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Thompson KMA, Gamble ASD, Kontro H, Lee JB, Burr JF. Low- and high-volume blood-flow restriction treadmill walking both improve maximal aerobic capacity independently of blood volume. Scand J Med Sci Sports 2024; 34:e14534. [PMID: 37961932 DOI: 10.1111/sms.14534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/22/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
AIM Assess the effect of low- and high-volume blood flow restriction training (BFR) on maximal aerobic capacity (VO2 max) and determine if alteration in VO2 max is mediated through changes in hemoglobin mass (Hbmass) and blood volume. METHODS Participants' Hbmass (CO-rebreathe), single, and double-leg VO2 max and blood volume regulating hormonal responses (renin and copeptin) were measured before and after BFR training. Training consisted of treadmill walking either (1) twice-daily for 4week (CON and BFRHV ) or (2) twice-weekly for 6week (BFRLV ). Each session consisted of five intervals (3 min, 5% incline, 5 km/h, 100% of lowest occlusion pressure), with 1 min of standing rest between sets. RESULTS VO2 max increased using both training exposures, in as quickly as 2-weeks (BFRLV baseline to 4week: +315 ± 241 mL (8.7%), p = 0.02; BFRHV baseline to 2week: +360 ± 261 mL (7.9%), p < 0.01), for the BFRLV and BFRHV groups, with no change in CON. Single- and double-leg VO2 max improved proportionately (single/double-leg VO2 max ratio: BFRLV 78 ± 4.9-78 ± 5.8%, BFRHV 79 ± 6.5-77 ± 6.5%), suggesting that the mechanism for increased VO2 max is not solely limited to central or peripheral adaptations. Hbmass remained unchanged across groups (CON: +10.2 ± 34 g, BFRLV : +6.6 ± 42 g, BFRHV : +3.2 ± 44 g; p = 0.9), despite a significant release of blood volume regulating hormones after initial BFR exposure (renin +20.8 ± 21.9 ng/L, p < 0.01; copeptin +22.0 ± 23.8 pmol/L, p < 0.01), which was blunted following BFRHV training (renin: +13.4 ± 12.4 ng/L, p = 0.09; copeptin: +1.9 ± 1.7 pmol/L, p = 0.98). CONCLUSION BFR treadmill walking increases VO2 max irrespective of changes in Hbmass or blood volume despite a large release of blood volume regulating hormones in response to BFR treadmill walking.
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Lee JB, Choi JS. Healthcare workers' epidemiology of occupational exposure to blood-borne viruses, post-exposure prophylaxis, and seroconversion over 10 years. J Hosp Infect 2023; 135:18-27. [PMID: 36805081 DOI: 10.1016/j.jhin.2023.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/25/2023] [Accepted: 02/06/2023] [Indexed: 02/19/2023]
Abstract
BACKGROUND Healthcare workers (HCWs) have an increased risk of blood-borne pathogen (BBP) infection due to occupational blood exposures (OBEs). Early reporting, detection, and post-exposure prophylaxis (PEP) allows for prevention of infections. AIM To investigate the incidence of OBEs, related epidemiological characteristics, PEP completion rate, time and reason for PEP discontinuation, and seroconversion rate reported over 10 years. METHODS We retrospectively analysed 1,086 OBE cases and staff PEP management from January 2012 to December 2021 in a South Korean tertiary hospital. FINDINGS The mean incidence of OBE was 7.82 per 100 beds and 3.0 per 100 HCWs. Among 1,086 cases, 633 (58.3%) required PEP, and 453 (41.7%) did not. After OBEs, 70.1% (444/633) of those subject to PEP completed tracking, and 29.9% (189/633) stopped PEP tracking (p < 0.001). The PEP completion rate showed a significant difference according to gender (p = 0.024), occupation (p < 0.001), and exposure frequency (p < 0.001). None of the 444 HCWs who completed PEP seroconverted to hepatitis B virus, hepatitis C virus, human immunodeficiency virus, or Treponema pallidum (syphilis). CONCLUSION Our findings demonstrate the need to improve follow-up care among HCWs following OBEs. There is a need for education in healthcare facilities; moreover, establishing a national surveillance system is necessary to ensure that HCWs proactively undergo PEP and complete their follow-up visits.
