editing in mammals.

neuroscience↗

bioRxiv2025

Wolbachia feminizes a spider host with assistance from co-infecting symbionts

Arthropods commonly harbor maternally-transmitted bacterial endosymbionts that manipulate host biology. Multiple heritable symbionts can co-infect the same individual, allowing these host-restricted bacteria to engage in cooperation or conflict, which can ultimately affect host phenotype. The spider Mermessus fradeorum is variably infected with up to five heritable symbionts: Rickettsiella (R), Tisiphia (T), and three strains of Wolbachia (W1-3). Quintuply infected spiders are feminized, causing genetic males to develop as phenotypic females and produce almost exclusively female offspring. By comparing feminization across nine infection combinations, we identified a feminizing strain of Wolbachia, W1. We also observed that spiders infected with both W1 and W3 produced [~]10% more females than those lacking W3. This increase in feminization rate does not seem to be due to direct changes in W1 titer, nor does W1 titer correlate with feminization rate. Instead, we observed subtle titer interactions among symbionts, with lower relative abundance of R and T symbionts in strongly feminized infections. This synergistic effect of co-infection on Wolbachia feminization may help promote the spread of all five symbionts in spider populations. These results confirm the first instance of Wolbachia-induced feminization in spiders and demonstrate that co-infecting symbionts can improve the efficacy of symbiont-induced feminization.

ecology↗

bioRxiv2023

Non-Negative Matrix Factorization for Analyzing State Dependent Neuronal Network Dynamics in Calcium Recordings

Calcium imaging allows recording from hundreds of neurons in vivo with the ability to resolve single cell activity. Evaluating and analyzing neuronal responses, while also considering all dimensions of the data set to make specific conclusions, is extremely difficult. Often, descriptive statistics are used to analyze these forms of data. These analyses, however, remove variance by averaging the responses of single neurons across recording sessions, or across combinations of neurons, to create single quantitative metrics, losing the temporal dynamics of neuronal activity, and their responses relative to each other. Dimensionally Reduction (DR) methods serve as a good foundation for these analyses because they reduce the dimensions of the data into components, while still maintaining the variance. Non-negative Matrix Factorization (NMF) is an especially promising DR analysis method for analyzing activity recorded in calcium imaging because of its mathematical constraints, which include positivity and linearity. We adapt NMF for our analyses and compare its performance to alternative dimensionality reduction methods on both artificial and in vivo data. We find that NMF is well-suited for analyzing calcium imaging recordings, accurately capturing the underlying dynamics of the data, and outperforming alternative methods in common use.

neuroscience↗

bioRxiv2023

Ageing impairs the regenerative capacity of regulatory T cells in central nervous system remyelination

Myelin regeneration (remyelination) is essential to prevent neurodegeneration in demyelinating diseases such as Multiple Sclerosis, however, its efficiency declines with age. Regulatory T cells (Treg) recently emerged as critical players in tissue regeneration, including remyelination. However, the effect of ageing on Treg-mediated regenerative processes is poorly understood. Here, we show that expansion of aged Treg does not rescue age-associated remyelination impairment due to an intrinsically diminished capacity of aged Treg to promote oligodendrocyte differentiation and myelination. This decline in regenerative Treg functions can be rescued by a young environment. We identified Melanoma Cell Adhesion Molecule 1 (MCAM1) and Integrin alpha 2 (ITGA2) as novel candidates of Treg-mediated oligodendrocyte differentiation that decrease with age. Our findings demonstrate that ageing limits the neuroregenerative capacity of Treg, likely limiting their remyelinating therapeutic potential in aged patients, and describe two novel mechanisms implicated in Treg-driven remyelination that may be targetable to overcome this limitation.

