Biology subjects

Kim, S.

Publications and source records attributed to Kim, S..

At least 415 records · Page 23Linked to original sources

bioRxiv2022

Listeria motility increases the efficiency of goblet cell invasion during intestinal infection

Listeria monocytogenes (Lm) is a food-borne pathogen that causes severe bacterial gastroenteritis, with high rates of hospitalization and mortality. Lm is ubiquitous in soil, water and livestock, and can survive and proliferate at low temperatures. Following oral ingestion of contaminated food, Lm crosses the epithelial through intestinal goblet cells in a mechanism depending on Lm InlA and host E-cadherin. Importantly, human infections typically occur with Lm growing at or below room temperature, which are flagellated and motile. Even though many important human bacterial pathogens are flagellated, little is known regarding the effect of bacterial motility on invasion and immune evasion. Here, we used complementary imaging and computer modeling approaches to test the hypothesis that bacterial motility helps Lm locate and engage target cells permissive for invasion. Imaging explanted mouse and human intestine, we confirmed that Lm grown at room temperature uses motility to scan the epithelial surface and preferentially attach to target cells. Furthermore, we integrated quantitative parameters from our imaging experiments to construct a versatile "layered" cellular Potts model (L-CPM) that simulates host-pathogen dynamics. Simulated data are consistent with the hypothesis that bacterial motility enhances invasion by allowing bacteria to search the epithelial surface for their preferred invasion targets. Indeed, our model consistently predicts that motile bacteria have invaded [~]2-fold more at the 1-hour mark. This invasion advantage persists even in the presence of host phagocytes, with the balance between invasion and phagocytosis governed almost entirely by bacterial motility. In conclusion, our simulations provide insight into host pathogen interactions and challenge fundamental assumptions regarding how phagocytes might limit bacterial invasion early during infection.

microbiology↗

bioRxiv2022

Three consecutive glycolysis enzymes are involved in autophagic flux regulation through monitoring nutrient availability

Autophagy serves as an important recycling route for growth and survival of eukaryotic organisms in nutrient-deficient conditions. When confronted with starvation, metabolic flux is coordinated by individual metabolic enzymes. Given that the metabolic diversity of carbon in eukaryotes is related to their lifestyle, autophagy may be modulated by metabolic enzymes by monitoring carbon flux. Here, we attempted to identify carbon metabolic genes that modulate autophagy using VIGS screening of 45 glycolysis- and the Calvin-Benson cycle-related genes. We report here that three consecutive triose-phosphate-processing enzymes involved in the cytosolic glycolysis, TPI (triose-phosphate-isomerase), GAPC (glyceraldehyde-3-phosphate dehydrogenase), and PGK (phosphoglycerate kinase), designated TGP, negatively regulate autophagy. Depletion of TGP enzymes result in spontaneous autophagy induction and increases ATG1 kinase activity. TGP enzymes interact with ATG101, a regulatory component of the ATG1 kinase complex. Spontaneous autophagy induction and abnormal growth under insufficient sugar in the TGP mutants is suppressed by crossing with the atg101 mutant. Considering that triose-phosphates are photosynthates transported to the cytosol from active chloroplasts, the TGP enzymes may be strategically positioned to monitor the flow of photosynthetic sugars and modulate autophagy accordingly. Collectively, these results suggest that TGP enzymes negatively control autophagy acting upstream of the ATG1 complex, which is critical for seedling development.

plant biology↗

bioRxiv2022

Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics

Functional magnetic resonance imaging (fMRI) with optogenetic neural manipulation is a powerful tool that enables brain-wide mapping of effective functional networks. To achieve flexible manipulation of neural excitation throughout the mouse cortex, we incorporated spatiotemporal programmable optogenetic stimuli generated by a digital micromirror device into an MR scanner via an optical fiber bundle for the first time. This approach offered versatility in space and time in planning the photostimulation pattern, combined with in situ optical imaging and cell-type or circuit-specific genetic targeting in individual mice. Brain-wide effective connectivity obtained by fMRI with optogenetic stimulation of atlas-based cortical regions is generally congruent with anatomically defined axonal tracing data but is affected by the types of anesthetics that act selectively on specific connections. fMRI combined with flexible optogenetics opens a new path to investigate dynamic changes in functional brain states in the same animal through high-throughput brain-wide effective connectivity mapping.