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Hassan NM, Lee JB. RADIOLOGICAL IMPACT OF USING DECORATIVE GRANITE AS AN ATTENUATOR OF IONIZING RADIATION. RADIATION PROTECTION DOSIMETRY 2023; 199:11-19. [PMID: 36309854 DOI: 10.1093/rpd/ncac213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 08/03/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Granite is a widely available rock, which can be used as a shielding material, for bulk in the form of the aggregate in concrete. It has the weakness that it is more radioactive than many other rocks, which can be used in concrete. This paper looks at its properties as a shielding material and the activity level. Thus, the concentrations of 226Ra, 232Th and 40K, in granite were measured using a high pure germanium detector (HPGe). They were ranged from (15 ± 4 to 49 ± 5) Bq kg-1 for 226Ra, (22 ± 4 to 78 ± 4 Bq kg-1) for 232Th and (791 ± 13 to 1231 ± 15 Bq kg-1) for 40K. Radiological indices of radium equivalent concentration (Raeq), external (Hex), internal (Hin) and annual effective dose were less than worldwide recommended limits. The results emphasized, the granite samples had no radiation hazard. Nevertheless, the mass attenuation coefficients of granite samples were measured for the gamma rays of energy range 122-1408 keV. The mass attenuation coefficients of the studied granite samples were ranged from 0.05 to 0.15 cm2 g-1. In addition, the average the half-value layer of granite was varied from 1.8 cm for 122 keV to 5.2 cm for 1408 keV. The results are that the attenuation characteristics are typical and match the values given by NIST for 'concrete' and that the activity levels of the samples examined are acceptable. Thus the granite may be used as an attenuator for ionizing radiation.
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Britton BM, London JA, Martin-Lopez J, Jones ND, Liu J, Lee JB, Fishel R. Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA. J Biol Chem 2022; 298:102505. [PMID: 36126773 PMCID: PMC9597889 DOI: 10.1016/j.jbc.2022.102505] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 12/30/2022] Open
Abstract
MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.
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Kim CM, Lee JB, Shin SJ, Ahn JB, Lee M, Kim HS. The efficacy of immune checkpoint inhibitors in elderly patients: a meta-analysis and meta-regression. ESMO Open 2022; 7:100577. [PMID: 36156450 PMCID: PMC9588901 DOI: 10.1016/j.esmoop.2022.100577] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/03/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022] Open
Abstract
Background Immune checkpoint inhibitor (ICI) therapy has improved patient survival in advanced cancers; however, the efficacy of ICIs in elderly patients is still elusive. This study assessed the efficacy of ICIs in elderly patients with advanced cancer in terms of overall survival (OS) and progression-free survival (PFS). Materials and methods We carried out a systematic review and identified 30 head-to-head phase II/III randomized controlled trials that compared immunotherapy with the standard of care in advanced solid tumor patients. The data on patients younger or over 65 years of age were indexed from PubMed-Medline, Embase, and Scopus and obtained for meta-analysis. The subgroup analyses were stratified by primary tumor type, line of treatment, or type of immunotherapy, and a meta-regression analysis was carried out after adjusting for all other variables. Results The study included 17 476 patients, comprising 58% (10 119) younger (<65 years old) and 42% (7357) elderly (≥65 years old) patients. The hazard ratio (HR) for OS was 0.77 [95% confidence interval (CI) 0.70-0.85] and 0.77 (95% CI 0.70-0.85) in the younger and elderly groups, respectively, suggesting similar efficacies of ICIs in these two age groups. The subgroup analyses revealed no significant relationship between age and treatment outcomes, except for the PFS benefit in younger patients with melanoma than in elderly patients (HR 0.44 in younger patients versus 0.65 in elderly patients, P = 0.04). These results were further supported by meta-regression analysis, which showed no statistically significant difference in OS (P = 0.954) and PFS (P = 0.555) between the two age groups. Conclusions The findings suggest that age-associated impairments of the immune system did not affect the efficacy of ICIs in elderly patients compared to younger patients. Therefore, the choice of ICIs for elderly patients can be considered, regardless of chronological age. We evaluated the efficacy of ICI in 17 476 patients, comprising 58% younger and 42% elderly patients. Meta-analysis resulted in the comparable efficacy of ICI between younger and older age groups. Further, meta-regression analysis showed no significant difference in OS and PFS. Our study suggests that chronological age does not lead to immunosenescence in response to ICI in immune-oncology.
