Biology subjects

Lee, S.-Y.

Publications and source records attributed to Lee, S.-Y..

45 records · Page 3Linked to original sources

bioRxiv2019

Mutation profiling of both cfDNAs and CTCs in gynecological cancer patients

In the recent years, microRNAs (miRNAs) have been discovered to play a very important role in biological processes such as development, differentiation, and apoptosis. The miRNA expression levels in cells are associated with diverse diseases including cancers. MiRNA inhibitors have been widely employed for studying the functions and targets of miRNAs by transfecting the inhibitors into cells. The concentrations of miRNA inhibitors used for such studies can vary depending on the types of miRNAs being tested, the cell lines under study, and the analysis methods. Therefore, in order to obtain accurate results, appropriate amounts of miRNA inhibitors have to be used in the experiments. Apart from amounts, the evaluation of inhibitors may also have to be conducted for functional studies.\n\nHere we developed capillary electrophoresis with laser-induced fluorescence (CE-LIF) method for evaluating miRNA inhibitor and for optimizing miRNA inhibitor concentrations, in the A549 lung cancer cell line. The target miRNAs, miRNA-23a and miRNA-24 are biomarker candidates in lung cancer cell lines. Our results showed that miRNA-23a and miRNA-24 were effectively inhibited upon transfection with 20 nM miRNA inhibitors using CE-LIF method. Furthermore, these results demonstrated the potential of CE for fast, specific, sensitive and specific analyses for the evaluation and determination of the optimal concentration of miRNA inhibitors for functional studies.\n\nAbstract Graphics\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/566786v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@2bbfeeorg.highwire.dtl.DTLVardef@45b7e3org.highwire.dtl.DTLVardef@12ba79borg.highwire.dtl.DTLVardef@108ec2f_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2019

Visualizing Conformational Transitions of the Lipid II Flippase MurJ

The biosynthesis of many polysaccharides, including bacterial peptidoglycan and eukaryotic N-linked glycans, requires transport of lipid-linked oligosaccharide (LLO) precursors across the membrane by specialized flippases. MurJ is the flippase for the lipid-linked peptidoglycan precursor Lipid II, a key player in bacterial cell wall synthesis, and a target of recently discovered antibacterials. However, the flipping mechanism of LLOs including Lipid II remains poorly understood due to a dearth of structural information. Here we report crystal structures of MurJ captured in inward-closed, inward-open, inward-occluded and outward-facing conformations. Together with cysteine accessibility, mass spectrometry, and complementation studies, we elucidate the conformational transitions in MurJ that mediate lipid flipping, identified the key ion for function, and provide a framework for the development of inhibitors.

biochemistry↗

bioRxiv2019

Symmetry transitions during gating of the TRPV2 ion channel in lipid membranes

The Transient Receptor Potential Vanilloid 2 (TRPV2) channel is a member of the temperature-sensing thermoTRPV family. Recent advances in cryo-electronmicroscopy (cryo-EM) and X-ray crystallography have provided many important insights into the gating mechanisms of thermoTRPV channels. Interestingly, crystallographic studies of ligand-dependent TRPV2 gating have shown that the TRPV2 channel adopts two-fold symmetric arrangements during the gating cycle. However, it was unclear if crystal packing forces played a role in stabilizing the two-fold symmetric arrangement of the channel. Here we employ cryo-EM to elucidate the structure of full-length rabbit TRPV2 in complex with the agonist resiniferatoxin (RTx) in nanodiscs and amphipol. We show that RTx induces two-fold symmetric conformations of TRPV2 in both environments. However, the two-fold symmetry is more pronounced in the native-like lipid environment of the nanodiscs. Our data offers insights into a gating pathway in TRPV2 involving symmetry transitions.

biophysics↗

bioRxiv2019

Sarcopenia is an independent predictor of hospitalization in chronic kidney disease outpatients