neuroscience↗

bioRxiv2022

Theta phase specific modulation of hippocampal memory neurons

I.The theta rhythm, a quasi-periodic 4-10 Hz oscillation, is observed during memory processing in the hippocampus, with different phases of theta hypothesized to separate independent streams of information related to the encoding and recall of memories. At the cellular level, the discovery of hippocampal memory cells (engram neurons), as well as the modulation of memory recall through optogenetic activation of these cells, has provided evidence that certain memories are stored, in part, in a sparse ensemble of neurons in the hippocampus. In previous research, however, engram reactivation has been carried out using open loop stimulation at fixed frequencies; the relationship between engram neuron reactivation and ongoing network oscillations has not been taken into consideration. To address this concern, we implemented a closed-loop reactivation of engram neurons that enabled phase-specific stimulation relative to theta oscillations in the local field potential. Using this real-time approach, we tested the impact of activating engram neurons during the peak (encoding phase) and trough (recall phase) of theta oscillations. Consistent with previously hypothesized functions of theta oscillations in memory function, we show that stimulating engram neurons at the trough of theta is more effective in eliciting behavioral recall than either fixed frequency stimulation or stimulation at the peak of theta. Moreover, phase-specific trough stimulation is accompanied by an increase in the coupling between gamma and theta oscillations in CA1 hippocampus. Oure results provide a causal link between phase-specific activation of engram cells and the behavioral expression of memory.

neuroscience↗

bioRxiv2022

Time or distance: predictive coding of Hippocampal cells

The discovery of place cells within the hippocampus has pointed to the importance of the hippocampus for navigation. The more recent discovery of hippocampal time cells has broadened the perspective of encoding in the hippocampus. An alternative hypothesis to the existence of time cells is based on the notion that hippocampal cells deduce location by integrating travelled distance ("path integration"). According to this alternate hypothesis, time cells, which fire at particular times when animals are running on a treadmill without changing location, actually encode accumulated distance on the treadmill. To examine this hypothesis, Kraus et al.1 performed treadmill experiments in which animals either ran for a fixed time or a fixed distance with varying velocities. Two distinct coding modes of hippocampal principal cells were found. Some cells encoded travelled distance and others elapsed time, thus refuting the notion that all hippocampal cells were performing path integration. Using the data from these experiments, we asked whether the two populations depended on the type of task the rats were engaged in. We show that the type of experiment determined the cells encoding, such that in fixed-distance experiments distance-encoding cells dominated, while on fixed-time experiments time-encoding cells dominated. These results suggest that the cells encoding contains a predictive element, dependent on the important variables of the experiment.

neuroscience↗

bioRxiv2022

Interneuronal network model of theta-nested fast oscillations predicts differential effects of heterogeneity, gap junctions and short term depression for hyperpolarizing versus shunting inhibition

Theta and gamma oscillations in the hippocampus have been hypothesized to play a role in the encoding and retrieval of memories. Recently, it was shown that an intrinsic fast gamma mechanism in medial entorhinal cortex can be recruited by optogenetic stimulation at theta frequencies, which can persist with fast excitatory synaptic transmission blocked, suggesting a contribution of interneuronal network gamma (ING). We calibrated the passive and active properties of a 100-neuron model network to capture the range of passive properties and frequency/current relationships of experimentally recorded PV+ neurons in the medial entorhinal cortex (mEC). The strength and probabilities of chemical and electrical synapses were also calibrated using paired recordings, as were the kinetics and short-term depression (STD) of the chemical synapses. Gap junctions that contribute a noticeable fraction of the input resistance were required for synchrony with hyperpolarizing inhibition; these networks exhibited theta-nested high frequencies ([~]200 Hz) similar to the putative ING observed experimentally in the optogenetically-driven PV-ChR2 mice. With STD included in the model, fast oscillations were only observed before the peak of the theta drive, whereas without STD, they were observed symmetrically before and after the peak. Because hyperpolarizing synapses provide a synchronizing drive that contributes to robustness in the presence of heterogeneity, synchronization decreases as the hyperpolarizing inhibition becomes weaker. In contrast, networks with shunting inhibition required non-physiological levels of gap junctions to synchronize using conduction delays within the measured range; synaptic depression of shunting synapses facilitated fast oscillations, suggesting that shunting inhibition in mEC is desynchronizing. Author SummaryFast oscillations nested within slower oscillations have been hypothesized to play a role in the encoding and retrieval of memories by chunking information within each fast cycle; networks of parvalbumin positive inhibitory interneurons contribute to the generation of fast oscillations. We show that, in the entorhinal cortex, the intrinsic dynamical properties of these neurons are sufficiently heterogeneous that electrical synapses are likely required to synchronize fast oscillations. Moreover, synchrony likely requires the chemical synapses to have a reversal potential that is negative relative to the action potential threshold of individual neurons during these oscillations. We show that the range of slow phases that support a fast oscillation is controlled by short term synaptic depression. The precise phase locking of the fast oscillation within the slow oscillations is hypothesized to allow for multiplexing of information.