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Lee JB, Choi JS. The effect of an isolation-coping programme on patients isolated for colonization or infection with multidrug-resistant organisms: a quasi-experimental study. J Hosp Infect 2022; 129:31-37. [PMID: 35987316 DOI: 10.1016/j.jhin.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The global increase in the prevalence of vancomycin-resistant enterococci (VRE) and carbapenem-resistant Enterobacterales (CRE) among multidrug-resistant organisms (MDROs) has necessitated contact precaution and isolation in medical institutions. Contact isolation has a negative effect on the mental health of patients, but few interventions have addressed this issue. AIM This study evaluated an isolation-coping programme developed for patients colonized or infected with VRE or CRE. METHODS To mitigate the negative effects of isolation due to having MDRO, an infection control nurse in the present study 1) developed an isolation-coping programme and 2) validated the programme's effect on the uncertainty, anxiety, depression, and knowledge of patients isolated because of MDRO (VRE or CRE) using a pre-post quasi-experimental design. FINDINGS The experimental group (n=56) received education and emotional support via the isolation-coping programme, while the control group (n=55) received only verbal isolation guidelines provided by the medical institution. Compared with the control group, the experimental group showed a reduction in uncertainty (t=-8.925), anxiety (Z=-6.131), and depression (Z=-5.379), and better knowledge (Z=-8.372) (p<.001 for all). CONCLUSION The novel isolation-coping programme is an effective intervention to improve uncertainty, anxiety, depression, and knowledge in patients isolated with VRE or CRE.
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Kim B, Park Y, Hwang HJ, Chang J, Kim YK, Lee JB. Single polysome analysis of mRNP. Biochem Biophys Res Commun 2022; 618:73-78. [PMID: 35716598 DOI: 10.1016/j.bbrc.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Eukaryotic translation is a complex process that involves the interplay of various translation factors to convert genetic information into a specific amino acid chain. According to an elegant model of eukaryotic translation initiation, the 3' poly(A) tail of an mRNA, which is occupied by poly(A)-binding proteins (PABPs), communicates with the 5'-cap bound by eIF4E to enhance translation. Although the circularization of mRNA resulting from the communication is widely understood, it has yet to be directly observed. To explore mRNA circularization in translation, we analyzed the level of colocalization of eIF4E, eIF4G, and PABP on individual mRNAs in polysomal and subpolysomal fractions using single polysome analysis. Our results show that the three tested proteins barely coexist in mRNA in either polysomal or subpolysomal fractions, implying that the closed-loop structure generated by the communication between eIF4E, eIF4G, and PAPB may be transient during translation.
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Chang M, Lee OC, Bu G, Oh J, Yunn NO, Ryu SH, Kwon HB, Kolomeisky AB, Shim SH, Doh J, Jeon JH, Lee JB. Formation of cellular close-ended tunneling nanotubes through mechanical deformation. SCIENCE ADVANCES 2022; 8:eabj3995. [PMID: 35353579 PMCID: PMC8967236 DOI: 10.1126/sciadv.abj3995] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Membrane nanotubes or tunneling nanotubes (TNTs) that connect cells have been recognized as a previously unidentified pathway for intercellular transport between distant cells. However, it is unknown how this delicate structure, which extends over tens of micrometers and remains robust for hours, is formed. Here, we found that a TNT develops from a double filopodial bridge (DFB) created by the physical contact of two filopodia through helical deformation of the DFB. The transition of a DFB to a close-ended TNT is most likely triggered by disruption of the adhesion of two filopodia by mechanical energy accumulated in a twisted DFB when one of the DFB ends is firmly attached through intercellular cadherin-cadherin interactions. These studies pinpoint the mechanistic questions about TNTs and elucidate a formation mechanism.
