Biology subjects

Kim, H.

Publications and source records attributed to Kim, H..

At least 325 records · Page 18Linked to original sources

bioRxiv2023

A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle

Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate the folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. In the open TRiC state, PhLP2A binds to the chambers equator while its N-terminal H3-domain binds to the apical domains of CCT3/4, thereby displacing PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to the positively charged inner surfaces formed by CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding. Highlights- Structural analysis of TRiC-mediated folding cycle with cochaperones PhLP2A and PFD. - The interactions of PhLP2A and PFD with TRiC are mutually exclusive. - PhLP2A domains interact in a subunit-specific manner with the TRiC chamber. - PhLP2A domains are rearranged in ATP-closed TRiC to contact actin across the ring interface

biophysics↗

bioRxiv2023

Lysine-Cysteine-Lysine (KCK) tag changes ParB action in vitro but not in vivo.

Due to the enhanced labeling capability of maleimide-based fluorescent probes, lysine-cysteine-lysine (KCK) tags are frequently added to proteins for visualization. In this study, we employed in vitro single-molecule DNA flow-stretching assay as a sensitive way to assess the impact of the KCK-tag on the property of DNA-binding proteins. Using Bacillus subtilis ParB as an example, we show that, although no noticeable changes were detected by in vivo fluorescence imaging and chromatin immunoprecipitation (ChIP) assays, the KCK-tag substantially altered ParBs DNA compaction rates, its response to nucleotide binding and to the presence of the specific sequence (parS) on the DNA. While it is typically assumed that short peptide tags minimally perturb protein function, our results urge researchers to carefully validate the use of tags for protein labeling. Our comprehensive analysis can be expanded and used as a guide to assess the impacts of other tags on DNA-binding proteins in single-molecule assays. MotivationSingle-molecule fluorescence microscopy has been extensively used in modern biology to define the molecular action of proteins. Appending short peptide tags is a common strategy to enhance fluorescence labeling. In this Resources article, we evaluate the impact of a commonly used tag, the lysine-cysteine-lysine (KCK) tag, on protein behavior in single-molecule DNA flow-stretching assay, which is a sensitive and versatile method to understand the action of DNA-binding proteins. Our motivation is to provide researchers with an experimental framework to validate the fluorescently labeled DNA-binding proteins in single-molecule methods.

biophysics↗

bioRxiv2023

Mesoscale volumetric light field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz

Various implementations of mesoscopes provide optical access for calcium imaging across multi-millimeter fields-of-view (FOV) in the mammalian brain. However, capturing the activity of the neuronal population within such FOVs near-simultaneously and in a volumetric fashion has remained challenging since approaches for imaging scattering brain tissues typically are based on sequential acquisition. Here, we present a modular, mesoscale light field (MesoLF) imaging hardware and software solution that allows recording from thousands of neurons within volumes of 4000 x 200 {micro}m, located at up to 400 {micro}m depth in the mouse cortex, at 18 volumes per second. Our optical design and computational approach enable up to hour-long recording of [~]10,000 neurons across multiple cortical areas in mice using workstation-grade computing resources.

neuroscience↗

bioRxiv2023

The Ralstonia pseudosolanacearum effector RipE1 is recognized at the plasma membrane by NbPtr1, Nicotiana benthamiana homolog of Pseudomonas tomato race 1.

The bacterial wilt disease caused by soil-borne bacteria of the Ralstonia solanacearum species complex (RSSC) threatens important crops worldwide. Only a few immune receptors conferring resistance to this devastating disease are known so far. Individual RSSC strains deliver around 70 different type III secretion system effectors into host cells to manipulate the plant physiology and dampen immune responses. RipE1 is an effector conserved across RSSC isolated from diverse plant species and triggers immune responses in the model Solanaceae Nicotiana benthamiana. Here, we used multiplexed virus-induced gene silencing of the nucleotide-binding and leucine-rich repeat receptor family to identify the genetic basis of RipE1 recognition in N. benthamiana. Specific silencing of the N. benthamiana homolog of Solanum lycopersicoides Pseudomonas tomato race 1 gene (NbPtr1) completely abolished RipE1-induced hypersensitive response and immunity to Ralstonia pseudosolanacearum. In Nb-ptr1 knock-out plants, expression of the native NbPtr1 coding sequence was sufficient to restore RipE1 recognition. In addition to the putative catalytic triad Cys-His-Asp, RipE1 association with the host cell plasma membrane was found necessary for NbPtr1-dependent recognition. Furthermore, we found that NbPtr1-dependent recognition of RipE1 natural variants is polymorphic suggesting the coevolutionary nature of this interaction. This work hence provides an additional evidence for the indirect mode of activation of NbPtr1 and supports NbPtr1 relevance for resistance to bacterial wilt disease in Solanaceae.