neuroscience↗

bioRxiv2020

Hippocampal cells multiplex positive and negative engrams

The hippocampus is involved in processing a variety of mnemonic computations specifically the spatiotemporal components and emotional dimensions of contextual memory.1-3 Recent studies have demonstrated vast structural and functional heterogeneity along the dorsal-ventral axis1, 5 of the hippocampus. The ventral hippocampus has been shown to be important in the processing of emotion and valence.6-9 Here, we combine transgenic and all-virus based activity-dependent tagging strategies to visualize multiple valence-specific engrams in the vHPC and demonstrate two partially segregated cell populations and projections that respond to appetitive and aversive experiences. Next, using RNA sequencing and DNA methylation sequencing approaches, we find that vHPC appetitive and aversive engram cells display distinct transcriptional programs and DNA methylation landscapes compared to a neutral engram population. Additionally, while optogenetic manipulation of tagged cell bodies in vHPC is not sufficient to drive appetitive or aversive behavior in real-time place preference, stimulation of tagged vHPC terminals projecting to the amygdala and nucleus accumbens (NAc), but not the prefrontal cortex (PFC), had the capacity drive preference and avoidance. These terminals can also undergo a "switch" or "reset" in their capacity to drive either, thereby demonstrating their adaptable contributions to behavior. We conclude that the vHPC contains genetically, cellularly, and behaviorally distinct populations of cells processing appetitive and aversive memory engrams. Together, our findings provide a novel means by which to visualize multiple engrams within the same brain and point to their unique genetic signatures as reference maps for the future development of new therapeutic strategies. One sentence summaryThe hippocampus contains neurons that correspond to positive and negative engrams, which are segregated by their molecular, cellular, and projection-specific features.

neuroscience↗

bioRxiv2020

Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+ T cells in vivo

Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here we show that it is possible to link antigen responsiveness, full proviral sequence, integration site, and T cell receptor {beta}-chain (TCR{beta}) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated Cytomegalovirus (CMV)- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCR{beta} repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCR{beta}-integration site analysis showed that infection could occur early or late in the course of a clones response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.

microbiology↗

bioRxiv2020

Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally-inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally-inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.

ecology↗

bioRxiv2019

μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells

Genome regulation depends on carefully programmed protein-DNA interactions that maintain or alter gene expression states, often by influencing chromatin organization. Most studies of these interactions to date have relied on bulk methods, which in many systems cannot capture the dynamic single-cell nature of these interactions as they modulate cell states. One method allowing for sensitive single-cell mapping of protein-DNA interactions is DNA adenine methyltransferase identification (DamID), which records a proteins DNA-binding history by methylating adenine bases in its vicinity, then selectively amplifies and sequences these methylated regions. These interaction sites can also be visualized using fluorescent proteins that bind to methyladenines. Here we combine these imaging and sequencing technologies in an integrated microfluidic platform (DamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We apply this system to generate paired single-cell imaging and sequencing data from a human cell line, in which we map and validate interactions between DNA and nuclear lamina proteins, providing a measure of 3D chromatin organization and broad gene regulation patterns. DamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions.

bioengineering↗