neuroscience↗

bioRxiv2022

A novel prion strain is responsible for the first case of chronic wasting disease in Finnish moose

Concern is mounting over the global emergence, expanding host range, and uncertain zoonotic potential of chronic wasting disease (CWD), a fatal, infectious disease of cervids caused by prions. Our previous studies using genetically modified CWD-susceptible mice showed that Norwegian and North American CWD are caused by different prion strains. Here we investigated the properties of prions causing the first case of Finnish moose CWD. While Finnish and Norwegian moose CWD prions share characteristics that distinguish them from North American CWD including the inability to replicate in lymphoid tissues, common responses to variations at residue 226 of host prion protein, and overlapping central nervous system profiles, they also exhibit pronounced conformational variation which is consistent with strain differences between Finnish and Norwegian moose CWD. Our findings support the existence of a surprisingly diverse portfolio of emergent CWD strains in Nordic countries that is etiologically distinct from North American CWD. Summary linePrion strain properties from the first case of chronic wasting disease in a Finnish moose are similar but not identical to Norwegian cases, supporting a growing population of strains in Nordic countries.

microbiology↗

bioRxiv2022

Causal role of the dorsolateral prefrontal cortex in modulating the balance between Pavlovian and instrumental systems in the punishment domain

Previous literature suggests that a balance between Pavlovian and instrumental decision-making systems is critical for optimal decision-making. Pavlovian bias (i.e., approach toward reward-predictive stimuli and avoid punishment-predictive stimuli) often contrasts with the instrumental response. Although recent neuroimaging studies have identified brain regions that may be related to Pavlovian bias, including the dorsolateral prefrontal cortex (dlPFC), it is unclear whether a causal relationship exists. Therefore, we investigated whether upregulation of the dlPFC using transcranial current direct stimulation (tDCS) would reduce Pavlovian bias. In this double-blind study, participants were assigned to the anodal or the sham group; they received stimulation over the right dlPFC for 3 successive days. On the last day, participants performed a reinforcement learning task known as the orthogonalized go/no-go task; this was used to assess each participants degree of Pavlovian bias in reward and punishment domains. We used computational modeling and hierarchical Bayesian analysis to estimate model parameters reflecting latent cognitive processes, including Pavlovian bias, go bias, and choice randomness. Several computational models were compared; the model with separate Pavlovian bias parameters for reward and punishment domains demonstrated the best model fit. When using a behavioral index of Pavlovian bias, the anodal group showed significantly lower Pavlovian bias in the punishment domain, but not in the reward domain, compared with the sham group. In addition, computational modeling showed that Pavlovian bias parameter in the punishment domain was lower in the anodal group than in the sham group, which is consistent with the behavioral findings. The anodal group also showed a lower go bias and choice randomness, compared with the sham group. These findings suggest that anodal tDCS may lead to behavioral suppression or change in Pavlovian bias in the punishment domain, which will help to improve comprehension of the causal neural mechanism. Author summaryA decision-making bias guided by the Pavlovian system (i.e., approach reward and avoid punishment) is often useful and predominant across species but it is also related to several psychiatric conditions. The dorsolateral prefrontal cortex (dlPFC) is known to be related to such "Pavlovian bias" but it is unclear whether a causal relationship exists between them. Here, we evaluated whether decision-making biases including Pavlovian bias could be modulated by exogenous brain stimulation, transcranial current direct stimulation, over the right dlPFC for 3 successive days. A combination of behavioral analysis and computational modeling revealed that the anodal group had lower Pavlovian bias in the punishment domain compared with the sham group. In addition, the anodal group showed lower go bias and choice randomness than the sham group, which can also hamper instrumental learning. These findings suggest a causal role for the dlPFC in modulating the balance between the Pavlovian and instrumental decision-making systems.

