Biology subjects

Kim, R.

Publications and source records attributed to Kim, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Learning and language in the unconscious human hippocampus

Consciousness is a fundamental component of cognition,1 but the degree to which higher-order pattern recognition relies on it remains disputed.2,3 Here we demonstrate the persistence of oddball discrimination, semantic processing, and online prediction in individuals under general anesthesia-induced loss of consciousness.4,5 Using high-density Neuropixels microelectrodes6 to record both single unit and local field potential neural activity in the human hippocampus while playing a series of tones to anesthetized patients, we found that hippocampal neurons and local oscillations retained some detection of oddball tones. This effect size grew over the course of the experiment ([~]10 minutes), demonstrating representational plasticity. A biologically plausible recurrent neural network model showed that learning and oddball representation are an emergent property of flexible tone discrimination. Moreover, when we played language stimuli, single units and local field potentials carried information about the semantic and grammatical features of natural speech, even predicting semantic information about upcoming words. Together these results indicate that in the hippocampus, which is anatomically and functionally distant from primary sensory cortices,7 complex processing of sensory stimuli occurs even in the unconscious state.

neuroscience↗

bioRxiv2025

Motion-corrected eye tracking (MoCET) improves gaze accuracy during visual fMRI experiments

Human eye movements are essential for understanding cognition, yet achieving high-precision eye tracking in fMRI remains challenging. Even slight head shifts from the initial calibration position can introduce drift in eye tracking data, leading to substantial gaze inaccuracies. To address this, we introduce Motion-Corrected Eye Tracking (MoCET), a novel approach that corrects drift using head motion parameters derived from the preprocessing of fMRI data. MoCET requires no additional hardware and can be applied retrospectively to existing datasets. We show that it outperforms traditional detrending methods with respect to accuracy of gaze estimation and offers higher spatial and temporal precision compared to MR-based eye tracking approaches. By overcoming a key limitation in integrating eye tracking with fMRI, MoCET facilitates investigations of naturalistic vision and cognition in fMRI research.

neuroscience↗

bioRxiv2025

Neutrophil arrest in myocardial capillaries drives hypoxia and impairs diastolic function in a mouse model of heart failure with preserved ejection fraction

Impairments in myocardial blood flow have been recognized for decades in human patients with and animal models of heart failure with preserved ejection fraction (HFpEF), but the underlying mechanisms and roles in pathogenesis remain poorly understood. Using intravital cardiac microcopy in a two-hit mouse model of HFpEF that combines high fat diet and inhibition of nitric oxide synthase, we identified an increase in slow or non-flowing neutrophils in capillaries compared to Control mice. In other mouse models of disease (e.g., in the brain of Alzheimers Disease mice), the presence of such stalled neutrophils leads to organ-wide decreases in perfusion and oxygenation. Administration of antibodies against the neutrophil surface protein Ly6G to deplete neutrophils reduced the number of arrested neutrophils in myocardial capillaries, leading to improvements in myocardial hypoxia, diastolic function, and exercise capacity. This study identifies a previously uncharacterized cellular mechanism that explains myocardial blood flow deficits in mouse models of HFpEF, and demonstrates that improving myocardial blood flow improves cardiac function, without necessitating reversal of pathologic remodeling. Restoring myocardial perfusion by decreasing neutrophil arrest in myocardial capillaries may provide a strategy for improving heart function in HFpEF patients in the future.

physiology↗

bioRxiv2024

Neutrophil extracellular traps promote tumor chemoresistance to anthracyclines

The microenvironment plays an important role in promoting tumor cell chemoresistance, but the mechanisms responsible for this effect are not clear. Here, using models of multiple myeloma (MM) and solid cancers, we demonstrate a novel mechanism mediated by neutrophils, a major cell population in the bone marrow (BM), that protects cancer cells from chemotherapeutics. We show that in response to tumor-derived soluble factors, BM neutrophils release their DNA in the form of neutrophil extracellular traps (NETs). Cell-free DNA derived from NETs is then taken up by tumor cells via endocytosis and localizes to the cytoplasm. We found that both NETs and cell-free DNA taken up by tumor cells can bind anthracyclines, leading to tumor cell resistance to this class of chemotherapeutic agents. Targeting cell-free DNA with Pulmozyme or blocking NET formation with a PAD4 inhibitor abrogates the chemoprotective effect of neutrophils and restores sensitivity of tumor cells to anthracyclines.

