Biology subjects

Kim, J.-S.

Publications and source records attributed to Kim, J.-S..

At least 37 records · Page 2Linked to original sources

bioRxiv2022

Decoding Imagined Musical Pitch from Human Scalp Electroencephalograms

Brain-computer interfaces (BCIs) can restore the functions of communication and control in people with paralysis. In addition to the currently proven functions restored by BCIs, it would enrich life if one could regain a function of musical activity. However, it remains largely unknown whether it is feasible to decode imagined musical information directly from neural activity. Among various musical information, this study aimed to decode pitch information directly from scalp electroencephalography (EEG). Twenty healthy participants performed a task to imagine one of the seven musical pitches (C4 - B4) randomly. To find EEG features for pitch imagination, we took two approaches: exploring multi-band spectral power at individual channels (IC); and exploring power differences between bilaterally symmetric channels (DC). We classified these features into the seven pitch classes using various types of classifiers. The selected spectral power features revealed marked contrasts between left and right hemispheres, between low-, (<13 Hz) and high-frequency (> 13 Hz) bands, and between frontal and parietal areas. The best classification performance for seven pitches was obtained using the IC feature and SVM with the average accuracy of 35.68{+/-}7.47% (max. 50%) and the average information transfer rate (ITR) of 0.37{+/-}0.22 bits/sec. Yet, when we decoded a different number of classes (K = 2 [~] 6) by grouping adjacent pitches, ITR was similar across K as well as between IC and DC features, suggesting efficiency of DC features. This study would be the first to demonstrate the feasibility of decoding imagined musical pitch directly from human EEG.

bioengineering↗

bioRxiv2022

Rescue of transcriptional pausing in metabolic genes jumpstarts Salmonella antioxidant defenses

Detoxification, scavenging and repair systems embody the archetypical antioxidant defenses of prokaryotic and eukaryotic cells1-3. Metabolic rewiring is an emergent aspect in the adaptation of bacteria to oxidative stress4, 5. Evolutionarily diverse bacteria combat the toxicity of reactive oxygen species by actively engaging the stringent response6-8, a metabolic program activated at the level of transcription initiation via guanosine tetraphosphate and the -helical DksA protein9. Studies herein with Salmonella demonstrate that the interactions of structurally related, but functionally unique, -helical Gre factors with the secondary channel of RNA polymerase elicit the expression of metabolic signatures that are associated with resistance to oxidative killing. Gre proteins resolve pauses in ternary elongation complexes of Embden-Meyerhof-Parnas (EMP) glycolysis and aerobic respiration genes. The Gre-directed utilization of glucose in overflow and aerobic metabolism satisfies the energetic and redox demands of Salmonella, while preventing the occurrence of amino acid bradytrophies. Moreover, the simultaneous utilization of lower glycolysis, the methylglyoxal pathway and the electron transport chain curtails the noxious coexistence of reductive and electrophilic stress. The resolution of transcriptional pauses in EMP glycolysis and aerobic respiration genes by Gre factors safeguards Salmonella from the cytotoxicity of phagocyte NADPH oxidase in the innate host response. Control of transcriptional elongation represents a pivotal breakpoint in the regulation of metabolic programs underlying bacterial pathogenesis.

microbiology↗

bioRxiv2022

Production of novel biosurfactant by a new yeast species isolated from Prunus mume Sieb. et Zucc.

Biosurfactants reduce surface and interfacial tension due to their amphiphilic properties, and are an eco-friendly alternative for chemical surfactants. In this study, a novel yeast strain JAF-11 that produces biosurfactant was selected using drop collapse method, and the properties of the material were investigated. The nucleotide sequences of the strain were compared with closely related strains and identified based on the D1/D2 domain of the large-subunit rDNA (LSU) and internal transcribed spacer (ITS) regions. Neodothiora populina CPC 39399T, the closest species with strain JAF-11 in the phylogenetic tree, showed a sequence similarity of 97.75% for LSU and 94.27% for ITS, respectively. The result suggests that the strain JAF-11 represent a distinct species which cannot be assigned to any existing genus or species in the family Dothideaceae. Strain JAF-11 was able to produce biosurfactant reducing the surface tension of medium to 34.5 mN/m on the 6th day of culture and the result of measuring the critical micelle concentration (CMC) by extracting the crude biosurfactant was found to be 24 mg l-1. The molecular weight 502 of the purified biosurfactant was confirmed by measuring the fast atom bombardment mass spectrum (FAB-MS). The chemical structure was analyzed by measuring 1H nuclear magnetic resonance (NMR), 13C NMR, two-dimensional NMRs of the compound. The molecular formula was C26H46O9, and it was composed of one octanoyl group and two hexanoyl group to myo-inositol moiety. The new biosurfactant is the first report of a compound produced by a novel yeast strain JAF-11. This new biosurfactant is proposed as potential candidate for use in a variety field.