plant biology↗

bioRxiv2023

Distinct roles of the orbitofrontal cortex, ventral striatum, and dopamine neurons in counterfactual thinking of decision outcomes

Individuals often assess past decisions by comparing what was gained with what would have been gained had they acted differently. Thoughts of past alternatives that counter what actually happened are called "counterfactuals". Recent theories emphasize the role of the prefrontal cortex in processing counterfactual outcomes in decision-making, although how subcortical regions contribute to this process remains to be elucidated. Here we report a clear distinction among the roles of the orbitofrontal cortex, ventral striatum and midbrain dopamine neurons in processing counterfactual outcomes in monkeys. Our findings suggest that actually-gained and counterfactual outcome signals are both processed in the cortico-subcortical network constituted by these regions but in distinct manners, and integrated only in the orbitofrontal cortex in a way to compare these outcomes. This study extends the prefrontal theory of counterfactual thinking and provides key insights regarding how the prefrontal cortex cooperates with subcortical regions to make decisions using counterfactual information. TeaserCortical and subcortical systems both contribute to counterfactual thinking of decision outcomes but in distinct manners.

neuroscience↗

bioRxiv2023

TEAD1 is crucial for myelination, Remak bundles and functional regeneration of peripheral nerves

Previously we showed that the hippo pathway transcriptional effectors, YAP and TAZ, are essential for Schwann cells (SCs) to develop, maintain and regenerate myelin (Grove et al., 2017; Grove, Lee, Zhao, & Son, 2020). Although TEAD1 has been implicated as a partner transcription factor, the mechanisms by which it mediates YAP/TAZ regulation of SC myelination are unclear. Here, using conditional and inducible knockout mice, we show that TEAD1 is crucial for SCs to develop and regenerate myelin. It promotes myelination by both positively and negatively regulating SC proliferation, enabling Krox20/Egr2 to upregulate myelin proteins, and upregulating the cholesterol biosynthetic enzymes FDPS and IDI1. We also show stage-dependent redundancy of TEAD1 and that non-myelinating SCs have a unique requirement for TEAD1 to enwrap nociceptive axons in Remak bundles. Our findings establish TEAD1 as a major partner of YAP/TAZ in developmental myelination and functional nerve regeneration and as a novel transcription factor regulating Remak bundle integrity.

neuroscience↗

bioRxiv2023

Acquired epithelial WNT secretion drives niche independence of developing gastric cancer

Recent studies have shed light on the signaling pathways required for gastric tissue maintenance and how aberrations in these key pathways lead to gastric cancer development. Although it has been shown that the WNT pathway is important for gastric epithelial homeostasis, the identity and source of the responsible canonical WNT ligands remain unknown. Furthermore, it is unclear how gastric cancer acquires WNT niche independence - an important early step in tumorigenesis. Using human and mouse gastric organoids and in vivo mouse models, we found that mesenchymal WNT2B and WNT7B maintain gastric epithelium in homeostasis. Next, mouse genetic studies and single-cell multi-omics analyses revealed that activation of MAPK signaling induces secretion of WNT7B in the epithelium itself. We further confirmed that in human gastric cancer, MAPK pathway activation through HER2 overexpression or copy number gains of WNT2 confers WNT independence. Importantly, the epithelium-intrinsic WNT expression could be therapeutically inhibited. Taken together, our results reveal that normal gastric epithelial turnover relies on WNT ligands secreted by niche mesenchymal cells, while transformation involves acquisition of a WNT secretory phenotype in the epithelium - representing a potential target for therapeutic interventions.