BackgroundPatients with chronic kidney disease (CKD) experience much more marked and earlier muscle wasting than subjects who do not have chronic illnesses. However, a few studies that have examined sarcopenia have been reported in CKD patients. We investigated the prevalence of sarcopenia in predialysis and dialysis outpatients with CKD and explored its relationship with the clinical outcomes.\n\nMeasurementsSarcopenia was defined as reduced muscle strength accompanied by decreased adjusted appendicular skeletal muscle (ASM), while those patients who exhibited only one of these characteristics were categorized as presarcopenic patients. ASM was measured by bioimpedence analysis, and muscle strength was evaluated by handgrips. ASM was adjusted by weight (ASM/wt). Patients were prospectively followed for up to 2 years.\n\nResultsOne hundred seventy-nine patients were recruited (114 male and 65 female patients who were classified into 103 predialysis patients and 76 dialysis patients, with 44.7% having diabetes). Their mean age was 60.6 {+/-} 13.5 years old. The prevalence of sarcopenia was 9.5%, while 55.9% of the patients were categorized as presarcopenic. The ASM/wt index showed significant correlations with age, handgrip strength, HOMA-IR and frailty scores. Multivariate Cox proportional hazards models demonstrated that the risk of hospitalization was significantly higher for patients with presarcopenia [hazard ratio (HR), 2.48; 95% confidence interval (CI), 1.180-5.230], and the risk of hospitalization was much higher for patients with sarcopenia than for patients in the nonsarcopenic group (HR, 9.11; 95% CI, 2.295-25.182)\n\nConclusionsSarcopenia and presarcopenia, which were defined using the ASM/wt index and handgrip strength, predicted a poorer, hospitalization-free survival in CKD patients

scientific communication and education↗

bioRxiv2019

Visualizing structural transitions of ligand-dependent gating of the TRPM2 channel

The calcium-permeable transient receptor potential melastatin 2 (TRPM2) channel plays a key role in redox sensation in many cell types 1-3. Channel activation requires binding of both ADP-ribose (ADPR) 2,4-6 and Ca2+ 7. The recently published TRPM2 structures from Danio rerio in the ligand-free and in the ADPR/Ca2+-bound conditions represent the channel in closed and open states, which uncover substantial tertiary and quaternary conformational rearrangements 8. However, it is unclear how these rearrangements occur within the tetrameric channel during channel gating. Here we report two cryo-electron microscopy structures of TRPM2 from the same species in complex with Ca2+ alone, and with both ADPR and Ca2+, determined to an overall resolution of ~3.8 [A] and ~4.2 [A] respectively. In comparison with the published results, our studies capture TRPM2 in two-fold symmetric intermediate states, offering a glimpse of the structural transitions within the tetramer that bridge the closed and open conformations.

biochemistry↗

bioRxiv2018

Conformational ensemble of the human TRPV3 ion channel

Transient receptor potential vanilloid channel 3 (TRPV3), a member of the thermosensitive TRP (thermoTRPV) channels, is activated by warm temperatures and serves as a key regulator of normal skin physiology through the release of pro-inflammatory messengers. Mutations in trpv3 have been identified as the cause of the congenital skin disorder, Olmsted syndrome. Unlike other members of the thermoTRPV channel family, TRPV3 sensitizes upon repeated simulation, yet a lack of structural information about the channel precludes a molecular-level understanding of TRPV3 sensitization and gating. Here, we present the cryo-electron microscopy structures of apo and sensitized human TRPV3, as well as several structures of TRPV3 in the presence of the common thermoTRPV agonist 2-aminoethoxydiphenyl borate (2-APB). Our results show -to-{pi}-helix transitions in the S6 during sensitization, and suggest a critical role for the S4-S5 linker {pi}-helix during ligand gating.

biochemistry↗

bioRxiv2018

Physiological Characteristics of Viable-but-nonculturable Vibrio parahaemolyticus upon Prolonged Exposure to the Refrigerator Temperature

