Journal of Analytical Science and Technology最新文献

{"title":"NMR structure and functional studies of the fourth FAS1 domain of human periostin","authors":"Hyosuk Yun, Jeong-Eun Seon, Kon-Young Ji, Hye Jung Min, Hyung-Sik Kang, Chul Won Lee","doi":"10.1186/s40543-024-00453-1","DOIUrl":"https://doi.org/10.1186/s40543-024-00453-1","url":null,"abstract":"Periostin is a matricellular protein that consists of several structural and functional domains, including EMILIN-like, four internal repeat fasciclin1 (FAS1) domains, and a carboxyl-terminal variable domain. It is known that periostin is associated with various fundamental biological processes and diseases, such as several types of cancer and chronic inflammatory diseases. Despite its important roles, the biological function of each domain is poorly understood. In this study, we expressed the fourth FAS1 (FAS1 IV) domain of human periostin, which was highly soluble and stable enough for structural and functional studies. The three-dimensional structure of FAS1 IV was determined using 3D NMR spectroscopy. The overall structure of FAS1 IV consists of six α-helices, one 310 helix, and eight β-strands. Two triangular α-helical modules formed by three α-helices each are located on one side of the molecule, while the orthogonal β-sheet sandwich module of FAS1 IV is located on the other side. The isolated FAS1 IV domain exhibited cell invasion, migration, and adhesion activities for cancer cell lines comparable to those of the full FAS1 I–IV domain. In conclusion, we propose that the FAS1 IV domain is functionally active in human periostin and provides valuable information for understanding the biological function of periostin.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141529293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative examination of analytical instruments for detecting pentachlorophenol in wood and environmental samples","authors":"K. Koushika, Quan He, H. Niati, C. U. Emenike","doi":"10.1186/s40543-024-00444-2","DOIUrl":"https://doi.org/10.1186/s40543-024-00444-2","url":null,"abstract":"","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141347728","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nail fold capillaroscopy as a potential tool to evaluate breast tumor","authors":"Minsuk Kim","doi":"10.1186/s40543-024-00449-x","DOIUrl":"https://doi.org/10.1186/s40543-024-00449-x","url":null,"abstract":"","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141364573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and validation of an LC–MS/MS method for the determination of BLU-945, a fourth-generation EGFR tyrosine kinase inhibitor, in rat and mouse plasma: application to a pharmacokinetic study in rats","authors":"Ji‐Hoon Oh, Thi-Thao-Linh Nguyen, H. Maeng","doi":"10.1186/s40543-024-00452-2","DOIUrl":"https://doi.org/10.1186/s40543-024-00452-2","url":null,"abstract":"","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141364860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of bladder tumor cells using motion features in urine","authors":"Minsuk Kim","doi":"10.1186/s40543-024-00451-3","DOIUrl":"https://doi.org/10.1186/s40543-024-00451-3","url":null,"abstract":"","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141360625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the interplay of contrast, defocus, and resolution in cryo-EM: a benchmark experiment for limited dataset screening","authors":"Hayeon Lee, Yeseul Lee, Jinseok Lee, Hyeongseop Jeong, Dong Keon Yon, Clarissa L. Durie, Bumhan Ryu, Jeong Min Chung","doi":"10.1186/s40543-024-00445-1","DOIUrl":"https://doi.org/10.1186/s40543-024-00445-1","url":null,"abstract":"The selection of defocus ranges for small datasets in cryo-electron microscopy (cryo-EM) is under-researched. We present a comprehensive benchmark experiment that aimed to evaluate the relationship between contrast, defocus, and resolution, particularly in the context of limited datasets. We conducted a detailed analysis of beta-galactosidase, apo-ferritin, and connexin-46/50 datasets to optimize pre-screening strategies for cryo-EM. Our approach involved classifying micrographs based on image contrast using an artificial intelligence (AI) model without considering the defocus level. This method allowed us to investigate the optimal defocus range for pre-screening in a limited dataset and its impact on the overall image processing. The micrographs were categorized into good, moderate, and bad contrast groups. Subsequent analysis revealed that, contrary to the prevailing assumption that lower contrast (associated with lower defocus) leads to higher resolution, in scenarios with limited datasets higher contrast images yield superior resolution. This finding was consistent across all three protein samples, underscoring the critical role of contrast in determining the quality of 3D reconstructions in limited datasets. This significant finding challenges conventional cryo-EM methodologies. In conclusion, our study provides new benchmarks for selecting appropriate contrast and defocus levels in cryo-EM, particularly for screening approaches that use limited datasets. This strategy promises to enhance the data quality and efficiency in structural biology research, particularly in resource-constrained scenarios.