microbiology↗

bioRxiv2022

Central role of Prominin-1 in lipid rafts during liver regeneration

Prominin-1 (PROM1), a lipid raft protein, is required for maintaining cancer stem cell properties in hepatocarcinoma cell lines, but its physiological roles in the liver have not been well studied. Here, we investigated the role of PROM1 in lipid rafts with a precise molecular mechanism during liver regeneration. We found that the expression of PROM1 increased during liver regeneration after 2/3 partial hepatectomy (PHx) or CCl4 injection. Interestingly, hepatocyte proliferation and liver regeneration were attenuated in liver-specific Prom1 knockout (Prom1LKO) mice compared to wild-type (Prom1f/f) mice. Detailed mechanistic studies revealed that PROM1 interacted with the interleukin-6 signal transducer glycoprotein 130 (GP130) and confined GP130 to lipid rafts so that STAT3 signaling by IL-6 was effectively activated. Moreover, the overexpression of the glycosylphosphatidylinsositol (GPI)-anchored first extracellular domain of PROM1 (PROM1GPI-EX1), which is a domain that binds to GP130, rescued the proliferation of hepatocytes and liver regeneration in Prom1LKO mice. PROM1 is upregulated in hepatocytes during liver regeneration, and upregulated PROM1 recruits GP130 into lipid rafts and activates the IL6-GP130-STAT3 axis. Thus, we conclude that PROM1 plays an important role in lipid rafts during liver regeneration and might be a promising target for therapeutic applications of liver transplantation.

cell biology↗

bioRxiv2021

In vivo mitochondrial matrix proteome profiling reveals RTN4IP1/OPA10 as an antioxidant NADPH oxidoreductase

Targeting proximity labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice expressing a mitochondrial matrix-targeted ascorbate peroxidase (MAX-Tg) to analyze tissue-specific matrix proteomes. Desthiobiotin-phenol labeling of muscle tissues from MAX-Tg mice allowed for efficient profiling of mitochondrial-localized proteins in these tissues. Comparative analysis of matrix proteomes from MAX-Tg muscle tissues revealed differential enrichment of mitochondrial proteins related to energy production in between different muscle groups. Reticulon 4 interacting protein 1 (RTN4IP1), also known as Optic Atrophy-10 (OPA10), was highly enriched in the cardiac and soleus muscles and was found to localize to the mitochondrial matrix via a strong mitochondrial targeting sequence at its N-terminus. Protein structure analysis revealed that RTN4IP1 is an NADPH oxidoreductase with structural homology to bacterial quinone oxidoreductase. Enzymatic activity assays, interactome analysis, and metabolite profiling confirmed a function for RTN4IP1 in coenzyme Q (CoQ) biosynthesis. Rtn4ip1-knockout C2C12 cells had reduced CoQ9 levels, were vulnerable to oxidative stress, and had decreased oxygen consumption rates and ATP production. Collectively, RTN4IP1 is a mitochondrial antioxidant NADPH oxidoreductase supporting oxidative phosphorylation activity in muscle tissue.

cell biology↗

bioRxiv2021

A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is maintained in xBrassicoraphanus. B. rapa-originated transposable elements were transcriptionally silenced in xBrassicoraphanus, rendered by gain of CHG methylation in trans via small RNAs derived from the same sequences of R. sativus subgenome. Our work proposes that not only transcription compatibility but also a certain extent of genome divergence supports hybrid genome stabilization, which may explain great diversification and expansion of angiosperms during evolution.

plant biology↗

bioRxiv2021

Enteric glial cells favour accumulation of anti-inflammatory macrophages during the resolution of muscularis inflammation

