Biology subjects

Kar, M.

Publications and source records attributed to Kar, M..

13 recordsLinked to original sources

bioRxiv2026

Prime editing of an evolutionarily informed PEPC residue enhances photosynthesis and grain nutrition in C₃ rice

C4 photosynthesis evolved through adaptive changes in key metabolic enzymes that enhance carbon fixation efficiency, yet transferring such traits into C3 crops has met limited success. Using precision prime editing, we introduced an evolutionarily conserved single amino acid substitution (Arg[->]Gly) into phosphoenolpyruvate carboxylase (PEPC) in rice. Edited plants exhibited enhanced PEPC activity in the presence of the feedback inhibitor malate, increased chlorophyll content, elevated photosynthetic rates under ambient CO2, and increased seed size and weight. Remarkably, seeds from the edited lines showed simultaneous enrichment of zinc (Zn), iron (Fe), and protein, hereafter referred to as ZiP rice. This work demonstrates that a single, evolutionarily guided residue change can reprogram core carbon metabolism in a C3 crop, enabling concurrent improvements in photosynthesis and grain nutritional quality.

plant biology↗

bioRxiv2025

Molecular Matchmakers: How ATP and Small Amphiphilic Molecules Fine-Tune FET Proteins Clusters

FET (FUS-EWSR1-TAF15) family proteins inherently form mesoscale molecular assemblies, known as clusters, under physiological conditions at concentrations well below the threshold for phase separation. This study demonstrates that adenosine triphosphate (ATP), an amphiphilic molecule and essential cellular metabolite, modulates the size of these sub-saturation mesoscale clusters in a concentration-dependent manner. At low concentrations (1-2 mM), ATP acts as a crosslinker for FET proteins, resulting in larger size clusters. At moderate concentrations (5 mM), the size of the clusters decreases but stabilizes. At high concentrations (10 mM), the cluster size further diminishes. Other amphiphilic molecules, including common hydrotropes like sodium xylene sulfonate, sodium toluene sulfonate, and hexanediol, exhibit comparable concentration-dependent effects on FET protein clustering. Notably, these effects cannot be explained solely by hydrotropic or kosmotropic mechanisms; instead, they stem from non-specific interactions between proteins and small molecules. The intrinsic chemical properties of the amphiphilic molecules and FET proteins play a crucial role in regulating mesoscale cluster formation at sub-saturation concentrations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/649119v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@90de68org.highwire.dtl.DTLVardef@f9bcb5org.highwire.dtl.DTLVardef@1d42e59org.highwire.dtl.DTLVardef@12eed97_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Eosinophils protect against SARS-CoV-2 following a vaccine breakthrough infection

Waning immunity and the emergence of immune evasive SARS-CoV-2 variants jeopardize vaccine efficacy leading to breakthrough infections. We have previously shown that innate immune cells play a critical role in controlling SARS-CoV-2. To investigate the innate immune response during breakthrough infections, we modeled breakthrough infections by challenging low-dose vaccinated mice with a vaccine-mismatched SARS-CoV-2 Beta variant. We found that low-dose vaccinated infected mice had a 2-log reduction in lung viral burden, but increased immune cell infiltration in the lung parenchyma, characterized by monocytes, monocyte-derived macrophages, and eosinophils. Single cell RNA-seq revealed viral RNA was highly associated with eosinophils that corresponded to a unique IFN-{gamma} biased signature. Antibody-mediated depletion of eosinophils in vaccinated mice resulted in increased virus replication and dissemination in the lungs, demonstrating that eosinophils in the lungs are protective during SARS-CoV-2 breakthrough infections. These results highlight the critical role for the innate immune response in vaccine mediated protection against SARS-CoV-2.