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Gu S, Jeon HM, Nam SW, Hong KY, Rahman MS, Lee JB, Kim Y, Jang SK. The flip-flop configuration of the PABP-dimer leads to switching of the translation function. Nucleic Acids Res 2021; 50:306-321. [PMID: 34904669 PMCID: PMC8754640 DOI: 10.1093/nar/gkab1205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
Poly(A)-binding protein (PABP) is a translation initiation factor that interacts with the poly(A) tail of mRNAs. PABP bound to poly(A) stimulates translation by interacting with the eukaryotic initiation factor 4G (eIF4G), which brings the 3′ end of an mRNA close to its 5′ m7G cap structure through consecutive interactions of the 3′-poly(A)–PABP-eIF4G-eIF4E-5′ m7G cap. PABP is a highly abundant translation factor present in considerably larger quantities than mRNA and eIF4G in cells. However, it has not been elucidated how eIF4G, present in limited cellular concentrations, is not sequestered by mRNA-free PABP, present at high cellular concentrations, but associates with PABP complexed with the poly(A) tail of an mRNA. Here, we report that RNA-free PABPs dimerize with a head-to-head type configuration of PABP, which interferes in the interaction between PABP and eIF4G. We identified the domains of PABP responsible for PABP–PABP interaction. Poly(A) RNA was shown to convert the PABP–PABP complex into a poly(A)–PABP complex, with a head-to-tail-type configuration of PABP that facilitates the interaction between PABP and eIF4G. Lastly, we showed that the transition from the PABP dimer to the poly(A)–PABP complex is necessary for the translational activation function.
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Kim KJ, Kim IS, Oh SH, Lee SM, Lee HJ, Kang SH, Lee JB, Ryu YL, Chang CL. Evaluation of an automated specimen processing system for staining and culture for acid-fast bacilli. Int J Tuberc Lung Dis 2021; 25:677-679. [PMID: 34330357 DOI: 10.5588/ijtld.21.0206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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El-Domyati M, El-Din WH, Rezk AF, Chervoneva I, Lee JB, Farber M, Uitto J, Igoucheva O, Alexeev V. Systemic CXCL10 is a predictive biomarker of vitiligo lesional skin infiltration, PUVA, NB-UVB and corticosteroid treatment response and outcome. Arch Dermatol Res 2021; 314:275-284. [PMID: 33866437 DOI: 10.1007/s00403-021-02228-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/24/2021] [Accepted: 04/03/2021] [Indexed: 10/21/2022]
Abstract
Vitiligo is an acquired pigmentary skin disorder that currently lacks standardized treatment and validated biomarkers to objectively evaluate disease state or therapeutic response. Although prior studies have linked vitiligo autoimmunity with CXCL10/CXCL9-mediated recruitment of leukocytes to the skin, only limited clinical data are available regarding CXCL10 as vitiligo biomarker. To evaluate the utility of systemic CXCL10 as a predictor of disease progression and treatment response on a large cohort of vitiligo patients. CXCL10 levels in lesional, perilesional, and unaffected skin of vitiligo patient (n = 30) and in the serum (n = 51) were measured by quantitative ELISA. CXCL10 expression, recruitment of leukocytes, and inflammatory infiltrates were evaluated by histochemical (n = 32) and immunofluorescence (n = 10) staining. Rigorous cross-sectional and longitudinal biostatistical analysis were employed to correlate CXCL10 levels with disease variables, treatment response, and outcome. We demonstrated that elevated CXCL10 level (2 pg/mm2 and higher) in lesional skin correlates with increased leukocytic infiltrate, disease duration (< 2 year), and its higher level in the serum (50 pg/ml and higher). Changes in CXCL10 serum levels in patients treated with psoralen plus UVA (PUVA) phototherapy, narrowband UVB (NB-UVB) phototherapy, and systemic steroids (SS) correlated with changes in the intralesional CXCL10 levels in repigmented skin. NB-UVB and SS regimens provided most consistent CXCL10 mean change, suggesting that these regimens are most effective in harnessing CXCR3-mediated inflammatory response. Serum CXCL10 is a useful vitiligo biomarker, which predicts lesional skin leukocytic infiltration, and vitiligo treatment response and outcome.