neuroscience↗

bioRxiv2022

DNA methylation is a widespread mechanism of light-induced circadian clock period plasticity

The suprachiasmatic nucleus (SCN) of the hypothalamus is a principal light-responsive circadian clock that adjusts circadian rhythms in mammalian physiology and behavior to changes in external light signals. Although mechanisms underlying how light acutely resets the timing of circadian rhythms have been characterized, it remains elusive how light signals induce lasting changes in circadian period, so-called period after-effects. Here we have found that the period after-effects on circadian behavior of changing photoperiods are blocked by application of DNA methyltransferase inhibitors directed to the SCN. At the level of single light pulses that act as clock-resetting stimulations, pharmacologically inhibiting DNA methylation in the SCN significantly attenuates period after-effects following acute phase shifts in behavioral rhythms in vivo, and blocks period after-effects on clock gene rhythms in the isolated ex vivo SCN. Acute clock resetting shifts themselves, however, do not appear to require DNA methylation at the SCN and behavioral levels, in contrast to subsequent period plasticity. Our results indicate that DNA methylation in the SCN mediates light-induced period after-effects in response to photoperiods, and single light pulses, and together with previous studies showing that DNA methylation in the SCN is essential for period after-effects of non-24hr light cycles (T-cycles), suggest that DNA methylation in the SCN is a widespread mechanism of light-induced circadian period plasticity.

neuroscience↗

bioRxiv2022

Exploring Taxonomic and Functional Microbiome of Hawaiian Stream and Spring Irrigation Water Systems Using Illumina and Oxford Nanopore Sequencing Platforms

Irrigation water is a potential source of contamination that carries plant and foodborne human pathogens and provides a niche for survival and proliferation of microbes in agricultural settings. This project investigated bacterial communities and their functions in the irrigation water from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and tank stored water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phyla in river stream source and associated wet taro field water samples. Cyanobacteria was also a dominant phylum from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. Whereas samples sequenced for full length 16S rRNA and shotgun metagenome, clearly illustrated that Oxford Nanopore MinION is a better choice to classify the microbes to the genus and species levels. In terms of functional analyses, only 12% of the genes were shared by two consortia. Total 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Description of microbial communities and their functions are essential for the development of better water management strategies to produce safer fresh produce and to protect plant, animal, human and environmental health. This project identified analytical tools to study microbiome of irrigation water.

microbiology↗

bioRxiv2022

Age-related Macular Degeneration patient deep phenotyping and whole genome sequencing analysis identifies coding variants linking small low-luminance visual deficit to fat storage defects

BackgroundThe basis of Age-related macular degeneration (AMD) genetic risk has been well documented; however, few studies have looked at genetic biomarkers of disease progression or treatment response within advanced AMD patients. Here we report the first genome-wide analysis of genetic determinants of low-luminance vision deficit (LLD), which is seen as predictive of visual acuity loss and anti-VEGF treatment response in neovascular AMD patients. MethodsAMD patients were separated into small- and large-LLD groups for comparison and whole genome sequencing was performed. Genetic determinants of LLD were assessed by common and rare variant genetic analysis. Follow-up functional analysis of rare coding variants identified by the burden test was then performed in vitro. ResultsWe identified four coding variants in the CIDEC gene. These rare variants were only present in patients with a small LLD, which has been previously shown to indicate better prognosis and better treatment response. Our in vitro functional characterization of these CIDEC alleles revealed that all decrease the binding affinity between CIDEC and the lipid droplet fusion effectors PLIN1, RAB8A and AS160. The rare CIDEC alleles all cause a hypomorphic defect in lipid droplet fusion and enlargement, resulting in a decreased fat storage capability in adipocytes. ConclusionsAs we did not detect CIDEC expression in the ocular tissue affected by AMD, our results suggest that the CIDEC variants do not play a direct role in the eye and influence low-luminance vision deficit via an indirect and systemic effect related to fat storage capacity. FundingNo external funding was received for this work.

genetics↗

bioRxiv2022

Precise modulation of transcription factor levels reveals drivers of dosage sensitivity