immunology↗

bioRxiv2024

CD4+ and CD8+ T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment

SARS-CoV-2 is the causative agent of COVID-19 and continues to pose a significant public health threat throughout the world. Following SARS-CoV-2 infection, virus-specific CD4+ and CD8+ T cells are rapidly generated to form effector and memory cells and persist in the blood for several months. However, the contribution of T cells in controlling SARS-CoV-2 infection within the respiratory tract are not well understood. Using C57BL/6 mice infected with a naturally occurring SARS-CoV-2 variant (B.1.351), we evaluated the role of T cells in the upper and lower respiratory tract. Following infection, SARS-CoV-2-specific CD4+ and CD8+ T cells are recruited to the respiratory tract and a vast proportion secrete the cytotoxic molecule Granzyme B. Using antibodies to deplete T cells prior to infection, we found that CD4+ and CD8+ T cells play distinct roles in the upper and lower respiratory tract. In the lungs, T cells play a minimal role in viral control with viral clearance occurring in the absence of both CD4+ and CD8+ T cells through 28 days post-infection. In the nasal compartment, depletion of both CD4+ and CD8+ T cells, but not individually, results in persistent and culturable virus replicating in the nasal compartment through 28 days post-infection. Using in situ hybridization, we found that SARS-CoV-2 infection persisted in the nasal epithelial layer of tandem CD4+ and CD8+ T cell-depleted mice. Sequence analysis of virus isolates from persistently infected mice revealed mutations spanning across the genome, including a deletion in ORF6. Overall, our findings highlight the importance of T cells in controlling virus replication within the respiratory tract during SARS-CoV-2 infection.

immunology↗

bioRxiv2023

Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions

Multivalent proteins undergo coupled segregative and associative phase transitions. Phase separation, a segregative transition, is driven by macromolecular solubility, and this leads to coexisting phases above system-specific saturation concentrations. Percolation is a continuous transition that is driven by multivalent associations among cohesive motifs. Contributions from percolation are highlighted by the formation of heterogeneous distributions of clusters in sub-saturated solutions, as was recently reported for Fused in sarcoma (FUS) and FET family proteins. Here, we show that clustering and phase separation are defined by a separation of length- and energy-scales. This is unmasked when glutamate is the primary solution anion. Glutamate is preferentially excluded from protein sites, and this enhances molecular associations. Differences between glutamate and chloride are manifest at ultra-low protein concentrations. These differences are amplified as concentrations increase, and they saturate as the micron-scale is approached. Therefore, condensate formation in supersaturated solutions and clustering in sub-saturated are governed by distinct energy and length scales. Glutamate, unlike chloride, is the dominant intracellular anion, and the separation of scales, which is masked in chloride, is unmasked in glutamate. Our work highlights how components of cellular milieus and sequence-encoded interactions contribute to amplifying distinct contributions from associative versus segregative phase transitions.

biophysics↗

bioRxiv2023

Condensate partitioning governs the mechanism of action of FUS phase separation modulators

Biomolecular phase separation plays a pivotal role in governing critical biological functions and arises from the collective interactions of large numbers of molecules. Characterising the underlying collective interactions of phase separation, however, has proven to be challenging with currently available tools. Here, we propose a general and easily accessible strategy to quantify collective interactions in biomolecular phase separation with respect to composition and energetics. By measuring the dilute phase concentration of one species only, we determine tie line gradients and free energy dominance as dedicated descriptors of collective interactions. We apply this strategy to dissect the role of salts and small molecules on phase separation of the protein fused in sarcoma (FUS). We discover that monovalent salts can display both exclusion from or preferential partitioning into condensates to either counteract charge screening or enhance non-ionic interactions. Moreover, we show that the common hydrophobic interaction disruptor 1,6-hexanediol inhibits FUS phase separation by acting as a solvation agent capable of expanding the protein polypeptide chain. Taken together, our work presents a widely applicable strategy that enables quantification of collective interactions and provides unique insights into the underlying mechanisms of condensate formation and modulation.

biophysics↗

bioRxiv2022

Vocalization categorization behavior explained by a feature-based auditory categorization model

Vocal animals produce multiple categories of calls with high between- and within-subject variability, over which listeners must generalize to accomplish call categorization. The behavioral strategies and neural mechanisms that support this ability to generalize are largely unexplored. We previously proposed a theoretical model that accomplished call categorization by detecting features of intermediate complexity that best contrasted each call category from all other categories. We further demonstrated that some neural responses in the primary auditory cortex were consistent with such a model. Here, we asked whether a feature-based model could predict call categorization behavior. We trained both the model and guinea pigs on call categorization tasks using natural calls. We then tested categorization by the model and guinea pigs using temporally and spectrally altered calls. Both the model and guinea pigs were surprisingly resilient to temporal manipulations, but sensitive to moderate frequency shifts. Critically, model performance quantitatively matched guinea pig behavior to a remarkable degree. By adopting different model training strategies and examining features that contributed to solving specific tasks, we could gain insight into possible strategies used by animals to categorize calls. Our results validate a model that uses the detection of intermediate-complexity contrastive features to accomplish call categorization.

