Biology subjects

Krishnamurthy, D.

Publications and source records attributed to Krishnamurthy, D..

11 recordsLinked to original sources

bioRxiv2026

Survival Benefits Outweigh Germline Competition Costs in Kin Chimeras

Chimerism, the coexistence of genetically distinct cells within an organism, is a widespread phenomenon in nature. In the colonial chordate Botryllus schlosseri, fusion between compatible colonies can lead to stem cell competition with a single genotype taking over the gonadal and/or somatic tissue of the chimera. Over five years, we quantified the frequency and consequences of chimeric formation among 809 larvae, assessing the rates of fusion after natural settlement and its long-term impact on colony survival. We found larvae preferentially settle near kin, facilitating high rates of successful fusion. Fusion was concentrated around the first month of life, boosting survival during this period of high mortality. At all timepoints chimerism significantly increased survival relative to naive and rejected colonies and extended overall lifespan. However, fusion triggered intense internal competition: in all cases tested, a single genotype achieved dominance over both germline and somatic tissues within several weeks post-fusion, regardless of initial genotype contribution. We estimate that among kin, the survival benefits of chimerism outweigh the potential costs of germline loss, extending Hamiltons kin selection framework to colonial marine organisms. In this context, chimerism functions as an adaptive strategy that enhances early survival while enabling selection among competing stem cell lineages.

evolutionary biology↗

bioRxiv2026

LUCas: Light-Uncaged Cas13a using photocleavable interfering guide RNAs

CRISPR diagnostics have emerged as powerful tools for detecting infectious diseases, with the RNA endonuclease Cas13a enabling sensitive and specific, amplification-free RNA detection through collateral trans-cleavage of fluorescent reporters. However, background cleavage from unbound enzyme, contaminating nucleases, and unsynchronized initiation of reactions limits assay sensitivity and interpretability. A strategy to precisely control the onset of Cas13a catalytic activity, essentially a molecular "starting gun", would address these challenges and expand assay design space. Here, we introduce Light-Uncaged Cas13a (LUCas), a light controllable system that directly gates Cas13a using a photocleavable interfering guide RNA (pc-igRNA) that suppresses trans-cleavage activity even in the presence of target RNA. Brief UV illumination releases this suppression, restoring full activity. Quantitative kinetic analysis reveals an approximately 100-fold suppression of trans-cleavage activity prior to photo-activation. Importantly, LUCas also suppresses target-independent background activity, enabling a predictive, background-limited determination of assay sensitivity. Using measured kinetic parameters, we predict and experimentally validate the limit-of-detection of the LUCas system. Finally, we demonstrate a multiplexed detection strategy termed "temporal barcoding," which enables quantitative detection of viral co-infections in a single bulk reaction. Together, these results establish LUCas as a general framework for mechanistically informed, light-based control of Cas13a activity.

bioengineering↗

bioRxiv2024

Target cell tension regulates macrophage trogocytosis

Macrophages are known to engulf small membrane fragments, or trogocytose, target cells and pathogens, rather than fully phagocytose them. However, little is known about what causes macrophages to choose trogocytosis versus phagocytosis. Here, we report that cortical tension of target cells is a key regulator of macrophage trogocytosis. At low tension, macrophages will preferentially trogocytose antibody-opsonized cells, while at high tension they tend towards phagocytosis. Using model vesicles, we demonstrate that macrophages will rapidly switch from trogocytosis to phagocytosis when membrane tension is increased. Stiffening the cortex of target cells also biases macrophages to phagocytose them, a trend that can be countered by increasing antibody surface density and is captured in a mechanical model of trogocytosis. This work suggests that a distinct molecular pathway for trogocytosis is not required to explain differences in trogocytosis among target cell types and points to a mechanism for target cells to modulate trogocytosis.

biophysics↗

bioRxiv2022

Towards A More Informative Representation of the Fetal-Neonatal Brain Connectome using Variational Autoencoder