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Chang J, Hwang HJ, Kim B, Choi YG, Park J, Park Y, Lee BS, Park H, Yoon MJ, Woo JS, Kim C, Park MS, Lee JB, Kim YK. TRIM28 functions as a negative regulator of aggresome formation. Autophagy 2021; 17:4231-4248. [PMID: 33783327 DOI: 10.1080/15548627.2021.1909835] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Selective recognition and elimination of misfolded polypeptides are crucial for protein homeostasis. When the ubiquitin-proteasome system is impaired, misfolded polypeptides tend to form small cytosolic aggregates and are transported to the aggresome and eventually eliminated by the autophagy pathway. Despite the importance of this process, the regulation of aggresome formation remains poorly understood. Here, we identify TRIM28/TIF1β/KAP1 (tripartite motif containing 28) as a negative regulator of aggresome formation. Direct interaction between TRIM28 and CTIF (cap binding complex dependent translation initiation factor) leads to inefficient aggresomal targeting of misfolded polypeptides. We also find that either treatment of cells with poly I:C or infection of the cells by influenza A viruses triggers the phosphorylation of TRIM28 at S473 in a way that depends on double-stranded RNA-activated protein kinase. The phosphorylation promotes association of TRIM28 with CTIF, inhibits aggresome formation, and consequently suppresses viral proliferation. Collectively, our data provide compelling evidence that TRIM28 is a negative regulator of aggresome formation.AbbreviationsBAG3: BCL2-associated athanogene 3; CTIF: CBC-dependent translation initiation factor; CED: CTIF-EEF1A1-DCTN1; DCTN1: dynactin subunit 1; EEF1A1: eukaryotic translation elongation factor 1 alpha 1; EIF2AK2: eukaryotic translation initiation factor 2 alpha kinase 2; HDAC6: histone deacetylase 6; IAV: influenza A virus; IP: immunoprecipitation; PLA: proximity ligation assay; polypeptidyl-puro: polypeptidyl-puromycin; qRT-PCR: quantitative reverse-transcription PCR; siRNA: small interfering RNA.
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Lee JB, Woo HK. Quality Evaluation of Mobile Applications for Fine dust Management. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Recently, the use of fine dust management mobile applications has been on the rise in South Korea. The aim of this study is to describe the current status of fine dust and air pollution mhealth apps used in Korea and to make qualitative assessments of them.
Methods
App search contents analysis 400 apps were searched using PM2.5, PM10 and yellow dust, the main keywords related to fine dust, referring to the preceding reference from December 30, 2019 to January 2, 2020. Among the apps searched, apps that meet all six criteria, such as those with 1) user score ≥4.0, 2) n of review Top 50, 3) those that do not duplicated, 4) apps that are related to the topic, 5) apps set in Korean, and 6) apps that do not have errors, were selected for the study. App assessment The app evaluation of the study utilizes the MARS scale, an app assessment tool developed overseas. The assessment was conducted for a week from January 3, 2020 to January 10, 2020. Each of the apps averaged scores evaluated over a week for each category and averaged over five categories for an overall quality score.
Results
The standard deviation of the information and functionality of the 30 apps was similar, with 3.62 (SD 0.38) and 3.58 (SD 0.43), respectively. On the other hand, engagement was the lowest with an average of 3.1 (SD 0.44). The average of aesthetics was 3.4 (SD 0.64), indicating that deviations between apps were very large
Conclusions
It is deemed necessary to improve the user interface (UI) and configuration of the app to enhance the application's engagement and aesthetics in order to increase the use of fine dust apps by consumers and gain effect.
Key messages
This research provided information that consumers can reasonably use and select mobile health apps by evaluating and reviewing the contents of fine dust and air pollution mobile health apps. this study is important in that it can serve as a reference for app developers to consider in future app development.
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Ryanggeun L, Liu J, Britton BM, Yang K, Lee JB, Fishel R. BIUXX. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Kim D, Rashid F, Cho Y, Zaher MS, Cho IIH, Hamdan SM, Jeong C, Lee JB. DNA skybridge: 3D structure producing a light sheet for high-throughput single-molecule imaging. Nucleic Acids Res 2019; 47:e107. [PMID: 31340015 PMCID: PMC6765118 DOI: 10.1093/nar/gkz625] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/01/2019] [Accepted: 07/12/2019] [Indexed: 11/14/2022] Open
Abstract
Real-time visualization of single-proteins or -complexes on nucleic acid substrates is an essential tool for characterizing nucleic acid binding proteins. Here, we present a novel surface-condition independent and high-throughput single-molecule optical imaging platform called ‘DNA skybridge’. The DNA skybridge is constructed in a 3D structure with 4 μm-high thin quartz barriers in a quartz slide. Each DNA end is attached to the top of the adjacent barrier, resulting in the extension and immobilization of DNA. In this 3D structure, the bottom surface is out-of-focus when the target molecules on the DNA are imaged. Moreover, the DNA skybridge itself creates a thin Gaussian light sheet beam parallel to the immobilized DNA. This dual property allows for imaging a single probe-tagged molecule moving on DNA while effectively suppressing interference with the surface and background signals from the surface.