neuroscience↗

bioRxiv2022

Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions

Macromolecular phase separation is thought to be one of the processes that drives the formation of membraneless biomolecular condensates in cells. The dynamics of phase separation, especially at low endogenous concentrations found in cells, are thought to follow the tenets of classical nucleation theory describing a sharp transition between a dense phase and a dilute phase characterized by dispersed monomers. Here, we used in vitro biophysical studies to study subsaturated solutions of phase separating RNA binding proteins with intrinsically disordered prion like domains (PLDs) and RNA binding domains (RBDs). Surprisingly, we find that subsaturated solutions are characterized by heterogeneous distributions of clusters comprising tens to hundreds of molecules. These clusters also include low abundance mesoscale species that are several hundreds of nanometers in diameter. Our results show that cluster formation in subsaturated solutions and phase separation in supersaturated solutions are strongly coupled via sequence-encoded interactions. Interestingly, however, cluster formation and phase separation can be decoupled from one another using solutes that impact the solubilities of phase separating proteins. They can also be decoupled by specific types of mutations. Overall, our findings implicate the presence of distinct, sequence-specific energy scales that contribute to the overall phase behaviors of RNA binding proteins. We discuss our findings in the context of theories of associative polymers. Significance StatementMembraneless biomolecular condensates are molecular communities with distinct compositional preferences and functions. Considerable attention has focused on phase separation as the process that gives rise to condensates. Here, we show that subsaturated solutions of RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions. The formation of clusters in subsaturated solutions and condensates in supersaturated solution are coupled through sequence-specific interactions. Given the low endogenous concentrations of phase separating proteins, our findings suggest that clusters in subsaturated conditions might be of functional relevance in cells.

biophysics↗

bioRxiv2021

A complex feature-based representation of vocalizations emerges in the superficial layers of primary auditory cortex

Early in auditory processing, neural responses faithfully reflect acoustic input. At higher stages of auditory processing, however, neurons become selective for particular call types, eventually leading to specialized regions of cortex that preferentially process calls at the highest auditory processing stages. We previously proposed that an intermediate step in how non-selective responses are transformed into call-selective responses is the detection of informative call features. But how neural selectivity for informative call features emerges from non-selective inputs, whether feature selectivity gradually emerges over the processing hierarchy, and how stimulus information is represented in non-selective and feature-selective populations remain open questions. In this study, using unanesthetized guinea pigs, a highly vocal and social rodent, as an animal model, we characterized the neural representation of calls in three auditory processing stages - the thalamus (vMGB), and thalamorecipient (L4) and superficial layers (L2/3) of primary auditory cortex (A1). We found that neurons in vMGB and A1 L4 did not exhibit call-selective responses and responded throughout the call durations. However, A1 L2/3 neurons showed high call-selectivity with about a third of neurons responding to only one or two call types. These A1 L2/3 neurons only responded to restricted portions of calls suggesting that they were highly selective for call features. Receptive fields of these A1 L2/3 neurons showed complex spectrotemporal structures that could underlie their high call feature selectivity. Information theoretic analysis revealed that in A1 L4 stimulus information was distributed over the population and was spread out over the call durations. In contrast, in A1 L2/3, individual neurons showed brief bursts of high stimulus-specific information, and conveyed high levels of information per spike. These data demonstrate that a transformation in the neural representation of calls occurs between A1 L4 and A1 L2/3, leading to the emergence of a feature-based representation of calls in A1 L2/3. Our data thus suggest that observed cortical specializations for call processing emerge in A1, and set the stage for further mechanistic studies.

neuroscience↗

bioRxiv2020

Pupillometry as a reliable metric of auditory detection and discrimination across diverse stimulus paradigms in animal models

Estimates of detection and discrimination thresholds are often used to explore broad perceptual similarities between human subjects and animal models. Pupillometry shows great promise as a non-invasive, easily-deployable method of comparing human and animal thresholds. Using pupillometry, previous studies in animal models have obtained threshold estimates to simple stimuli such as pure tones, but have not explored whether similar pupil responses can be evoked by complex stimuli, what other stimulus contingencies might affect stimulus-evoked pupil responses, and if pupil responses can be modulated by experience or short-term training. In this study, we used an auditory oddball paradigm to estimate detection and discrimination thresholds across a wide range of stimuli in guinea pigs. We demonstrate that pupillometry yields reliable detection and discrimination thresholds across a range of simple (tones) and complex (conspecific vocalizations) stimuli; that pupil responses can be robustly evoked using different stimulus contingencies (low-level acoustic changes, or higher level categorical changes); and that pupil responses are modulated by short-term training. These results lay the foundation for using pupillometry as a high-throughput method of estimating thresholds in large experimental cohorts, and unveil the full potential of using pupillometry to explore broad similarities between humans and animal models.