cancer biology↗

bioRxiv2024

Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography

Influenza viruses are enveloped, negative sense single-stranded RNA viruses covered in a dense layer of glycoproteins. Hemagglutinin (HA) accounts for 80-90% of influenza glycoprotein and plays a role in host cell binding and membrane fusion. While previous studies have characterized structures of receptor-free and receptor-bound HA in vitro, the effect of receptor binding on HA organization and structure on virions remains unknown. Here, we used cryo-electron tomography (cryoET) to visualize influenza virions bound to a sialic acid receptor mimic. Overall, receptor binding did not result in significant changes in viral morphology; however, we observed rearrangements of HA trimer organization and orientation. Compared to the even inter-glycoprotein spacing of unliganded HA trimers, receptor binding promotes HA trimer clustering and formation of a triplet of trimers. Subtomogram averaging and refinement yielded 8-10 [A] reconstructions that allowed us to visualize specific contacts between HAs from neighboring trimers and identify molecular features that mediate clustering. Taken together, we present new structural evidence that receptor binding triggers clustering of HA trimers, revealing an additional layer of HA dynamics and plasticity.

biophysics↗

bioRxiv2024

Highly sensitive mapping of in vitro type II topoisomerase DNA cleavage sites with SHAN-seq

Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seqs exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.

biochemistry↗

bioRxiv2024

Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer

While colorectal cancer (CRC) patients with microsatellite instability (MSI) respond well to immunotherapy those with microsatellite stable (MSS) tumors rely on conventional chemotherapy, often with poor outcomes. Both types frequently carry mutations in KRAS or BRAF proto-oncogenes, rendering them more resistant to treatment. New therapeutic biomarkers and treatments remain a clinical need, especially for MSS tumors. We performed whole exome and RNA-Sequencing from 28 tumors of the Athens Comprehensive Cancer Center CRC cohort, and molecularly characterized colorectal cancer patients based on their MSI status, SNVs/CNAs, and pathway/transcription factor activities at the individual patient level. Variants were classified using a new computational score for integrative cancer variant annotation and prioritization. Complementing this molecular data with public multi-omics datasets, we identified activation of transforming growth factor beta (TGF{beta}) signaling to be stronger activated in the MSS patients whereas JAK-STAT and MAPK molecular cascades were activated specifically in MSI. We unraveled mechanisms consistently perturbed in the transcriptional and mutational circuits and identified RUNX transcription factors as putative novel targets. Assessing the immunogenicity of CRC tumors in the context of RAS/RAF mutations and MSI/MSS status revealed a critical impact KRAS mutations have on immunogenicity particularly in the MSS patient subgroup, with implications for diagnosis and treatment.

cancer biology↗

bioRxiv2024

Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus

We recently described the evolution of a community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 variant responsible for an outbreak of skin and soft tissue infections. Acquisition of a mosaic version of the {Phi}11 prophage (m{Phi}11) that increases skin abscess size was an early step in CA-MRSA adaptation that primed the successful spread of the clone. The present report shows how prophage m{Phi}11 exerts its effect on virulence for skin infection without encoding a known toxin or fitness genes. Abscess size and skin inflammation were associated with DNA methylase activity of an m{Phi}11-encoded adenine methyltransferase (designated pamA). pamA increased expression of fibronectin-binding protein A (fnbA; FnBPA), and inactivation of fnbA eliminated the effect of pamA on abscess virulence without affecting strains lacking pamA. Thus, fnbA is a pamA-specific virulence factor. Mechanistically, pamA was shown to promote biofilm formation in vivo in skin abscesses, a phenotype linked to FnBPAs role in biofilm formation. Collectively, these data reveal a novel mechanism--epigenetic regulation of staphylococcal gene expression--by which phage can regulate virulence to drive adaptive leaps by S. aureus. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/589803v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@b97d6forg.highwire.dtl.DTLVardef@1da30f1org.highwire.dtl.DTLVardef@1c34311org.highwire.dtl.DTLVardef@6834df_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Evaluation of intracochlear pressure and distribution during fluid application in cochlea models and human petrous bone