Transcriptional regulation displays extensive robustness, but human genetics indicate sensitivity to transcription factor (TF) dosage. Reconciling such observations requires quantitative studies of TF dosage effects at trait-relevant ranges, which are lacking to date. TFs play central roles in both normal-range and disease-associated variation in facial morphology; we therefore developed an approach to precisely modulate TF levels in human facial progenitors and applied it to SOX9, a TF associated with craniofacial variation and disease (Pierre Robin Sequence, PRS). We found that most SOX9-dependent regulatory elements (REs) are buffered against small decreases in SOX9 dosage, but REs directly and primarily regulated by SOX9 show heightened sensitivity to SOX9 dosage; these RE responses predict gene expression responses. Sensitive REs and genes underlie the vulnerability of chondrogenesis and PRS-like craniofacial shape variation to SOX9 dosage perturbation. We propose that such REs and genes drive the sensitivity of specific phenotypes to TF dosage, while buffering of other genes leads to robust, nonlinear dosage-to-phenotype relationships.

genetics↗

bioRxiv2022

Off-manifold coding in visual cortex revealed by sleep

Low-dimensional neural manifolds are controversial in part because it is unclear how to reconcile them with high-dimensional representations observed in areas such as primary visual cortex (V1). We addressed this by recording neuronal activity in V1 during slow-wave sleep, enabling us to identify internally-generated low-dimensional manifold structure and evaluate its role during visual processing. We found that movements and visual stimuli were both encoded in the "on-manifold" subspace preserved during sleep. However, only stimuli were encoded in the "off-manifold" subspace, which contains activity patterns that are less likely than chance to occur spontaneously during sleep. This off-manifold activity comprises sparse firing in neurons with the strongest low-dimensional modulation by movement, which paradoxically prevents movement-evoked activity from interfering with stimulus representations. These results reveal an unexpected link between low-dimensional dynamics and sparse coding, which together create a protected off-manifold coding space keeping high-dimensional representations separable from movement-evoked activity.

neuroscience↗

bioRxiv2022

A dual gene-specific mutator system installs all transition mutations at similar rates in vivo

Targeted in vivo hypermutation accelerates directed evolution of proteins through concurrent DNA diversification and selection. Among recently developed methods, the systems employing a fusion protein of a nucleobase deaminase and T7 RNA polymerase present gene-specific targeting. However, their mutational spectra have been largely limited to exclusive or dominant C:G[->]T:A mutations. Here we describe eMutaT7transition, a new gene-specific mutator system, that installs all the transition mutations (C:G[->]T:A and A:T[->]G:C) at comparable rates. By using two mutator proteins in which two efficient deaminases, PmCDA1 and TadA-8e, are separately fused to T7 RNA polymerase, we obtained similar numbers of C:G[->]T:A and A:T[->]G:C mutations at a sufficiently high rate ([~]3.4 x 10-5 mutations per base per generation or [~]1.3 mutations per 1 kb per day). Through eMutaT7transition-mediated TEM-1 evolution for antibiotic resistance, we generated many mutations also found in clinical isolates. Overall, with a fast mutation rate and wider mutational spectrum, eMutaT7transition is a potential first-line method for gene-specific in vivo hypermutation.

synthetic biology↗

bioRxiv2022

Hydrodynamic dissection of single cells in a microfluidic system

Stentor coeruleus, a single-cell ciliated protozoan, is a model organism for wound healing and regeneration studies. Despite Stentors large size (up to 2 mm in extended state), microdissection of Stentor remains challenging. In this work, we describe a hydrodynamic cell splitter, consisting of a cross junction, capable of splitting Stentor cells in a non-contact manner at a high throughput of [~]500 cells/min under continuous operation. Introduction of asymmetry in the flow field at the cross junction leads to asymmetric splitting of the cells to generate cell fragments as small as [~]8.5 times the original cell size. Characterization of cell fragment viability shows reduced 5-day survival as fragment size decreases and as the extent of hydrodynamic stress imposed on the fragments increases. Our results suggest that cell fragment size and composition, as well as mechanical stress, play important roles in the long-term repair of Stentor cells and warrant further investigations. Nevertheless, the hydrodynamic splitter can be useful for studying phenomena immediately after cell splitting, such as the closure of wounds in the plasma membrane which occurs on the order of 100 - 1000 seconds in Stentor.