ObjectiveMonocyte-derived macrophages (M{varphi}s) are crucial regulators during muscularis inflammation. However, it is unclear which microenvironmental factors are responsible for monocyte recruitment and neurotrophic M{varphi} differentiation in this paradigm. Here, we investigate M{varphi} heterogeneity at different stages of muscularis inflammation and determine how environmental cues can attract and activate tissue protective M{varphi}s. DesignSingle cell RNA sequencing was performed on immune cells from the muscularis of wild-type and CCR2-/- mice at different timepoints after muscularis inflammation. CX3CR1GFP/+ and CX3CR1CreERT2 R26YFP mice were analyzed by flow cytometry and immunofluorescence. The transcriptome of enteric glial cells (EGCs) was investigated using PLPCreERT2 Rpl22HA mice. In addition, we assessed the effect of supernatant from neurosphere-derived EGCs on monocyte differentiation based on the expression of pro- and anti-inflammatory factors. ResultsMuscularis inflammation induced marked alterations in mononuclear phagocyte populations associated with a rapid infiltration of Ly6c+ monocytes that locally acquired unique transcriptional states. Trajectory inference analysis revealed two main pro-resolving M{varphi} subpopulations during the resolution of muscularis inflammation, i.e. Cd206+ MhcIIhi and Timp2+ MhcIIlo M{varphi}s, which were both derived from CCR2+ monocytes. Interestingly, we found that EGCs were able to sense damage to the muscularis to stimulate monocyte recruitment and differentiation towards pro-resolving M{varphi}s via CCL2 and CSF1, respectively. ConclusionOur study provides a comprehensive insight into pro-resolving M{varphi} differentiation and their regulators during muscularis inflammation. We deepened our understanding in the interaction between EGCs and M{varphi}s, thereby highlighting pro-resolving M{varphi} differentiation as a potential novel therapeutic strategy for the treatment of intestinal inflammation.

immunology↗

bioRxiv2021

Endomembrane systems are reorganized by ORF3a and Membrane (M) of SARS-CoV-2

The endomembrane reticulum (ER) is largely reorganized by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 ORF3a and membrane (M) protein expression affects ER-derived structures including cubic membrane and double membrane vesicles in coronavirus-infected cells; however, the molecular mechanisms underlying ER remodeling remain unclear. We introduced a "plug and playable" proximity labeling tool (TurboID-GBP) for interactome mapping of GFP-tagged SARS-CoV-2 ORF3a and M proteins. Through mass spectrometric identification of the biotinylated lysine residue (K+226 Da) on the viral proteins using Spot-TurboID workflow, 117 and 191 proteins were robustly determined as ORF3a and M interactomes, respectively, and many, including RNF5 (E3 ubiquitin ligase), overlap with the mitochondrial-associated membrane (MAM) proteome. RNF5 expression was correlated to ORF3a ubiquitination. MAM formation and secreted proteome profiles were largely affected by ORF3a expression. Thus, SARS-CoV-2 may utilize MAM as a viral assembly site, suggesting novel anti-viral treatment strategies for blocking viral replication in host cells. HighlightsO_LISARS-CoV-2 proteins ORF3a and M alter endoplasmic reticulum proteome profile C_LIO_LIORF3a affects mitochondrial-associated membrane formation C_LIO_LISARS-CoV-2 may utilize mitochondrial-associated membrane as viral assembly site C_LIO_LIORF3a and M interactome proteins may serve as targets for COVID-19 treatment C_LI eTOC BlurbER remodelling by SARS-CoV-2 ORF3a and M protein

biochemistry↗

bioRxiv2021

Escherichia coli Cryptic Prophages Sense Nutrients to Control Persister Cell Resuscitation

We determined previously that some cryptic prophages are not genomic junk but instead enable cells to combat myriad stresses as part of an active stress response. However, how these phage fossils affect the extreme stress response of dormancy; i.e., how cryptic prophages affect persister cell formation and resuscitation, has not been fully explored. Persister cells form as a result of stresses such as starvation, antibiotics, and oxidative conditions, and resuscitation of these persister cells likely causes recurring infections such as those associated with tuberculosis, cystic fibrosis, and Lyme disease. Unlike for the active stress response, here we find that deletion of each of the nine Escherichia coli cryptic prophages has no effect on persister cell formation. Strikingly, elimination of each cryptic prophage results in an increase in persister cell resuscitation with a dramatic increase in resuscitation upon deleting all nine prophages. This increased resuscitation includes eliminating the need for a carbon source and is due to activation of the phosphate import system as a result of inactivating transcriptional regulator AlpA of the CP4-57 cryptic prophage, since we found {Delta}alpA increases persister resuscitation, and AlpA represses phosphate regulator PhoR. Therefore, we report a novel cellular stress mechanism controlled by cryptic prophages: regulation of phosphate uptake which controls the exit of the cell from dormancy and prevents premature resuscitation in the absence of nutrients.

