Journal of Analytical Science and Technology最新文献

{"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":"70 1","pages":""},"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":"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":"14 1","pages":""},"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":"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":"76 1","pages":""},"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":"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":"44 1","pages":""},"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":"Development of non-destructive isotope measurement of the natural galena (PbS) using negative muon beams","authors":"K. Terada, K. Ninomiya, A. Sato, D. Tomono, Y. Kawashima, M. Inagaki, A. Nambu, T. Kudo, T. Osawa, M. K. Kubo","doi":"10.1186/s40543-024-00440-6","DOIUrl":"https://doi.org/10.1186/s40543-024-00440-6","url":null,"abstract":"In Earth and planetary science, Pb isotopic composition is well known to play a key role in deciphering the origin and evolution of materials because they provide unique chronological and/or indigenous regional information as a radiogenic daughter nuclide from U and Th. To determine such an isotopic composition, mass spectrometers have been widely used over several decades, which requires a destructive/consuming treatment such as sputtering, laser ablation and thermal ionization. Here, we first report the non-destructive Pb isotopic measurement of natural galena (PbS) using the energy shift of muon-induced characteristic X-rays. The observed Pb isotopic composition of the natural galena is in good agreement with that obtained by conventional mass spectrometry. Such a muon-based Pb isotopic analysis method is expected to be applied to identify the production area of archaeological artefacts (e.g. bronze products), where non-destructive analysis is highly desirable compared to conventional mass spectrometry.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"29 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884913","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":"Fast, accessible and reliable method for elemental analysis of metals in solution by ED-XRF spectroscopy","authors":"Filipe M. J. Figueiredo, José M. Carretas, João P. Leal, José M. Sardinha","doi":"10.1186/s40543-024-00442-4","DOIUrl":"https://doi.org/10.1186/s40543-024-00442-4","url":null,"abstract":"The measurement of metals in solution is usually performed using inductive coupled plasma hyphenated techniques or atomic absorption. Although very sensitive and accurate, these analytical techniques are quite expensive and do not allow field measurements. The present work takes advantage of energy-dispersive X-ray fluorescence (ED-XRF) ease-of-use features to determine the concentration of rare earth elements (Y, Pr, Nd, Eu) and others (S, Fe, Ni, Cu, Zn) in aqueous solutions, after appropriate sample treatment. The approach turned out to be a reliable and very convenient procedure for field analysis. The simplicity, speed and reliability of the methodology used combined with the possibility of simultaneous analysis and low cost of the method can be advantageous in industrial context. The approach relies on the suspension of the target solutions in a cellulose matrix that is further converted into a pellet for direct analysis. Calibration curves obtained by regression analysis at 5% significance are shown for a variety of elements (S, Fe, Ni, Cu, Zn, Y, Pr, Nd, Eu) with correlation coefficients between 0.9555 and 0.9980. Higher coefficients of variance were obtained for the calibration of S and Pr due to low sensitivity and the overlapping with the L lines of Nd, respectively. The performed calibrations were not affected by the presence of other analytes in the matrix. Results obtained showed that it is possible to use the proposed methodology to accurately quantify d and f block metals in aqueous solutions by ED-XRF after sequestering the chemical content into a cellulose powder matrix and further processing into a pellet. ","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"63 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140889618","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":"SIMS study of fine-scale distribution of U, Th and Pb in meteorites","authors":"Keewook Yi, Yuri Amelin","doi":"10.1186/s40543-024-00439-z","DOIUrl":"https://doi.org/10.1186/s40543-024-00439-z","url":null,"abstract":"We report developing a procedure for measuring concentrations of U, Th and Pb (including all natural Pb isotopes) to establish the distribution of these elements in meteorite minerals and correctly interpret Pb-isotopic ages of meteorites. The concentrations were measured on KBSI SHRIMP IIe by peak jumping using a discrete-dynode secondary electron multiplier. The concentrations were calculated relative to BCR-2G glass and monitored by analysis of the NIST glasses SRM-615 and SRM-617 as secondary reference materials. The detection limits using the spot sizes of ca. 180 μm2, primary O2− beam current of 10.6 nA, and with amplifier dark noise of 0.015 counts per second are ~ 0.2 parts per billion (ppb) for U (500 s integration), ~ 0.6 ppb for Pb (100 s integration for each of the major isotopes), and ~ 1.2 ppb for Th (100 s integration). Analyses of the NIST glasses confirm that the measured concentrations of U and Th are consistent with their certified values, while the Pb concentrations are about four times too low, most likely due to the compositional mismatch between the primary and secondary reference materials. The achieved level of sensitivity and concentration precision (~ 20–30%) is adequate for measuring U, Th and Pb distributions in both rock-forming and accessory minerals in chondrites, achondrites, and their components.