cancer biology↗

bioRxiv2023

Single cell and spatial alternative splicing analysis with long read sequencing

Long-read sequencing has become a powerful tool for alternative splicing analysis. However, technical and computational challenges have limited our ability to explore alternative splicing at single cell and spatial resolution. The higher sequencing error of long reads, especially high indel rates, have limited the accuracy of cell barcode and unique molecular identifier (UMI) recovery. Read truncation and mapping errors, the latter exacerbated by the higher sequencing error rates, can cause the false detection of spurious new isoforms. Downstream, there is yet no rigorous statistical framework to quantify splicing variation within and between cells/spots. In light of these challenges, we developed Longcell, a statistical framework and computational pipeline for accurate isoform quantification for single cell and spatial spot barcoded long read sequencing data. Longcell performs computationally efficient cell/spot barcode extraction, UMI recovery, and UMI-based truncation- and mapping-error correction. Through a statistical model that accounts for varying read coverage across cells/spots, Longcell rigorously quantifies the level of inter-cell/spot versus intra-cell/ spot diversity in exon-usage and detects changes in splicing distributions between cell populations. Applying Longcell to single cell long-read data from multiple contexts, we found that intra-cell splicing heterogeneity, where multiple isoforms co-exist within the same cell, is ubiquitous for highly expressed genes. On matched single cell and Visium long read sequencing for a tissue of colorectal cancer metastasis to the liver, Longcell found concordant signals between the two data modalities. Finally, on a perturbation experiment for 9 splicing factors, Longcell identified regulatory targets that are validated by targeted sequencing.

bioinformatics↗

bioRxiv2023

Neural Systems Underlying the Implementation of Working Memory Removal Operations

Recently multi-voxel pattern analysis has verified the removal of information from working memory (WM) via three distinct operations replacement, suppression, or clearing compared to information being maintained (Kim et al., 2020). Univariate analyses and classifier importance maps indicate that some brain regions commonly contribute to these operations. This study aimed to use multivariate approaches to determine whether, within these commonly activated brain regions, each of these operations is being represented in a similar or distinct manner. To do so, we used Leiden community detection to identify brain networks that are characterized by similar multi-voxel patterns of activity with regard to these WM operations. Four networks were identified. The Visual Network shows similar multi-voxel patterns for maintain and replace, which are highly dissimilar from suppress and clear, suggesting this network differentiates whether an item is held in WM or not. The Somatomotor Network shows distinct multi-voxel patterns for clear relative to the other operations, suggesting that this network diff in clearing information from WM. The Default Mode Network has distinct patterns for suppress and clear, also suggesting that clearing information from WM is distinct from suppressing it. The Frontoparietal Control Network displays distinct multi-voxel patterns for each of the four operations, suggesting that this network has high involvement in regulating the flow of information within WM. These results indicate that how information is removed from WM depends on distinct brain networks that each have a particular manner in which their co-activation patterns represent these operations. SIGNIFICANCE STATEMENTThe ability to actively remove, manipulate and maintain information in working memory (WM) is required for encoding of new information and for controlling thoughts. This study revealed that different brain networks show characteristic multi-voxel activity patterns across four distinct WM operations: maintenance of information, replacement of one item by another, suppression of a specific item, and clearing the mind of all thought. One network, the Frontoparietal Control Network, differentiates all four operations, suggesting it may play a critical role in the controlled removal of information from WM.

neuroscience↗

bioRxiv2023

IQGAP2 regulates blood-brain barrier immune dynamics

Brain endothelial cells (BECs) play an important role in maintaining central nervous system (CNS) homeostasis through blood-brain barrier (BBB) functions. BECs express low baseline levels of adhesion receptors, which limits entry of leukocytes. However, the molecular mediators governing this phenotype remain mostly unclear. Here, we explored how infiltration of immune cells across the BBB is influenced by the scaffold protein IQ motif containing GTPase activating protein 2 (IQGAP2). In mice and zebrafish, we demonstrate that loss of Iqgap2 increases infiltration of peripheral leukocytes into the CNS under homeostatic and inflammatory conditions. Using single-cell RNA sequencing and immunohistology, we further show that BECs from mice lacking Iqgap2 exhibit a profound inflammatory signature, including extensive upregulation of adhesion receptors and antigen-processing machinery. Human tissue analyses also reveal that Alzheimers disease is associated with reduced hippocampal IQGAP2. Overall, our results implicate IQGAP2 as an essential regulator of BBB immune privilege and immune cell entry into the CNS.