Although it has been reported that viable-but-nonculturable (VBNC) cells of Vibrio parahaemolyticus can be developed by a prolonged duration of cold-starvation there are restricted cellular characteristics available on understanding the exact mechanisms governing the entry of pathogens into the VBNC state. Therefore, this research was aimed at determining the cellular profile of VBNC cells of V. parahaemolyticus upon exposure to the refrigerator temperature. Strains of V. parahaemolyticus were incubated in artificial sea water (ASW) microcosms (pH 6) added with different amounts of NaCl at 4{degrees}C until these pathogens entered into such a dormant state. At a regular time-interval, both culturability and viability of these bacteria were enumerated, and then cellular profiling were carried out in terms of cellular membrane permeability, enzymatic activity, hydrophobicity, fatty acid composition, and morphological changes after cells of V. parahaemolyticus became the VBNC state. Three strains of V. parahaemolyticus used in this study showed that VBNC cells retained the strong virulent properties to Vero and CACO-2 cell lines, re-gained the cytotoxicity even after resuscitation, became permeabilized in terms of the outer membrane, showed lower levels of enzymatic (catalase and glutathione-S-transferase) activities, exerted the increasing hydrophobicity, and then exhibited increasing amounts of saturated fatty acids.\n\nIMPORTANCETo the current best knowledge, there are restricted information available on understanding the physiological characterization of viable-but-nonculturable cells. Most previous studies are still making a degree of efforts in discovering the causative effector causing microorganisms to be induced into the VBNC state. Herein, the present study showed that pathogenic V. parahaemolyticus can enter into the VBNC state when challenged by a certain environmental stress where higher amounts of NaCl combined with acidic pHs was artificially controlled. Importantly, it was indicated that VBNC V. parahaemolyticus maintained peculiarly different physiological characteristics. Furthermore, this study proposed a novel approach on the transient/stepwise conversion of the bacteria into the VBNC state. Specific alternative tools for measuring and controlling the incidence of VBNC pathogens on food are not established until now. In this aspect, results obtained from this study will used to provide an effective insight in determining physiological properties of viable-but-nonculturable V. parahaemolyticus.

microbiology↗

bioRxiv2018

Analysis of the Resuscitation-Availability of Viable-But-Nonculturable Cells of Vibrio parahaemolyticus upon Exposure to the Refrigerator Temperature

Major pathogenic strains of Vibrio parahaemolyticus can enter into the viable-but-nonculturable (VBNC) state when subjected to environmental conditions commonly encountered during food processing. Especially, VBNC cells can be recovered to the culturable state reversibly by removing the causative stress, expressing higher levels of virulence factors. Therefore, the aim of this study was to determine if VBNC V. parahaemolyticus strains retain the resuscitation-availability upon eliminating the adverse condition, followed by the enrichment in developed resuscitation-facilitating buffers. Bacterial cells were shown to enter into the VBNC state in artificial sea water (ASW, pH 6) microcosms at 4{degrees}C within 70 days. VBNC cells were harvested, inoculated in formulated resuscitation-buffers, and then incubated at 25{degrees}C for several days. TSB (pH 8) supplemented with 3% NaCl (TSBA) exhibited the higher resuscitation-availability of VBNC cells. It was also shown that TSBA containing 10,000 U/mg/protein catalase, 2% sodium pyruvate, 20 mM MgSO4, 5 mM ethylenediaminetetraacetic acid (EDTA), and cell free supernatants extracted from the pure cultures of V. parahaemolyticus was more effective in resuscitating VBNC cells of V. parahaemolyticus, showing by 7.69-8.91 log10 CFU/ml.\n\nIMPORTANCEGenerally, higher concentrations ([≤]40%) of NaCl are used for preserving different sorts of food products from bacterial contaminations. However, it was shown from the present study that strains of V. parahaemolyticus were able to persist in maintaining the cellular viability, thereby entering into the VBNC state upon exposure to the refrigerator temperature for 80 days. Hence, the ability of VBNC V. parahaemolyticus to re-enter into the culturable state was examined, using various resuscitation buffers that were formulated in this study. VBNC cells re-gained the culturability successfully when transferred onto the resuscitation-buffer D, and then incubated at 25{degrees}C for several days. Resuscitation-facilitating agent D is consisting of antioxidizing agents, mineral, an emulsifier, and cell free supernatants from the actively growing cells of V. parahaemolyticus. It appeared that such a reversible conversion of VBNC cells to the culturable state would depend on multiple resuscitation-related channels.

microbiology↗

bioRxiv2018

Immuno-genomic PanCancer Landscape Reveals Diverse Immune Escape Mechanisms and Immuno-Editing Histories

Immune reactions in the tumor micro-environment are one of the cancer hallmarks and emerging immune therapies have been proven effective in many types of cancer. To investigate cancer genome-immune interactions and the role of immuno-editing or immune escape mechanisms in cancer development, we analyzed 2,834 whole genomes and RNA-seq datasets across 31 distinct tumor types from the PanCancer Analysis of Whole Genomes (PCAWG) project with respect to key immuno-genomic aspects. We show that selective copy number changes in immune-related genes could contribute to immune escape. Furthermore, we developed an index of the immuno-editing history of each tumor sample based on the information of mutations in exonic regions and pseudogenes. Our immuno-genomic analyses of pan-cancer analyses have the potential to identify a subset of tumors with immunogenicity and diverse background or intrinsic pathways associated with their immune status and immuno-editing history.

genomics↗