biophysics↗

bioRxiv2022

ECPAS/Ecm29-Mediated 26S Proteasome Disassembly Is an Adaptive Response to Glucose Starvation

The 26S proteasome consists of loosely associated 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in eukaryotic cells exist as free 20S complexes; however, our mechanistic and physiological understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation in mammalian cells results in the uncoupling of 26S holoenzymes into intact 20S and 19S subcomplexes. Subcomplex affinity-purification and quantitative mass spectrometry revealed that Ecm29 proteasome adaptor and scaffold (ECPAS) is a crucial mediator of this structural remodeling. The loss of ECPAS abrogated 26S dissociation, leading to decreased degradation of 20S proteasome substrates such as puromycylated polypeptides and lysine-less cyclin B. In silico modeling analysis suggested that the conformational changes of ECPAS may commence the disassembly process. ECPAS was also essential for proper endoplasmic reticulum stress response and cell survival during glucose starvation. In addition, we evaluated the role of ECPAS in vivo using the mouse xenograft model and observed that glucose-deprived tumor tissues had significantly elevated 20S proteasome levels. Collectively, our results indicate that the 20S-19S disassembly mediated by ECPAS is a novel mechanism adapting global proteolysis to physiological needs and an effective cellular strategy against proteotoxic stress.

biochemistry↗

bioRxiv2022

Proteome-wide microarray-based screening of PAR-binding proteins

Poly(ADP-ribose) (PAR) plays a crucial role in intracellular signaling and scaffolding through covalent modification or non-covalent binding to target proteins. The non- covalent binding PARylome has not been extensively characterized. Here we performed a PAR-binding screen using a human protein microarray that covers most of the human proteome to characterize the non-covalent binding PARylome. A total of 356 PAR- binding proteins were identified. The PAR-binding PARylome suggests that PAR- binding regulates a variety of biological processes beyond well-characterized DNA damage signaling and DNA repair. Proteins that may be reprogrammed by PAR-binding include signaling molecules, transcription factors, nucleic acid binding proteins, calcium binding proteins, ligases, oxidoreductases, enzymes, transferases, hydrolases, and receptors. The global database of PAR-binding proteins that we established will be a valuable tool for further in-depth analysis of the role of PARylation in a wide range of biological contexts.

biochemistry↗

bioRxiv2022

FcRγ- NK cell induction by specific CMV and expansion by subclinical viral infections in rhesus macaques

Long-lived memory-like NK cells, characterized by FcR{gamma}-deficiency and enhanced responsiveness to antibody-bound virus-infected cells, have been found in certain human cytomegalovirus (HCMV)-seropositive individuals. Because humans are exposed to numerous microbes and environmental agents, specific relationships between HCMV and FcR{gamma}-deficient NK cells (also known as g-NK cells) have been challenging to define. Here, we show that a subgroup of rhesus cytomegalovirus (RhCMV)-seropositive macaques possesses FcR{gamma}-deficient NK cells that stably persist and display phenotype resembling human FcR{gamma}-deficient NK cells. Moreover, these macaque NK cells resembled human FcR{gamma}-deficient NK cells with respect to functional characteristics, including enhanced responsiveness to RhCMV-infected target in an antibody-dependent manner and hypo-responsiveness to tumor and cytokine stimulation. These cells were not detected in specific-pathogen-free (SPF) macaques free of RhCMV and six other viruses; however, experimental infection of SPF animals with RhCMV strain UCD59, but not RhCMV strain 68-1 or SIV, led to induction of FcR{gamma}-deficient NK cells. In non-SPF macaques, co-infection by RhCMV with other common viruses was associated with higher frequencies of FcR{gamma}-deficient NK cells. These results support a causal role for specific cytomegalovirus strain(s) in the induction of FcR{gamma}-deficient NK cells, and suggest that co-infection by other viruses further expands this memory-like NK cell pool.