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"43 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140832088","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":"Aptamer-based protein molecule detection via cyclic reverse transcription coupling with self-priming hairpin-triggered CRISPR-Cas12a system","authors":"Jie Gao, Xiaoqing Yang","doi":"10.1186/s40543-024-00441-5","DOIUrl":"https://doi.org/10.1186/s40543-024-00441-5","url":null,"abstract":"Protein biomarkers (e.g. thrombin) are of great significance for the biological process of the organism, and its aberrant expression is closely associated with the development of diseases. With thrombin, a serine protease that plays a crucial role in maintaining homeostasis and promoting blood clotting, as detection target, this study introduces a novel approach for sensitive and accurate measurement of protein biomarker expression by utilization of cyclic reverse transcription (CRT) in combination with the self-priming hairpin-triggered CRISPR-Cas12a system. In this method, an elegantly designed sensing probe is utilized to specifically bind with the thrombin protein and convert the protein signals to nucleic acids signals, following by the CRT and CRISPR-Cas12a system-based signal amplification strategy. Taking the merit of the two-stage amplification, this assay has the capability to detect thrombin at the fM level. In addition, due to the aptamer sequence’s strong selectivity to thrombin protein and the dual-check process in the signal amplification process (first in the CRT and second in the CRISPR system), the proposed test demonstrates exceptional specificity in detecting thrombin. By re-designing the sensing probe, the established method could be extended to various protein biomarker detection. Ultimately, this assay has successfully enabled the accurate evaluation of biomarker levels in constructed clinical samples, showing significant potential for application in the realm of clinical molecular diagnosis.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"108 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140831909","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":"Performance assessment of activated carbon thermally modified with iron in the desulfurization of biogas in a static batch system supported by headspace gas chromatography","authors":"Mayerlin Edith Acuña Montaño, Luciane Effting, Carmen Luisa Barbosa Guedes, Gregorio Guadalupe Carbajal Arizaga, Renata Mello Giona, Patricia Hissae Yassue Cordeiro, César Ricardo Teixeira Tarley, Alesandro Bail","doi":"10.1186/s40543-024-00432-6","DOIUrl":"https://doi.org/10.1186/s40543-024-00432-6","url":null,"abstract":"A static batch arrangement composed of anti-leak vials coupled to gas chromatography is proposed as a complementary system for performance assessment of biogas desulfurization by adsorption. For testing, a modified commercial activated carbon produced by controlled thermal treatment in the presence of iron(III) species improved biogas desulfurization. The adsorbents showed a superior hydrogen sulfide removal compared to ordinary one. Pseudo-first-order, pseudo-second-order, and Bangham’s kinetic models were used to fit experimental data. All studied samples followed pseudo-first-order model, indicating the predominance of physisorption, and Bangham’s model, confirming that the micropores structure played an important role for gases diffusion and adsorbent capacity. Additionally, the materials were characterized by N2 adsorption–desorption, X-ray diffraction, infrared spectroscopy, scanning electron microscopy and energy-dispersive spectroscopy. The thermal treatment associated with iron impregnation caused significant modifications in the surface of the materials, and the iron species showed two main benefits: an expressive increase in the specific area and the formation of specific adsorption sites for hydrogen sulfide removal. The results reinforce the advantages of iron-modified adsorbents in relation to their non-modified counterparts. The analytical methodology based on the confinement of multiple gases contributes to improving the understanding of the hydrogen sulfide adsorption process using pressure swing adsorption technology. ","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"52 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589917","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":"Direct and accurate miRNA detection based on CRISPR/Cas13a-triggered exonuclease-iii-assisted colorimetric assay","authors":"Yunxiao Li, Qiuxia Wang, Yali Wang","doi":"10.1186/s40543-024-00434-4","DOIUrl":"https://doi.org/10.1186/s40543-024-00434-4","url":null,"abstract":"The abnormally expressed microRNAs (miRNAs) serve as crucial indicators for disease diagnosis and are strongly associated with the progression of various diseases. The quantification of miRNAs is highly significant for the clinical diagnosis and treatment of various types of cancers. This study utilizes the CRISPR/Cas13a system, which combines CRISPR RNA (crRNA) and CRISPR-associated Cas13a, to recognize the miRNA directly and specifically, thus activating the trans-cleavage activity of Cas13a. By integrating the CRISPR-Cas13a system with an exonuclease-iii (Exo-iii)-assisted chain cleavage of silver ions (Ag+)-aptamer and an Ag+ -based color reaction, a method for the detection of miRNA that is specific and sensitive is developed. This approach demonstrated exceptional sensitivity in detecting miRNA, with a low detection limit of 5.12 fM. Moreover, the suggested method was effectively utilized to precisely measure the amount of miRNA in intricate biological samples, demonstrating its practical applicability. Furthermore, due to its elevated sensitivity and simple probe design and fluorophore labeling, the suggested colorimetric technique holds great potential for use in clinical diagnostics.","PeriodicalId":14967,"journal":{"name":"Journal of Analytical Science and Technology","volume":"213 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140589464","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}