animal behavior and cognition↗

bioRxiv2019

Rapid adaptation to elevated extracellular potassium in the pyloric circuit of the crab, Cancer borealis

Elevated [K+] is often used to alter excitability in neurons and networks by shifting the potassium equilibrium potential (EK) and, consequently, the resting membrane potential. We studied the effects of increased extracellular [K+] on the well-described pyloric circuit of the crab, Cancer borealis. A 2.5-fold increase in extracellular [K+] (2.5x[K+]) depolarized Pyloric Dilator (PD) neurons and resulted in short-term loss of their normal bursting activity. This period of silence was followed within 5-10 minutes by the recovery of spiking and/or bursting activity during continued superfusion of 2.5x[K+] saline. In contrast, when PD neurons were pharmacologically isolated from pyloric presynaptic inputs, they exhibited no transient loss of spiking activity in 2.5x[K+], suggesting the presence of an acute inhibitory effect mediated by circuit interactions. Action potential threshold in PD neurons hyperpolarized during an hour-long exposure to 2.5x[K+] concurrent with the recovery of spiking and/or bursting activity. Thus, the initial loss of activity appears to be mediated by synaptic interactions within the network, but the secondary adaptation depends on changes in the intrinsic excitability of the pacemaker neurons. The complex sequence of events in the responses of pyloric neurons to elevated [K+] demonstrates that electrophysiological recordings are necessary to determine both the transient and longer-term effects of even modest alterations of K+ concentrations on neuronal activity. Significance StatementSolutions with elevated extracellular potassium are commonly used as a depolarizing stimulus. Moreover, hyperkalemia is associated with a number of disease states, including epileptic seizures and brain traumas. We studied the effects of high [K+] saline on the well-described pyloric circuit of the crab stomatogastric ganglion. A 2.5-fold increase in extracellular [K+] led to a transient loss of activity in pyloric neurons that was not due to depolarization block. This was followed by a rapid increase in excitability and concurrent recovery of spiking and rhythmic bursting activity within minutes. These results suggest that effects of high [K+] on neuronal circuits can be complex and non-stationary.

neuroscience↗

bioRxiv2018

Active gelation breaks time-reversal-symmetry of mitotic chromosome mechanics

In cell division, mitosis is the phase in which duplicated sets of chromosomes are mechanically aligned to form the metaphase plate before being segregated in two daughter cells. Irreversibility is a hallmark of this process, despite the fundamental laws of Newtonian mechanics being time symmetric.\n\nHere we show experimentally that mitotic chromosomes receive the arrow of time by time-reversal-symmetry breaking of the underlying mechanics in prometaphase. By optically inducing hydrodynamic flows within prophase nuclei, we find that duplicated chromatid pairs initially form a fluid suspension in the nucleoplasm: although showing little motion on their own, condensed chromosomes are free to move through the nucleus in a time-reversible manner. Actively probing chromosome mobility further in time, we find that this viscous suspension of chromatin transitions into a gel after nuclear breakdown. This gel state, in which chromosomes cannot be moved by flows, persists even when chromosomes start moving to form the metaphase plate. Complemented by minimal reconstitution experiments, our active intra-nuclear micro-rheology reveals time-reversal-symmetry breaking of chromosome mechanics to be caused by the transition from a purely fluid suspension into an active gel.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC=\"FIGDIR/small/296566_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@15b00edorg.highwire.dtl.DTLVardef@199eb2dorg.highwire.dtl.DTLVardef@1f0550org.highwire.dtl.DTLVardef@95cb5a_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryFlows induced in living cell nuclei reveal the rheological changes that bring chromosomes under mechanical control during mitosis.

biophysics↗

bioRxiv2018

Compartmentalized RNA catalysis in membrane - free coacervate protocells

Phase separation of mixtures of oppositely charged polymers provides a simple and direct route to compartmentalization via coacervation, which may have been important for driving primitive reactions as part of the RNA world hypothesis. However, to date, RNA catalysis has not been reconciled with coacervation. Here we demonstrate that RNA catalysis is viable within coacervate microdroplets and further show that these membrane-free droplets can selectively retain longer length RNAs while permitting transfer of lower molecular weight oligonucleotides.

biophysics↗