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Liu J, Lee R, Britton BM, London JA, Yang K, Hanne J, Lee JB, Fishel R. MutL sliding clamps coordinate exonuclease-independent Escherichia coli mismatch repair. Nat Commun 2019; 10:5294. [PMID: 31757945 PMCID: PMC6876574 DOI: 10.1038/s41467-019-13191-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 10/22/2019] [Indexed: 01/09/2023] Open
Abstract
A shared paradigm of mismatch repair (MMR) across biology depicts extensive exonuclease-driven strand-specific excision that begins at a distant single-stranded DNA (ssDNA) break and proceeds back past the mismatched nucleotides. Historical reconstitution studies concluded that Escherichia coli (Ec) MMR employed EcMutS, EcMutL, EcMutH, EcUvrD, EcSSB and one of four ssDNA exonucleases to accomplish excision. Recent single-molecule images demonstrated that EcMutS and EcMutL formed cascading sliding clamps on a mismatched DNA that together assisted EcMutH in introducing ssDNA breaks at distant newly replicated GATC sites. Here we visualize the complete strand-specific excision process and find that long-lived EcMutL sliding clamps capture EcUvrD helicase near the ssDNA break, significantly increasing its unwinding processivity. EcSSB modulates the EcMutL–EcUvrD unwinding dynamics, which is rarely accompanied by extensive ssDNA exonuclease digestion. Together these observations are consistent with an exonuclease-independent MMR strand excision mechanism that relies on EcMutL–EcUvrD helicase-driven displacement of ssDNA segments between adjacent EcMutH–GATC incisions. The mechanics of MMR strand specific excision that begins at a distant ssDNA break are not yet clear. Here the authors have used multiple single molecule imaging techniques to visualize the behavior of MMR components on mismatched DNA substrates and reveal an exonuclease-independent mechanism for E.coli MMR.
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Abstract
Single-molecule techniques have been used successfully to visualize real-time enzymatic activities, revealing transient complex properties and heterogeneity of various biological events. Especially, conventional force spectroscopy including optical tweezers and magnetic tweezers has been widely used to monitor change in DNA length by enzymes with high spatiotemporal resolutions of ~ nanometers and ~ milliseconds. However, DNA metabolism results from coordination of a number of components during the processes, requiring efficient monitoring of a complex of proteins catalyzing DNA substrates. In this min-review, we will introduce a simple and multiplexed single-molecule assay to detect DNA substrates catalyzed by enzymes with high-throughput data collection. We conclude with a perspective of possible directions that enhance capability of the assay to reveal complex biological events with higher resolution.
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Hanne J, Britton BM, Park J, Liu J, Martin-Lopez J, Jones N, Schoffner M, Klajner P, Bundschuh R, Lee JB, Fishel R. Muts Homolog Sliding Clamps Shield the DNA from Binding Proteins. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Liu J, Lee RG, Britton B, London J, Hanne J, Lee JB, Fishel R. DNA Mismatch Repair Relies Entirely on Stochastic Transactions. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Kim D, Fishel R, Lee JB. Coordinating Multi-Protein Mismatch Repair by Managing Diffusion Mechanics on the DNA. J Mol Biol 2018; 430:4469-4480. [PMID: 29792877 PMCID: PMC6388638 DOI: 10.1016/j.jmb.2018.05.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
Abstract
DNA mismatch repair (MMR) corrects DNA base-pairing errors that occur during DNA replication. MMR catalyzes strand-specific DNA degradation and resynthesis by dynamic molecular coordination of sequential downstream pathways. The temporal and mechanistic order of molecular events is essential to insure interactions in MMR that occur over long distances on the DNA. Biophysical real-time studies of highly conserved components on mismatched DNA have shed light on the mechanics of MMR. Single-molecule imaging has visualized stochastically coordinated MMR interactions that are based on thermal fluctuation-driven motions. In this review, we describe the role of diffusivity and stochasticity in MMR beginning with mismatch recognition through strand-specific excision. We conclude with a perspective of the possible research directions that should solve the remaining questions in MMR.