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141259926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spectroscopic and antibacterial activities of cobalt and nickel nanoparticles: a comparative analysis","authors":"Sheriff A. Balogun, Tesleem O. Abolarinwa, Funmilola A. Adesanya, Collins N. Ateba, Omolola E. Fayemi","doi":"10.1186/s40543-024-00446-0","DOIUrl":"https://doi.org/10.1186/s40543-024-00446-0","url":null,"abstract":"This study aimed to compare the spectroscopy, morphological, electrocatalytic properties, and antibacterial activities of cobalt nanoparticles (CoNPs) with nickel nanoparticles (NiNPs). Cobalt nanoparticles and NiNPs were prepared via a chemical reduction approach and characterized utilizing transmission electron microscopy (TEM), energy-dispersive X-ray (EDX), and X-ray diffraction (XRD) techniques. The result from XRD and TEM analysis revealed that the synthesized nanoparticles exhibit face-centered cubic with smooth spherical shape, having average particles size of 12 nm (NiNPs) and 18 nm (CoNPs). The electrochemical properties of the nanoparticles were examined via cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques. The CV results showed that GCE-Ni (35.6 μA) has a higher current response compared to GCE-Co (10.5 μA). The EIS analysis revealed that GCE-Ni (1.39 KΩ) has faster electron transport capability compared to GCE-Co (2.99 KΩ) as indicated in their Rct values. The power density of the synthesized nanoparticles was obtained from their \"knee\" frequency (f°) values, with GCE-Ni (3.16 Hz) having higher f° values compared to GCE-Co (2.00 Hz). The antibacterial activity of the nanoparticles was evaluated against multidrug-resistant Escherichia coli O157, Escherichia coli O177, Salmonella enterica, Staphylococcus aureus, and Vibrio cholerae. The result from the antibacterial study revealed that at low concentrations both CoNPs and NiNPs have significant antibacterial activities against E. coli O157, E. coli O177, S. enterica, S. aureus, and V. cholerae. NiNPs showed better antibacterial activities at low concentrations of 61.5, 61.5, 125, 61.5, and 125 µg/mL compared to CoNPs with minimum inhibitory concentrations of 125, 125, 250, 61.5, and 125 µg/mL against E. coli O157, E. coli O177, S. enterica, S. aureus, and V. cholerae, respectively. These promising antibacterial activities emphasize the potential of CoNPs and NiNPs as effective antibacterial agents, which could aid in the development of novel antibacterial medicines.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141259813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Raman spectroscopic comparison of zearalenone and its derivatives for non-destructive rapid detection","authors":"Won-Seok Kang, Sung-Wook Choi, Hyo-Sop Kim, Jae-Ho Kim, Jae-Hyeok Lee","doi":"10.1186/s40543-024-00448-y","DOIUrl":"https://doi.org/10.1186/s40543-024-00448-y","url":null,"abstract":"Raman spectroscopy is used to investigate the absorption and dispersion of zearalenone (ZEN) and its derivatives. The C=C stretching vibration modes of ZEN and zearalenol (ZENOL) were appeared at 975–990 cm−1. The C=O vibration mode was present at 1680–1690 cm−1 for ZEN and zearalanone (ZAN), but it was absent for ZENOL and zearalanol (ZANOL) which have –OH group instead of –C=O group in ZEN and ZAN molecular structures. On the basis of this characterization, Raman spectra of specific chemical groups and linkages corresponding to the structural difference of ZEN and its derivatives were identified. These results indicated that Raman spectroscopy can apply for the identification of ZEN and its derivatives and has a potential for the non-destructive rapid detection of these compounds in food.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141254524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of acyl carrier protein in de novo fatty acid synthesis by Enterococcus faecalis based on NMR spectroscopy and molecular dynamics simulation","authors":"Sujung Oh, Chaeyoung Lee, Minwon Son, Jiwon Yeon, Yangmee Kim","doi":"10.1186/s40543-024-00447-z","DOIUrl":"https://doi.org/10.1186/s40543-024-00447-z","url":null,"abstract":"Fatty acid synthesis (FAS) is essential for the production of biological components such as cell membrane building blocks and metabolism-related compounds. There are two types of bacterial FAS: de novo FAS and FAS through the incorporation of external fatty acids. Enterococcus faecalis possesses two distinct acyl carrier proteins (ACPs), AcpA (EfAcpA) and AcpB (EfAcpB), which serve as cofactors in the two types of FAS. We previously showed through NMR spectroscopy that EfAcpA comprises only three long helices, while EfAcpB consists of four helices, including a short α3 helix, similar to other bacterial ACPs. An increase in melting temperature (Tm) from 64.0 to 76.1 °C confirmed that protein structural stability increased in the presence of calcium ions. Using NMR spectroscopy, two metal binding sites were identified in EfAcpA: site A was located at the start of the α2 helix while site B was situated near the α2 helix and α2α3 loop. To understand the importance of structural flexibility of EfAcpA in de novo FAS, we investigated its motional properties using backbone spin relaxation and molecular dynamics simulations. The α2α3 loop in EfAcpA displayed high flexibility, as indicated by low heteronuclear NOE values. The residues Val51, Glu54, and Gly58 exhibited significant R2 values, likely due to the movement of this loop. EfAcpA created a novel cavity towards the α1α2 loop, in contrast to conventional cavity formation in most bacterial ACPs. This unique behavior was attributed to the flexibility exhibited by the α2α3 loop. The structural and motional characteristics of EfAcpA confirmed that its conformational plasticity is a crucial factor influencing acyl chain transfers in de novo FAS. Given the increasing antibiotic resistance observed for E. faecalis in clinical settings, the findings of this study may contribute to the development of more effective pathogen management strategies targeting FAS.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141167516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Target recognition-initiated allosteric probe-based multiple signal amplification strategy for sensitive and direct Pseudomonas aeruginosa detection","authors":"Kun Xue, Shuhong Kang","doi":"10.1186/s40543-024-00443-3","DOIUrl":"https://doi.org/10.1186/s40543-024-00443-3","url":null,"abstract":"","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140966959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}