immunology↗

bioRxiv2022

Glia-mediated cerebellar pain modulation

Clinical studies have revealed that the cerebellum is activated by noxious stimuli or pathological pain, and its removal results in somatosensory dysfunction. However, the neural circuits and molecular mechanisms underlying the processing of noxious information in the cerebellum remain unknown. Using two-photon microscopy and optogenetics in mice, we found that the locus coeruleus (LC) terminals in the cerebellar cortex release noradrenaline (NA) in response to cutaneous noxious electrical stimuli. Most Bergmann glia (BG) accumulated this LC-NA noxious information by increasing intracellular calcium in an integrative manner. This global calcium activation of BG, referred to as "flare," was also elicited in response to an intraplantar capsaicin injection. Chemogenetic inactivation of LC terminals or BG in the cerebellar cortex suppressed BG flares and reduced licking, a nocifensive behavior associated with capsaicin-induced pain. BG-specific knockdown of -1 adrenergic receptors also suppressed capsaicin-induced BG flares and licking. Chemogenetic activation of BG or an intraplantar capsaicin injection reduced Purkinje cell firings, which disinhibited the output activity of the deep cerebellar nuclei. These results suggest that BG in the cerebellar cortex play an essential role in computing noxious information ascending from the LC and modulate pain-related behaviors by controlling the activity of the cerebellar neural circuits. One Sentence SummaryBergmann glia mediate noxious information processing in the cerebellum

neuroscience↗

bioRxiv2022

The regulatory landscapes of human ovarian ageing

Summary paragraphThe ovary is the first organ to age in the human body, affecting both fertility and overall health in women1-8. However, the biological mechanisms underlying human ovarian ageing remain poorly understood. Here we performed single-nuclei multi-omics analysis of young and reproductively aged human ovaries to understand the molecular and cellular basis of ovarian ageing in humans. Our analysis reveals coordinated changes in transcriptomic output and chromatin accessibility across cell types during ageing, including elevated mTOR and MAPK signaling, decreased activity of the oxidative phosphorylation and DNA damage repair pathways, and an increased signature of cellular senescence. By constructing cell type-specific regulatory networks, we uncover enhanced activity of the transcription factor CEBPD across cell types in the aged ovary, with a corresponding significant loss of activity of most cell identity-associated transcription factors. Moreover, by performing integrative analyses of our single-nuclei multi-omics data with common genetic variants associated with age at natural menopause (ANM) from genome-wide association studies, we demonstrate a global impact of functional variants on changes in gene regulatory networks across ovarian cell types. Finally, we nominate about a dozen of functional non-coding variants, their target genes and cell types and regulatory mechanisms that underlie genetic association with ANM. This work provides a comprehensive multimodal landscape of human ovarian ageing and mechanistic insights into inherited variation of ANM.

genomics↗

bioRxiv2022

Entorhinal-hippocampal circuit integrity is related to mnemonic discrimination and amyloid-β pathology in older adults

Mnemonic discrimination, a cognitive process that relies on hippocampal pattern separation, is one of the first memory domains to decline in aging and preclinical Alzheimers disease. We tested if functional connectivity (FC) within the entorhinal-hippocampal circuit, measured with high-resolution resting state fMRI, is associated with mnemonic discrimination and A{beta} pathology, measured with PET, in nondemented older adults. Low object mnemonic discrimination performance was specifically associated with increased FC between anterolateral entorhinal cortex (alEC) and dentate gyrus (DG)/CA3, supporting the importance of this connection to object memory. This hyperconnectivity between alEC-DG/CA3 was related to A{beta} pathology and decreased entorhinal cortex volume. In contrast, spatial mnemonic discrimination was not associated with altered FC. A{beta} was further associated with decreased FC and volume within hippocampal subfields. Our findings suggest that A{beta} may indirectly lead to memory impairment through entorhinal-hippocampal circuit dysfunction and neurodegeneration, and provide a mechanism for vulnerability of object mnemonic discrimination.

neuroscience↗