neuroscience↗

bioRxiv2023

C3 in the 10-20 system may not be the best target for the motor hand area

The C3 region in the international 10-20 system for electroencephalography (EEG) recording is assumed to represent the right motor hand area. Therefore, in the absence of transcranial magnetic stimulation (TMS) or a neuronavigational system, neuromodulation methods, such as transcranial direct current stimulation, target C3 or C4, based on the international 10-20 system, to influence the cortical excitability of the right and left hand, respectively. The purpose of this study is to compare the peak-to-peak motor evoked potential (MEP) amplitudes of the right first dorsal interosseus (FDI) muscle after single-pulse TMS at C3, C3h, and C1. Using an intensity of 110% of the resting motor threshold, 15 individual MEPs from each of C3, C3h, C1, and hotspots were randomly recorded from FDI for sixteen right-handed undergraduate students. Average MEPs were greatest at C3h and C1, with both being larger than those recorded at C3. These data are congruent with recent findings using topographic analysis of individual MRIs that revealed poor correspondence between C3/C4 and the respective hand knob. Implications for the use of scalp locations determined using the 10-20 system for localizing the hand area are highlighted. HighlightsO_LIMEPs recorded at C3h and C1 were larger than those recorded at C3. C_LIO_LIScalp locations other than C3 offer a more accurate estimation of human hand area. C_LI

neuroscience↗

bioRxiv2023

Mucociliary Clearance Augmenting Drugs Block SARS-Cov-2 Replication in Human Airway Epithelial Cells

The coronavirus disease (COVID-19) pandemic, caused by SARS-CoV-2 coronavirus, is devastatingly impacting human health. A prominent component of COVID-19 is the infection and destruction of the ciliated respiratory cells, which perpetuates dissemination and disrupts protective mucociliary transport (MCT) function, an innate defense of the respiratory tract. Thus, drugs that augment MCT could improve barrier function of the airway epithelium, reduce viral replication and, ultimately, COVID-19 outcomes. We tested five agents known to increase MCT through distinct mechanisms for activity against SARS-CoV-2 infection using a model of human respiratory epithelial cells terminally differentiated in an air/liquid interphase. Three of the five mucoactive compounds tested showed significant inhibitory activity against SARS-CoV-2 replication. An archetype mucoactive agent, ARINA-1, blocked viral replication and therefore epithelial cell injury, thus, it was further studied using biochemical, genetic and biophysical methods to ascertain mechanism of action via improvement of MCT. ARINA-1 antiviral activity was dependent on enhancing the MCT cellular response, since terminal differentiation, intact ciliary expression and motion was required for ARINA-1-mediated anti-SARS-CoV2 protection. Ultimately, we showed that improvement of cilia movement was caused by ARINA-1-mediated regulation of the redox state of the intracellular environment, which benefited MCT. Our study indicates that Intact MCT reduces SARS-CoV-2 infection, and its pharmacologic activation may be effective as an anti-COVID-19 treatment.

microbiology↗

bioRxiv2023

tRNA m1G9 modification depends on substrate-specific RNA conformational changes induced by the methyltransferase Trm10