microbiology↗

bioRxiv2021

Calbindin regulates Kv4.1 trafficking and excitability of dentate granule cells via CaMKII-dependent phosphorylation

Calbindin, a major Ca2+ buffer in dentate granule cells (GCs), plays a critical role in shaping Ca2+ signals, yet how it regulates neuronal functions remains largely unknown. Here, we found that calbindin knock-out mice (CBKO) exhibited hyperexcitability in dentate GCs and impaired pattern separation, which was concurrent with reduced K+ current due to downregulated surface expression of Kv4.1. Consistently, manipulation of the calbindin expression in HT22 led to changes in CaMKII activation and the level of surface localization of Kv4.1 through phosphorylation at serine 555, confirming the mechanism underlying neuronal hyperexcitability in CBKO. We also discovered that Ca2+ buffering capacity was significantly reduced in the GCs of Tg2576 to the level of CBKO GCs, and this reduction was restored to normal levels by antioxidants, suggesting that calbindin is a target of oxidative stress. Our data suggest that regulation of CaMKII signaling by Ca2+ buffer is crucial for neuronal excitability regulation.

neuroscience↗

bioRxiv2021

Spc1 regulates substrate selection for signal peptidase

Signal peptidase (SPase) cleaves the signal sequences (SSs) of secretory precursors. It contains an evolutionarily conserved membrane protein subunit, Spc1 that is dispensable for the catalytic activity of SPase, and its role remains elusive. In the present study, we investigated the function of yeast Spc1. First, we set up an in vivo SPase cleavage assay using secretory protein CPY variants with SSs modified in the n and h regions. When comparing the SS cleavage efficiencies of these variants in cells with or without Spc1, we found that signal-anchored sequences become more susceptible to cleavage by SPase without Spc1. Further, SPase-mediated processing of transmembrane (TM) segments in model membrane proteins was reduced upon overexpression of Spc1. Spc1 was co-immunoprecipitated with membrane proteins carrying uncleaved signal-anchored or TM segments. These results suggest a role of Spc1 in shielding TM segments from SPase action, thereby contributing to accurate substrate selection for SPase.

biochemistry↗

bioRxiv2021

Strain variation in Bacillus cereus biofilms and their susceptibility to extracellular matrix-degrading enzymes

Bacillus cereus is a foodborne pathogen and can form biofilms on food contact surfaces, which causes food hygiene problems. While it is necessary to understand strain-dependent variation to effectively control these biofilms, strain-to-strain variation in the structure of B cereus biofilms is poorly understood. In this study, B. cereus strains from tatsoi and the ATCC 10987 reference strain were incubated at 30{degrees}C to form biofilms in the presence of the extracellular matrix-degrading enzymes DNase I, proteinase K, dispase II, cellulase, amyloglucosidase, and -amylase to assess the susceptibility to these enzymes. The four strains exhibited four different patterns in terms of biofilm susceptibility to the enzymes as well as morphology of surface-attached biofilms or suspended cell aggregates. DNase I inhibited the biofilm formation of strains ATCC 10987 and BC4 but not of strains BC10 and BC72. This result suggests that some strains may not have extracellular DNA, or their extracellular DNA may be protected in their biofilms. In addition, the strains exhibited different patterns of susceptibility to protein- and carbohydrate-degrading enzymes. While other strains were resistant, strains ATCC 10987 and BC4 were susceptible to cellulase, suggesting that cellulose or its similar polysaccharides may exist and play an essential role in their biofilm formation. Our compositional analysis of strains ATCC 10987 and BC4 suggested that the physicochemical properties of their biofilms are distinct, as calculated by the carbohydrate to protein ratio. Taken together, our study suggests that the extracellular matrix of B. cereus biofilms may be highly diverse and provides insight into the diverse mechanisms of biofilm formation among B. cereus strains.

microbiology↗

bioRxiv2020

The SARS-CoV-2 RNA interactome

SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its ability to repurpose host RNA-binding proteins (RBPs) to form its own RNA interactome. Here, we developed and applied a robust ribonucleoprotein capture protocol to uncover the SARS-CoV-2 RNA interactome. We report 109 host factors that directly bind to SARS-CoV-2 RNAs including general antiviral factors such as ZC3HAV1, TRIM25, and PARP12. Applying RNP capture on another coronavirus HCoV-OC43 revealed evolutionarily conserved interactions between viral RNAs and host proteins. Network and transcriptome analyses delineated antiviral RBPs stimulated by JAK-STAT signaling and proviral RBPs responsible for hijacking multiple steps of the mRNA life cycle. By knockdown experiments, we further found that these viral-RNA-interacting RBPs act against or in favor of SARS-CoV-2. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions.