IntroductionThe important factor during the application of substances for an inner ear therapy is the atraumatic execution as well as a homogeneous distribution over the cochlea in a reasonable time frame. Since faster delivery can be obtained with higher pressure but, higher pressure will lead to traumatic execution, there are certain constrains for the delivery process. Because of this, an optimized procedure for intracochlear delivery is needed, which enables reduction of intracochlear pressure during perfusion in reasonable time. Hence, the aim of this study was to compare different techniques of substance application and their effects on intracochlear pressure in different models. Material and MethodsIntracochlear pressure was measured by fiberoptic pressure sensors in artificial cochlea models and in a human temporal bone. The pressure sensor was introduced into the inner ear models via an additional channel or the lateral arcade of the temporal bone. In all models the substance was applied by means of an inner ear catheter (MED-EL, Innsbruck, Austria) via the round window with methylene blue with or without second access to the cochlea (helicotrema/oval window). ResultsThe application of substances showed significant differences in intracochlear pressure and substance distribution at the same velocity between the models with and without second access. ConclusionUsing a second-hole technique leads to a faster homogeneous distribution, as well as a lower intracochlear pressure, which can be assumed to be an essential factor for hearing preservation during substance application.

biophysics↗

bioRxiv2024

Neural Manifold Capacity Captures Representation Geometry, Correlations, and Task-Efficiency Across Species and Behaviors

From an eagle spotting a fish in shimmering water to a scientist extracting patterns from noisy data, many cognitive tasks require untangling overlapping signals. Neural circuits achieve this by transforming complex sensory inputs into distinct, separable representations that guide behavior. Data-visualization techniques convey the geometry of these transformations, and decoding approaches quantify performance efficiency. However, we lack a framework for linking these two key aspects. Here we address this gap by introducing a data-driven analysis framework, which we call Geometry Linked to Untangling Efficiency (GLUE) with manifold capacity theory, that links changes in the geometrical properties of neural activity patterns to representational untangling at the computational level. We applied GLUE to over seven neuroscience datasets--spanning multiple organisms, tasks, and recording techniques--and found that task-relevant representations untangle in many domains, including along the cortical hierarchy, through learning, and over the course of intrinsic neural dynamics. Furthermore, GLUE can characterize the underlying geometric mechanisms of representational untangling, and explain how it facilitates efficient and robust computation. Beyond neuroscience, GLUE provides a powerful framework for quantifying information organization in data-intensive fields such as structural genomics and interpretable AI, where analyzing high-dimensional representations remains a fundamental challenge.

neuroscience↗

bioRxiv2024

A multi-institutional study to investigate the sparing effect after whole brain electron FLASH in mice: Reproducibility and temporal evolution of functional, electrophysiological, and neurogenic endpoints

PurposeUltra-high dose-rate radiotherapy (FLASH) has been shown to mitigate normal tissue toxicities associated with conventional dose rate radiotherapy (CONV) without compromising tumor killing in preclinical models. A prominent challenge in preclinical radiation research, including FLASH, is validating both the physical dosimetry and the biological effects across multiple institutions. MethodsWe previously demonstrated dosimetric reproducibility of two different electron FLASH devices at separate institutions using standardized phantoms and dosimeters. In this study, we compared the outcome of FLASH and CONV 10 Gy whole brain irradiation on female adult mice at both institutions to evaluate the reproducibility and temporal evolution of multiple endpoints. ResultsFLASH sparing of behavioral performance on novel object recognition (4 months post-irradiation) and electrophysiologic long-term potentiation (LTP, 5-months post-irradiation) was reproduced between institutions. Interestingly, differences between FLASH and CONV on the endpoints of hippocampal neurogenesis (Sox2, doublecortin), neuroinflammation (microglial activation), and electrophysiology (LTP) at late times were not observed at early times. ConclusionsIn summary, we demonstrated reproducible FLASH sparing effects between two beams and two institutions with validated dosimetry. FLASH sparing effects on the endpoints evaluated manifested at late but not early time points.

cancer biology↗

bioRxiv2024

Whole-cortex simulation reveals spatiotemporal patterns emerging from the interplay of network connectivity and intracellular dynamics