Recent advances in functional magnetic resonance imaging (fMRI) have helped elucidate previously inaccessible trajectories of early-life prenatal and neonatal brain development. To date, the interpretation of fetal-neonatal fMRI data has relied on linear analytic models, akin to adult neuroimaging data. However, unlike the adult brain, the fetal and newborn brain develops extraordinarily rapidly, far outpacing any other brain development period across the lifespan. Consequently, conventional linear computational models may not adequately capture these accelerated and complex neurodevelopmental trajectories during this critical period of brain development along the prenatal-neonatal continuum. To obtain a nuanced understanding of fetal-neonatal brain development, including non-linear growth, for the first time, we developed quantitative, systems-wide representations of neuronal circuitry in a large sample (>700) of fetuses, preterm, and full-term neonates using an unsupervised deep generative model called Variational Autoencoder (VAE), a model previously shown to be superior to linear models in representing complex resting state data in healthy adults. Here, we demonstrated that non-linear brain features, i.e., latent variables, derived with the VAE, carried important individual neural signatures, leading to improved representation of prenatal-neonatal brain maturational patterns and more accurate and stable age prediction compared to linear models. Using the VAE decoder, we also revealed distinct functional brain networks spanning the sensory and default mode networks. Using the VAE, we are able to reliably capture and quantify complex, non-linear fetal-neonatal functional neural connectivity. This will lay the critical foundation for detailed mapping of healthy and aberrant functional brain signatures that have their origins in fetal life.

neuroscience↗

bioRxiv2022

Emergent Programmable Behavior and Chaos in Dynamically Driven Active Filaments

AO_SCPLOWBSTRACTC_SCPLOWHow the behavior of single cells emerges from their constituent sub-cellular biochemical and physical parts is an outstanding challenge at the intersection of biology and physics. A remarkable example of single-cell behavior is seen in the ciliate Lacrymaria olor, which hunts by striking its prey via rapid movements and protrusions of a slender neck, many times the size of the original cell body. This dynamics of the cell neck is powered by active injection of energy into this slender filamentous structure via a coat of cilia across its length and specialized cilia at the tip. How a cell can program this dynamical active filament to produce desirable behaviors like search and homing to a target remains unknown. By constructing a coupled active-elastic and hydrodynamic model of a slender filament with activity at the tip, here we uncover how cell behavior (filament shape dynamics) can be controlled via activity dynamics. Our model captures two key features of this system - dynamic activity patterns (extension and compression cycles) and active stresses that are uniquely aligned with the filament geometry - leading to a so-called "follower force" constraint. We show that active filaments under deterministic, time-varying follower forces display rich behaviors including periodic and aperiodic shape dynamics over long times. We further show that aperiodic dynamics occur due to a transition to chaos in regions of a biologically accessible parameter space. By further dissecting the non-linear dynamics of this active filament system, we discover a simple iterative map of filament shape that predicts long-term behavior. Lastly, using these iterative maps as a design tool, we demonstrate examples of how a cell could "program" filament behaviors by using frequency and amplitude modulated activity patterns. Overall, our results serve as a framework to mechanistically understand behavior in single cells such as L. olor and present a novel chaotic dynamical system in active elastohydrodynamics. Our work also offers a direct framework for designing programmable active matter systems using filament geometries. Significance statementSingle-celled protozoa display remarkable animal-like behaviors without the aid of neurons. Mechanistically understanding how this dynamic behavior emerges from underlying physical and biochemical components is an outstanding challenge. In this work, using an active filament model, we uncover the fundamental non-linear dynamics and non-variational mechanics that underlie the complex behaviors of single cells like Lacrymaria olor. In doing so we discover a novel route to chaos in active elastohydrodynamic systems and the first-ever description of how chaos can drive single-cell behaviors. Lastly, we present a framework for how filament behaviors can be "programmed" using dynamic, modulated activity patterns. Overall our work provides mechanistic insights into single-cell behaviors and offers a new framework for the design of filamentous active matter systems to achieve diverse functions.

biophysics↗

bioRxiv2021

Active Sinking Particles: Sessile Suspension Feeders significantly alter the Flow and Transport to Sinking Aggregates