The methyltransferase Trm10 modifies a subset of tRNAs on the base N1 position of the 9th nucleotide in the tRNA core. Trm10 is conserved throughout Eukarya and Archaea, and mutations in the human gene (TRMT10A) have been linked to neurological disorders such as microcephaly and intellectual disability, as well as defects in glucose metabolism. Of the 26 tRNAs in yeast with guanosine at position 9, only 14 are substrates for Trm10. However, no common sequence or other posttranscriptional modifications have been identified among these substrates, suggesting the presence of some other tRNA feature(s) which allow Trm10 to distinguish substrate from nonsubstrate tRNAs. Here, we show that substrate recognition by Saccharomyces cerevisiae Trm10 is dependent on both intrinsic tRNA flexibility and the ability of the enzyme to induce specific tRNA conformational changes upon binding. Using the sensitive RNA structure-probing method SHAPE, conformational changes upon binding to Trm10 in tRNA substrates, but not nonsubstrates, were identified and mapped onto a model of Trm10-bound tRNA. These changes may play an important role in substrate recognition by allowing Trm10 to gain access to the target nucleotide. Our results highlight a novel mechanism of substrate recognition by a conserved tRNA modifying enzyme. Further, these studies reveal a strategy for substrate recognition that may be broadly employed by tRNA-modifying enzymes which must distinguish between structurally similar tRNA species.

biochemistry↗

bioRxiv2023

GABA-mediated inhibition in visual feedback neurons fine-tunes Drosophila male courtship

Vision is critical for the regulation of mating behaviors in many species. Here, we discovered that the Drosophila ortholog of human GABAA-receptor-associated protein (GABARAP) is required to fine-tune male courtship by modulating the activity of visual feedback neurons, lamina tangential cells (Lat). GABARAP is a ubiquitin-like protein that regulates cell-surface levels of GABAA receptors. Knocking down GABARAP or GABAA receptors in Lat neurons or hyperactivating them induces male courtship toward other males. Inhibiting Lat neurons, on the other hand, delays copulation by impairing the ability of males to follow females. Remarkably, the human ortholog of Drosophila GABARAP restores function in Lat neurons. Using in vivo two-photon imaging and optogenetics, we show that Lat neurons are functionally connected to neural circuits that mediate visually-guided courtship pursuits in males. Our work reveals a novel physiological role for GABARAP in fine-tuning the activity of a visual circuit that tracks a mating partner during courtship.

neuroscience↗

bioRxiv2023

Gesture profiles distinguish primary progressive aphasia variants

Primary progressive aphasia (PPA) is a neurodegenerative syndrome characterized by progressive language deficits. There are three main variants of PPA - semantic (svPPA), logopenic (lvPPA), and nonfluent (nfvPPA) - that can be challenging to distinguish. Limb praxis may also be affected in PPA, but it is unclear whether different variants of PPA are associated with differences in gesture production. Prior research with neurotypical individuals indicates that the left temporal lobe is a critical locus of manipulable object and hand posture representations. Moreover, when imitating gestures, individuals whose strokes include the left temporal lobe show reduced benefit of gesture meaning and disproportionate impairment in hand posture as compared to arm kinematics. We tested the hypothesis that svPPA - who typically exhibit primarily temporal lobe atrophy - would differentially show these expected patterns of gesture imitation performance. Nineteen participants with PPA completed meaningful and meaningless gesture imitation tasks, and performance was scored for hand posture and arm kinematics accuracy. Generalized logistic mixed-effect regression models controlling for dementia severity showed overall benefits from gesture meaning, and greater impairments in hand posture than arm kinematics. We also found that svPPA participants were the most impaired in gesture imitation overall. Critically, there was also a significant three-way interaction of group, meaning, and gesture component: only svPPA participants showed relative impairments of hand posture for meaningful gestures as well as meaningless gestures. Thus, unlike lvPPA and nfvPPA, the hand postures of svPPA failed to benefit from gesture meaning. This research extends prior findings on the role of the temporal lobe in hand posture representations associated with manipulable objects, and is the first to indicate that there may be distinct gesture imitation patterns as a function of PPA variant. Characterizing componential gesture deficits in PPA may help to inform differential diagnosis, compensatory communication strategies, and cognitive praxis models of PPA.

neuroscience↗

bioRxiv2023

Predicting the efficacy of BH3 mimetics through the profiling of multiple protein complexes