Recent advances in Graphics Processing Unit (GPU) computing have allowed for computational models of whole-brain activity at unprecedented scales. In this work, we use desktop computers to build and simulate a whole-cortex mouse brain model using Hodgkin-Huxley type models for all the most active neurons in the mouse cortex. We compare the model dynamics over different types of connectivity, ranging from uniform random to realistic connectivity derived from experimental data on cell positions and the Allen Brain Atlas. By changing the external drive and coupling strength of neurons in the network, we can produce a wide range of oscillations in the gamma through delta bands. While the global mean-field behaviors of different connectivities share some similarities, an experimentally determined hierarchical connectivity allows for complex, heterogeneous behaviors typically seen in EEG recordings that are not observed in networks with nearest neighbors or uniform coupling. Moreover, our simulations reveal a wide range of spatiotemporal patterns, such as rotational or planar traveling waves, that are observed in experiments. Different traveling waves are observed with different connectivity and coupling strengths on the same connectivity. Our simulations show that many cortical behaviors emerge at scale with the full complexity of the network structure and ionic dynamics. We also provide a computational framework to explore these cortex- wide behaviors further.

neuroscience↗

bioRxiv2023

Whole-genome sequences reveal zygotic composition in chimeric twins

The monochorionic placenta in dizygotic twins allows in utero exchange of embryonic cells, resulting in chimerism in the twins. In practice, this chimerism is incidentally identified on mixed ABO blood types or in the presence of cells with a discordant sex chromosome. Here, we applied whole-genome sequencing to one triplet and one twin families to precisely understand their zygotic compositions, using millions of genomic variants as barcodes of zygotic origins. Peripheral blood showed asymmetrical contributions from two sister zygotes, where one of the zygotes was the major clone in both twins. Single-cell RNA sequencing of peripheral blood tissues further showed differential contributions from the two sister zygotes across blood cell types. In contrast, buccal tissues were pure in genetic composition, suggesting that in utero cellular exchanges were confined to the blood tissues. Our study illustrates the cellular history of twinning during human development, which is critical for managing the health of chimeric individuals in the era of genomic medicine.

genomics↗

bioRxiv2023

Antibody-based immunotherapy targeting FAM19A5 reverses synaptic loss and improves cognitive function in Alzheimer's disease.

IntroductionAlzheimers disease (AD) is characterized by the dysregulation of synaptic balance, with progressive loss of synapses outpacing formation, ultimately leading to cognitive decline. However, the lack of effective strategies for restoring lost synapses poses a major barrier to improving clinical outcomes. MethodsWe developed NS101, a monoclonal antibody targeting FAM19A5, a brain-secreted protein. Its preclinical efficacy in restoring synapses and cognition was evaluated using APP/PS1 and P301S mice. The clinical safety and target engagement of NS101 were examined in human participants. ResultsFAM19A5 binds to LRRC4B, a postsynaptic adhesion molecule, leading to synapse reduction. Blocking this interaction with NS101 normalized the rate of synapse elimination in AD mice. This synaptic rebalancing restored the number and function of synapses, resulting in improved cognition. Systemically administered NS101 facilitated the transport of brain FAM19A5 into the bloodstream. DiscussionTargeting FAM19A5 may hold clinical promise for treating AD by restoring synaptic balance.

neuroscience↗

bioRxiv2023

Top-down signaling dynamically mediates information processing in biologically inspired RNNs

Recent studies have proposed employing biologically plausible recurrent neural networks (RNNs) to investigate flexible decision-making in the brain. However, the mechanisms underlying the integration of bottom-up sensory inputs and temporally varying top-down factors (such as task instructions and selective attention) remain poorly understood, both within the context of these models and the brain. To address this knowledge gap, we trained biologically inspired RNNs on complex cognitive tasks that require adaptive integration of these factors. Through comprehensive analyses of RNNs and neural activity from mouse primary visual cortex, we show that sensory neurons in low-level areas possess the remarkable ability to multiplex and dynamically combine both bottom-up and top-down information via local inhibitory-to-inhibitory connections. Our results shed light on the role of disinhibitory circuits in the intricate interplay between bottom-up and top-down factors to enable flexible decision processes.

neuroscience↗

bioRxiv2023

Distinct subpopulations of ventral pallidal cholinergic neurons encode valence of olfactory stimuli