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Liu J, Lee JB, Fishel R. Stochastic Processes and Component Plasticity Governing DNA Mismatch Repair. J Mol Biol 2018; 430:4456-4468. [PMID: 29864444 PMCID: PMC6461355 DOI: 10.1016/j.jmb.2018.05.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/09/2018] [Accepted: 05/28/2018] [Indexed: 02/06/2023]
Abstract
DNA mismatch repair (MMR) is a DNA excision-resynthesis process that principally enhances replication fidelity. Highly conserved MutS (MSH) and MutL (MLH/PMS) homologs initiate MMR and in higher eukaryotes act as DNA damage sensors that can trigger apoptosis. MSH proteins recognize mismatched nucleotides, whereas the MLH/PMS proteins mediate multiple interactions associated with downstream MMR events including strand discrimination and strand-specific excision that are initiated at a significant distance from the mismatch. Remarkably, the biophysical functions of the MLH/PMS proteins have been elusive for decades. Here we consider recent observations that have helped to define the mechanics of MLH/PMS proteins and their role in choreographing MMR. We highlight the stochastic nature of DNA interactions that have been visualized by single-molecule analysis and the plasticity of protein complexes that employ thermal diffusion to complete the progressions of MMR.
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Hanne J, Britton BM, Park J, Liu J, Martín-López J, Jones N, Schoffner M, Klajner P, Bundschuh R, Lee JB, Fishel R. MutS homolog sliding clamps shield the DNA from binding proteins. J Biol Chem 2018; 293:14285-14294. [PMID: 30072380 DOI: 10.1074/jbc.ra118.002264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 07/31/2018] [Indexed: 11/06/2022] Open
Abstract
Sliding clamps on DNA consist of evolutionarily conserved enzymes that coordinate DNA replication, repair, and the cellular DNA damage response. MutS homolog (MSH) proteins initiate mismatch repair (MMR) by recognizing mispaired nucleotides and in the presence of ATP form stable sliding clamps that randomly diffuse along the DNA. The MSH sliding clamps subsequently load MutL homolog (MLH/PMS) proteins that form a second extremely stable sliding clamp, which together coordinate downstream MMR components with the excision-initiation site that may be hundreds to thousands of nucleotides distant from the mismatch. Specific or nonspecific binding of other proteins to the DNA between the mismatch and the distant excision-initiation site could conceivably obstruct the free diffusion of these MMR sliding clamps, inhibiting their ability to initiate repair. Here, we employed bulk biochemical analysis, single-molecule fluorescence imaging, and mathematical modeling to determine how sliding clamps might overcome such hindrances along the DNA. Using both bacterial and human MSH proteins, we found that increasing the number of MSH sliding clamps on a DNA decreased the association of the Escherichia coli transcriptional repressor LacI to its cognate promoter LacO. Our results suggest a simple mechanism whereby thermal diffusion of MSH sliding clamps along the DNA alters the association kinetics of other DNA-binding proteins over extended distances. These observations appear generally applicable to any stable sliding clamp that forms on DNA.
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Achita P, Dervovic D, Ly D, Lee JB, Haug T, Joe B, Hirano N, Zhang L. Infusion of ex-vivo expanded human TCR-αβ + double-negative regulatory T cells delays onset of xenogeneic graft-versus-host disease. Clin Exp Immunol 2018; 193:386-399. [PMID: 30066399 DOI: 10.1111/cei.13145] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2018] [Indexed: 12/25/2022] Open
Abstract
Despite the demonstration of potent immunosuppressive function of T cell receptor (TCR)-αβ+ double-negative regulatory T cells (DN Tregs ), scarce numbers and lack of effective expansion method limit their clinical applications. Here we describe an approach that allows for ∼3500-fold ex-vivo expansion of human DN Tregs within 3 weeks with > 97% purity. Ex-vivo-expanded DN Tregs suppress proliferation of polyclonally stimulated autologous T and B cells in vitro through direct cell-to-cell contact. In vivo, we demonstrate for the first time that infusion of human DN Tregs delayed an onset of xenogeneic graft-versus-host disease (GVHD) significantly in a humanized mouse model. Furthermore, preincubation of ex-vivo-expanded DN Tregs with a mechanistic target of rapamycin (mTOR) inhibitor rapamycin enhanced their immune regulatory function further. Taken together, this study demonstrates that human DN Tregs can be expanded ex vivo to therapeutic numbers. The expanded DN Tregs can suppress proliferation of T and B cells and attenuate GVHD, highlighting the potential clinical use of DN Tregs to mitigate GVHD.