microbiology↗

bioRxiv2020

Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice

Here we describe iSLET (in situ Secretory protein Labeling via ER-anchored TurboID) which labels secretory pathway proteins as they transit through the ER-lumen to enable dynamic tracking of tissue-specific secreted proteomes in vivo. We expressed iSLET in the mouse liver and demonstrated efficient in situ labeling of the liver-specific secreted proteome which could be tracked and identified within circulating blood plasma. iSLET is a versatile and powerful tool for studying spatiotemporal dynamics of secretory proteins, a valuable class of biomarkers and therapeutic targets.

biochemistry↗

bioRxiv2020

ERH as a component of the Microprocessor facilitates the maturation of suboptimal microRNAs

The Microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here we identify Enhancer of Rudimentary Homolog (ERH) as a new component of the Microprocessor. ERH binds to a conserved region in the N-terminus of DGCR8. Knockdown of ERH or deletion of the DGCR8 N-terminus results in a decrease of processing of primary miRNAs with suboptimal hairpin structures that reside in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate "cluster assistance" in which the Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA pathway.

molecular biology↗

bioRxiv2019

Prominin-1-Radixin Axis controls hepatic gluconeogenesis by regulating PKA activity

Prominin-1 (Prom1) is a major cell surface marker of cancer stem cells, but its physiological functions in the liver have not been elucidated. We analyzed the levels of mRNA transcripts in serum-starved primary Prom1+/+ and Prom1-/- mouse hepatocytes using RNA-sequencing (RNA-seq) data, and found that CREB target genes were down-regulated. This initial observation led us to determine that the Prom1 deficiency inhibited cAMP response element binding protein (CREB) activation and gluconeogenesis, but not cyclic AMP (cAMP) accumulation, in glucagon-, epinephrine-, or forskolin-treated liver tissues and primary hepatocytes, and mitigated glucagon-induced hyperglycemia. Because Prom1 interacted with radixin, the Prom1 deficiency prevented radixin from localizing to the plasma membrane. Moreover, systemic adenoviral knockdown of radixin inhibited CREB activation and gluconeogenesis in glucagon-treated liver tissues and primary hepatocytes, and mitigated glucagon-elicited hyperglycemia. Based on these results, we conclude that Prom1 regulates hepatic PKA signaling via radixin functioning as an A kinase-anchored protein (AKAP).

cell biology↗

bioRxiv2019

Comparative analysis of CreER transgenic mice for the study of brain macrophages - a case study

Conditional mutagenesis and fate mapping have contributed considerably to our understanding of physiology and pathology. Specifically, Cre recombinase-based approaches allow the definition of cell type-specific contributions to disease development and inter-cellular communication circuits in respective animals models. Here we compared Cx3cr1CreER and Sall1CreER transgenic mice and their use to decipher the brain macrophage compartment as a showcase to discuss recent technological advances. Specifically, we highlight the need to define the accuracy of Cre recombinase expression, as well as strengths and pitfalls of these particular systems that should be taken into consideration when applying these models.

immunology↗

bioRxiv2019

NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs

Maintenance and expression of mitochondrial DNA is indispensable for proper function of the oxidative phosphorylation machinery. Post-transcriptional modification of mitochondrial RNA has emerged as one of the key regulatory steps of human mitochondrial gene expression. Mammalian NOP2/Sun RNA Methyltransferase Family Member 2 (NSUN2) has been characterised as an RNA methyltransferase that introduces 5-methylcytosine (m5C) in nuclear-encoded tRNAs, mRNAs, microRNA and noncoding RNAs. In these roles, NSUN2 has been associated with cell proliferation and differentiation. Pathogenic variants in NSUN2 have been linked with neurodevelopmental disorders. Here we employ spatially restricted proximity labelling and immunodetection to demonstrate that NSUN2 is imported into the matrix of mammalian mitochondria. Using three genetic models for NSUN2 inactivation - knockout mice, patient-derived fibroblasts and CRISPR/Cas9 knockout in human cells - we show that NSUN2 in necessary for the generation of m5C at positions 48, 49 and 50 of several mammalian mitochondrial tRNAs. Finally, we show that inactivation of NSUN2 does not have a profound effect on mitochondrial tRNA stability and oxidative phosphorylation in differentiated cells. We discuss the importance of the newly discovered function of NSUN2 in the context of human disease.

biochemistry↗