The ventral pallidum (VP) mediates motivated behaviors largely via the action of VP GABA and glutamatergic neurons. In addition to these neuronal subtypes, there is a population of cholinergic projection neurons in the VP, whose functional significance remains unclear. To understand the functional role of VP cholinergic neurons, we first examined behavioral responses to an appetitive (APP) odor that elicited approach, and an aversive (AV) odor that led to avoidance. To examine how VP cholinergic neurons were engaged in APP vs. AV responses, we used an immediate early gene marker and in-vivo fiber photometry, examining the activation profile of VP cholinergic neurons in response to each odor. Exposure to each odor led to an increase in the number of cFos counts and increased calcium signaling of VP cholinergic neurons. Activity and cre-dependent viral vectors were designed to label engaged VP cholinergic neurons in two distinct contexts: (1) exposure to the APP odor, (2) followed by subsequent exposure to the AV odor, and vice versa. These studies revealed two distinct, non-overlapping subpopulations of VP cholinergic neurons: one activated in response to the APP odor, and a second distinct population activated in response to the AV odor. These two subpopulations of VP cholinergic neurons are spatially intermingled within the VP, but show differences in electrophysiological properties, neuronal morphology, and projections to the basolateral amygdala. Although VP cholinergic neurons are engaged in behavioral responses to each odor, VP cholinergic signaling is only required for approach behavior. Indeed, inhibition of VP cholinergic neurons not only blocks approach to the APP odor, but reverses the behavior, leading to active avoidance. Our results highlight the functional heterogeneity of cholinergic projection neurons within the VP. These two subpopulations of VP cholinergic neurons differentially encode valence of olfactory stimuli and play unique roles in approach and avoidance behaviors.

neuroscience↗

bioRxiv2023

Sex Chromosomes and Gonads Shape the Sex-Biased Transcriptomic Landscape in Tlr7-Mediated Demyelination During Aging

Demyelination occurs in aging and associated diseases, including Alzheimers disease. Several of these diseases exhibit sex differences in prevalence and severity. Biological sex primarily stems from sex chromosomes and gonads releasing sex hormones. To dissect mechanisms underlying sex differences in demyelination of aging brains, we constructed a transcriptomic atlas of cell type-specific responses to illustrate how sex chromosomes, gonads, and their interaction shape responses to demyelination. We found that sex-biased oligodendrocyte and microglial responses are driven by interaction of sex chromosomes and gonads prior to myelin loss. Post demyelination, sex chromosomes mainly guide microglial responses, while gonadal composition influences oligodendrocyte signaling. Significantly, ablation of the X-linked gene Toll-like receptor 7 (Tlr7), which exhibited sex-biased expression during demyelination, abolished the sex-biased responses and protected against demyelination. One-sentence summaryCell type-specific processes underlying aged demyelination are sex-biased and mediated by Tlr7.

neuroscience↗

bioRxiv2023

SARS-CoV-2 ORF8 modulates lung inflammation and clinical disease progression

The virus severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the causative agent of the current COVID-19 pandemic. It possesses a large 30 kilobase (kb) genome that encodes structural, non-structural, and accessory proteins. Although not necessary to cause disease, these accessory proteins are known to influence viral replication and pathogenesis. Through the synthesis of novel infectious clones of SARS-CoV-2 that lack one or more of the accessory proteins of the virus, we have found that one of these accessory proteins, ORF8, is critical for the modulation of the host inflammatory response. Mice infected with a SARS-CoV-2 virus lacking ORF8 exhibit increased weight loss and exacerbated macrophage infiltration into the lungs. Additionally, infection of mice with recombinant SARS-CoV-2 viruses encoding ORF8 mutations found in variants of concern reveal that naturally occurring mutations in this protein influence disease severity. Our studies with a virus lacking this ORF8 protein and viruses possessing naturally occurring point mutations in this protein demonstrate that this protein impacts pathogenesis. SignificanceSince its emergence in 2019, SARS-CoV-2 has accrued mutations throughout its 30kb genome. Of particular interest are the mutations present in the ORF8 protein, which occur in every major variant. The precise function and impact of this protein on disease severity and pathogenesis remains understudies. Our studies reveal that the ORF8 protein modulates the immune response by impacting macrophage infiltration into the lungs. Additionally, we have shown that the ORF8 protein of SARS-CoV-2 has accrued mutations throughout its evolution that lead to a loss of function phenotype in this protein. Our work reveals that the ORF8 protein of SARS-CoV-2 contributes significantly to disease progression through modulation of the inflammatory response.

microbiology↗