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Kim SK, You HR, Kim SH, Yun SJ, Lee SC, Lee JB. Skin photorejuvenation effects of light-emitting diodes (LEDs): a comparative study of yellow and red LEDs in vitro and in vivo. Clin Exp Dermatol 2018; 41:798-805. [PMID: 27663159 DOI: 10.1111/ced.12902] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2015] [Indexed: 11/27/2022]
Abstract
BACKGROUND Red-coloured light-emitting diodes (LEDs) can improve skin photorejuvenation and regeneration by increasing cellular metabolic activity. AIM To evaluate the effectiveness of visible LEDs with specific wavelengths for skin photorejuvenation in vitro and in vivo. METHODS Normal human dermal fibroblasts (HDFs) from neonatal foreskin were cultured and irradiated in vitro by LEDs at different wavelengths (410-850 nm) and doses (0-10 J/cm(2) ). In vivo experiments were performed on the skin of hairless mice. Expression of collagen (COL) and matrix metalloproteinases (MMPs) was evaluated by semi-quantitative reverse transcription PCR (semi-qRT-PCR), western blotting and a procollagen type I C-peptide enzyme immunoassay (EIA). Haematoxylin and eosin and Masson trichrome stains were performed to evaluate histological changes. RESULTS In HDFs, COL I was upregulated and MMP-1 was downregulated in response to LED irradiation at 595 ± 2 and 630 ± 8 nm. In the EIA, a peak result was achieved at a dose of 5 J/cm(2) with LED at 595 ± 2 nm. In vivo, COL I synthesis was upregulated in a dose-dependent manner to both 595 and 630 nm LED irradiation, and this effect was prolonged to 21 days after a single irradiation with a dose of 100 J/cm(2) . These histological changes were consistent with the results of semi-qRT-PCR and western blots. CONCLUSION Specific LED treatment with 595 ± 2 and 630 ± 8 nm irradiation was able to modulate COL and MMPs in skin, with the effects persisting for at least 21 days after irradiation. These findings suggest that yellow and red LEDs might be useful tools for skin photorejuvenation.
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Hwang YJ, Kim N, Lee HS, Lee JB, Choi YJ, Yoon H, Shin CM, Park YS, Lee DH. Reversibility of atrophic gastritis and intestinal metaplasia after Helicobacter pylori eradication - a prospective study for up to 10 years. Aliment Pharmacol Ther 2018; 47:380-390. [PMID: 29193217 DOI: 10.1111/apt.14424] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/31/2017] [Accepted: 10/27/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Atrophic gastritis and intestinal metaplasia are premalignant conditions for gastric cancer. Their reversibility by Helicobacter pylori eradication remains controversial. AIM To evaluate the reversibility of atrophic gastritis and intestinal metaplasia by H. pylori eradication with long-term follow-up. METHODS 598 subjects were prospectively enrolled and followed for up to 10 years. They were categorised as H. pylori-negative (n = 65), H. pylori non-eradicated (n = 91), and H. pylori-eradicated (n = 442). Histological assessment was performed for antrum and corpus by Sydney classification. RESULTS Histological follow-up was performed regularly at 1, 2, 3-4 and ≥5 years, with mean follow-up of 1.07 ± 0.21, 2.29 ± 0.83, 3.93 ± 1.02, and 6.45 ± 1.28 years, respectively. Atrophic gastritis in antrum and corpus gradually and significantly (both P < .05 for all timepoints) improved only in the H. pylori-eradicated group compared to that at baseline. Significant difference in atrophic gastritis between H. pylori-eradicated and H. pylori-negative groups disappeared from 1-year follow-up. Similarly, intestinal metaplasia in antrum and corpus improved significantly (both P < .05 for all timepoints) only in the H. pylori-eradicated group in comparison with that at baseline. Significant difference in intestinal metaplasia between H. pylori-eradicated and H. pylori-negative groups disappeared from ≥5 years of follow-up in the antrum and from 3 years of follow-up in the corpus. CONCLUSION H. pylori eradication may be a preventative strategy for intestinal-type gastric cancer by regression of atrophic gastritis and intestinal metaplasia.
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