BH3 mimetics are protein-protein interaction (PPI) inhibitors that saturate anti-apoptotic proteins in the BCL2 family to induce apoptosis in cancer cells, a prominent example of protein complex-targeting therapies. Despite the remarkable success of the BH3 mimetic ABT-199 in treating hematological malignancies, only a fraction of patients respond to ABT-199 and eventually develop resistance, necessitating the predictive biomarkers for both initial responses and resistance development. We here used the single-molecule pull-down and co-immunoprecipitation platform to quantify more than 20 different types of PPI complexes using [~]1.2x106 cells in total, revealing the rewired status of the BCL2 family PPI network. By comparing the obtained multi-dimensional data with BH3 mimetic efficacies determined ex vivo, we constructed an analysis model for ABT-199 efficacy that designates the BCL2-BAX and BCLxL-BAK complexes as the primary mediators of drug effectiveness and resistance. We then applied this model to assist in therapeutic decision-making for acute myeloid leukemia patients in a prospective manner. Our work demonstrates a capability for the extensive characterization of PPI complexes in clinical specimens, potentially opening a new avenue of precision medicine for protein complex-targeting therapies.

molecular biology↗

bioRxiv2022

Electrophysiological Activity of Primary Cortical Neuron-Glia Mixed Cultures

BackgroundWe have previously described a tri-culture of neurons, astrocytes, and microglia that accurately mimics the in vivo neuroinflammatory response (both neurotoxic and neuroprotective) to a wide range of neuroinflammatory stimuli. Electrophysiological activity is an essential measure of neuronal function, which is influenced by neuroinflammation. Microelectrode array (MEA) technology is a versatile tool to non-invasively study in vitro neural networks by simultaneously recording electrophysiological activity from multiple sites. In this study, we used extracellular recordings to determine the effect of microglia on neural network formation and stability in primary cortical cultures and monitor the changes in neural activity in response to neuroinflammatory stimuli. MethodsPrimary neonatal rat cortical tri-cultures of neurons, astrocytes, and microglia or co-cultures of neurons and astrocytes were cultured on custom MEAs and the neural activity was monitored for 21 days in vitro to assess culture maturation and network formation. Quantification of synaptic puncta and averaged spike waveforms were used to determine the difference in excitatory to inhibitory neuron ratio (E/I ratio) of the neurons in tri- and co-cultures. The electrophysiological response to lipopolysaccharide (LPS) treatment of both culture types were compared. ResultsThe tri- and co-culture showed minimal difference in electrophysiological markers of neural network formation and stability with the exception of a significant increase in spike frequency in the tri-culture at later timepoints (DIV 17 and 21). Additionally, there was no significant difference in the density of either post-synaptic or excitatory pre-synaptic puncta between the culture types. However, characterization of the average spike waveforms revealed that the tri-culture had an E/I ratio much closer to that found in the rat cortex. Finally, only the tri-culture displayed a significant decrease in both the number of active channels and spike frequency following LPS exposure. ConclusionsThis study demonstrates that the microglia in the tri-culture do not disrupt neural network formation and stability as quantified using extracellular recordings and may be a better representation of the in vivo cortex due to the closer E/I ratio than more traditional isolated neuron and neuron-astrocyte co-cultures. Additionally, the tri-culture is better able to mimic the neuroinflammatory response to LPS, which was quantified via changes in neural electrophysiological activity.

neuroscience↗

bioRxiv2022

Restoring glucose homeostasis with stomach-derived human insulin-secreting organoids

Gut stem cells are accessible by biopsy and propagate robustly in culture, offering an invaluable resource for autologous cell therapies. Insulin-producing cells can be induced in mouse gut, but it has not been possible to generate abundant and durable insulin-secreting cells from human gut tissues to evaluate their potential as a cell therapy for diabetes. Here we describe a protocol to differentiate cultured human gastric stem cells (hGSCs) into pancreatic islet-like organoids containing gastric insulin-secreting (GINS) cells that resemble {beta}-cells in molecular hallmarks and function. Sequential activation of the inducing factors NGN3 and PDX1-MAFA led hGSCs onto a novel differentiation path, including a SOX4High endocrine and GalaninHigh GINS precursor, before adopting {beta}-cell identity, at efficiencies close to 70%. GINS organoids acquired glucose-stimulated insulin secretion in 10 days and restored glucose homeostasis for over 100 days in diabetic mice after transplantation, providing proof of concept for a new approach to treat diabetes.

cell biology↗