AO_SCPLOWBSTRACTC_SCPLOWSinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are "active," since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these "active sinking particles," has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical tracking microscopy." Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached Vorticella cause substantial changes to the flow around aggregates in a dynamic manner and reshape mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking significantly changes how aggregates interact with the water-column at larger scales by modifying the encounter and plume cross-sections and by inducing sustained aggregate rotations. In this way our work suggests an important role of biological activity in understanding the growth, degradation, composition and sinking speeds of aggregates with consequences for predicting vertical material fluxes in marine, freshwater and man-made environments. 1 Significance StatementSinking aggregates are a critical part of aquatic ecosystems. Plentiful sinking aggregates account for the majority of carbon sequestration in the oceans. These aggregates are densely colonized by microorganisms, including many that generate feeding currents. Utilizing a novel instrument for high resolution imaging of sinking particles, we demonstrate that these feeding currents significantly change how water flows near the aggregates. We show that these changes in flow are likely to affect aquatic system processes, including aggregation rates, degradation rates, sinking speeds, and aggregate composition. Our work provides a starting point for exploring the larger-scale implications of attached organisms on these system processes, which, in turn, are critical for understanding carbon sequestration in the oceans or efficiency in waste-water treatment plants.

biophysics↗

bioRxiv2020

Squid: Simplifying Quantitative Imaging Platform Development and Deployment

With rapid developments in microscopy methods, highly versatile, robust and affordable implementations are needed to enable rapid and wide adoption by the biological sciences community. Here we report Squid, a quantitative imaging platform with a full suite of hardware and software components and configurations for deploying facility-grade widefield microscopes with advanced features like flat field fluorescence excitation, patterned illumination and tracking microscopy, at a fraction of the cost of commercial solutions. The open and modular nature (both in hardware and in software) lowers the barrier for deployment, and importantly, simplifies development, making the system highly configurable and experiments that can run on the system easily programmable. Developed with the goal of helping translate the rapid advances in the field of microscopy and microscopy-enabled methods, including those powered by deep learning, we envision Squid will simplify roll-out of microscopy-based applications - including at point of care and in low resource settings, make adoption of new or otherwise advanced techniques easier, and significantly increase the available microscope-hours to labs.

bioengineering↗

bioRxiv2019

Interleukin-33 promotes type 1 cytokine expression via p38 MAPK in human natural killer cells

This study tests the hypothesis that activation of mitogen-activated protein kinase (MAPK) by physiologically-relevant concentrations of interleukin-33 (IL-33) contributes to enhanced cytokine expression by IL-12 stimulated human natural killer (NK) cells. While IL-33 canonically triggers type 2 cytokine responses, this cytokine can also synergize with type 1 cytokines like IL-12 to provoke interferon-gamma (IFN-{gamma}). We show that picogram concentrations of IL-12 and IL-33 are sufficient to promote robust secretion of IFN-{gamma} by human NK cells that greatly exceeds responses to either cytokine alone. Nanogram doses of IL-33, potentially consistent with levels in tissue microenvironments, synergize with IL-12 to induce secretion of additional cytokines, including tumor necrosis factor (TNF) and granulocyte-macrophage colony-stimulating factor (GM-CSF). IL-33-induced activation of the p38 MAPK pathway in human NK cells is crucial for enhanced release of IFN-{gamma} and TNF in response to IL-12. Mechanistically, IL-33-induced p38 MAPK signaling enhances stability of IFNG transcripts and triggers ADAM17-mediated cleavage of TNF from the cell surface. These data support our hypothesis and suggest that altered sensitivity of NK cells to IL-12 in the presence of IL-33 may have important consequences in diseases associated with mixed cytokine milieus, like asthma and chronic obstructive pulmonary disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/777847v2_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@c1f7c9org.highwire.dtl.DTLVardef@72d47dorg.highwire.dtl.DTLVardef@dc84d4org.highwire.dtl.DTLVardef@194b42f_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2019

Scale-free Vertical Tracking Microscopy: Towards Bridging Scales in Biological Oceanography

Understanding key biophysical phenomena in the ocean often requires one to simultaneously focus on microscale entities, such as motile plankton and sedimenting particles, while maintaining the macroscale context of vertical transport in a highly stratified environment. This poses a conundrum: How to measure single organisms, at microscale resolution, in the lab, while allowing them to freely move hundreds of meters in the vertical direction? We present a solution in the form of a scale-free, vertical tracking microscope based on a circular \"hydrodynamic-treadmill\". Our technology allows us to transcend physiological and ecological scales, tracking organisms from marine zooplankton to single-cells over vertical scales of meters while resolving microflows and behavioral processes. We demonstrate measurements of sinking particles, including marine snow as they sediment tens of meters while capturing sub-particle-scale phenomena. We also demonstrate depth-patterned virtual-reality environments for novel behavioral analyses of microscale plankton. This technique offers a new experimental paradigm in microscale ocean biophysics by combining physiological-scale imaging with free movement in an ecological-scale patterned environment.\n\nOne sentence summaryScale-free vertical tracking microscopy captures, for the first time, untethered behavioral dynamics at cellular resolution for marine plankton.

biophysics↗

bioRxiv2018

Ddx3x regulates B-cell development and light chain recombination in mice

The X chromosome gene, DDX3X, is an ATP-dependent RNA helicase with roles in transcription, splicing, nuclear export, and translation. Loss of function mutations in DDX3X are linked to a variety of neoplasms, including B-cell lymphoma. We find that conditional homozygous deletion (Mb1-Cre) of Ddx3x in developing mouse B cells in female mice results in a complete absence of mature peripheral B cells associated with an absolute block at the pro-B cell stage of development in the bone marrow. In male mice with Vav1-Cre or Mb1-Cre mediated hemizygous deletion of Ddx3x, there are less severe reductions in peripheral B-cell frequencies with skewing towards the marginal zone lineage, suggesting that the Y chromosome homolog Ddx3y or other male factors may partially compensate for loss of Ddx3x. Loss of Ddx3x in male mice is associated with perturbations at developmental time points linked to cell cycle arrest and immunoglobulin chain rearrangement. Mechanistically, loss of Ddx3x in pre-B cells is associated with reduced expression of the histone reader Brwd1, failure to curtail proliferation, and defective Igk rearrangement, which skews the peripheral B cell receptor repertoire toward lambda light chain usage. These data reveal that Ddx3x plays an essential role in B-cell development by supporting proliferative and epigenetic changes necessary for rearrangement of immunoglobulin genes.

immunology↗

bioRxiv2018

Coupled active systems encode emergent behavioral dynamics of the unicellular predator Lacrymaria olor

Multiple active systems in a cell work together to produce sophisticated cellular behaviors such as motility and search. However, it is often unclear how this coupling specifies the complex emergent dynamics that define such behaviors. As a model system, we analyzed the hunting strategy of Lacrymaria olor, a unicellular predatory ciliate that uses extreme morphological changes to extend, contract and whip an apparent \"cell neck\" over many body lengths to capture prey. Tracking millions of unique subcellular morphologies over time revealed that these fast dynamics encode a comprehensive local search behavior apparent only at longer timescales. This hunting behavior emerges as a tug-of-war between active sub-cellular structures that use surface cilia and cortex contractility to deform the structure of the neck. The resulting search space can be described mathematically using a small number of normal shape modes that change amplitude rapidly during hunts. The distribution of these shape modes in space and time reveals a transition point between tense and compressed neck morphologies at the mean neck length, such that new shapes are readily sampled by repeatedly extending and retracting across this critical length. Molecular perturbations to the cell-signaling controller show that coupling between ciliary and contractile programs is needed to maintain this length/shape relationship; neither system alone provides the dynamic repertoire of shapes necessary for comprehensive search. Our results highlight the utility of coupling antagonistic active systems as a strategy for encoding or engineering complex behaviors in molecular machines.\n\nOne Sentence Summary: Analysis of millions of unique cellular morphologies of the highly dynamic single-celled predator Lacrymaria olor reveals that it programs a comprehensive search space and emergent hunting behavior through coupling surface based active cilia and cortex based contractile molecular systems together.

systems biology↗