Pub Date : 2023-07-13DOI: 10.3389/frans.2023.1124741
Edison Zhamungui Sánchez, Hassan Y. Hijazi, Jana Haidar, Enrica Mecarelli, Elda Bauda, Isabelle Petit-Härtlein, J. Teulon, J. Pellequer, Elisabetta Boeri Erba
Membrane proteins are key players in many cellular events and represent crucial drug targets. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is a valuable approach to investigate them. To our knowledge, there are only a few reports of sequencing small membrane proteins using MALDI in-source decay (ISD). We report the successful fragmentation and sequencing of membrane proteins up to 46 kDa by MALDI-ISD. We have 1) investigated key MALDI parameters that influence the sequencing of a soluble protein; 2) used atomic force microscopy to observe our samples and correlate their topological features with MALDI data, which allowed us to optimize fragmentation conditions; 3) sequenced N- and C-termini of three membrane proteins (SpoIIIAF, TIM23, and NOX), solubilized in three different ways. Our results indicate that detergent and buffer type are of key importance for successful MALDI-ISD sequencing. Our findings are significant because sequencing membrane proteins enables the unique characterization of challenging biomolecules. The resulting fragmentation patterns provide key insights into the identity of proteins, their sequences, modifications, and other crucial information, such as the position of unexpected truncation.
{"title":"Sequencing intact membrane proteins using MALDI mass spectrometry","authors":"Edison Zhamungui Sánchez, Hassan Y. Hijazi, Jana Haidar, Enrica Mecarelli, Elda Bauda, Isabelle Petit-Härtlein, J. Teulon, J. Pellequer, Elisabetta Boeri Erba","doi":"10.3389/frans.2023.1124741","DOIUrl":"https://doi.org/10.3389/frans.2023.1124741","url":null,"abstract":"Membrane proteins are key players in many cellular events and represent crucial drug targets. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is a valuable approach to investigate them. To our knowledge, there are only a few reports of sequencing small membrane proteins using MALDI in-source decay (ISD). We report the successful fragmentation and sequencing of membrane proteins up to 46 kDa by MALDI-ISD. We have 1) investigated key MALDI parameters that influence the sequencing of a soluble protein; 2) used atomic force microscopy to observe our samples and correlate their topological features with MALDI data, which allowed us to optimize fragmentation conditions; 3) sequenced N- and C-termini of three membrane proteins (SpoIIIAF, TIM23, and NOX), solubilized in three different ways. Our results indicate that detergent and buffer type are of key importance for successful MALDI-ISD sequencing. Our findings are significant because sequencing membrane proteins enables the unique characterization of challenging biomolecules. The resulting fragmentation patterns provide key insights into the identity of proteins, their sequences, modifications, and other crucial information, such as the position of unexpected truncation.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48987475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-04DOI: 10.3389/frans.2023.1202074
F. Donati, L. Concetti, X. de la Torre, Xinmiao Zhou, Lisi Zhang, F. Botré
Background: In doping control, the presence of the exon5 c.577del variant in the human erythropoietin gene may be a confounding factor in the interpretation of the results from the analytical method currently in force for the detection of human recombinant erythropoietin, based on immunoelectrophoresis on SDS-PAGE and/or SAR-PAGE. This variant, determining the transcription of a higher molecular weight protein, can erroneously suggest the presence of recombinant erythropoietin in a biological sample, causing the possibility of a false positive result. Although the variant was now identified only in East Asian populations and with a very low frequency, it can threaten the reliability of current anti-doping tests.Methods: We have implemented a genetic test to identify the presence of this variant in the biological samples that are presently collected for anti-doping analysis (whole blood, urine, and dried blood spots). The test is based on the Sanger sequencing of the human erythropoietin gene exon 5, where the c.577del variant falls.Results and Discussion: The method has a specificity of 100% and allows identification of the possible presence of the variant starting from 100 pg of genomic DNA extracted from each biological sample. The efficacy of the test has been confirmed by the analysis of real samples from subjects showing and not showing the exon c.577del variant.
{"title":"Detection of exon 5 c.577del variant of human erythropoietin gene in whole blood, dried blood spots and urine samples for doping control","authors":"F. Donati, L. Concetti, X. de la Torre, Xinmiao Zhou, Lisi Zhang, F. Botré","doi":"10.3389/frans.2023.1202074","DOIUrl":"https://doi.org/10.3389/frans.2023.1202074","url":null,"abstract":"Background: In doping control, the presence of the exon5 c.577del variant in the human erythropoietin gene may be a confounding factor in the interpretation of the results from the analytical method currently in force for the detection of human recombinant erythropoietin, based on immunoelectrophoresis on SDS-PAGE and/or SAR-PAGE. This variant, determining the transcription of a higher molecular weight protein, can erroneously suggest the presence of recombinant erythropoietin in a biological sample, causing the possibility of a false positive result. Although the variant was now identified only in East Asian populations and with a very low frequency, it can threaten the reliability of current anti-doping tests.Methods: We have implemented a genetic test to identify the presence of this variant in the biological samples that are presently collected for anti-doping analysis (whole blood, urine, and dried blood spots). The test is based on the Sanger sequencing of the human erythropoietin gene exon 5, where the c.577del variant falls.Results and Discussion: The method has a specificity of 100% and allows identification of the possible presence of the variant starting from 100 pg of genomic DNA extracted from each biological sample. The efficacy of the test has been confirmed by the analysis of real samples from subjects showing and not showing the exon c.577del variant.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46732167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-03DOI: 10.3389/frans.2023.1229003
Luke Valencia
Septicemia is a prominent disease with a mortality rate of over 20%, making it one of the most expensive illnesses for hospitals in the United States. Many cells throughout the body release procalcitonin (PCT) in response to severe bacterial infection. This literature review attempts to assess PCT testing as a potential addition to sepsis protocols and to identify recommendations when implementing PCT testing into sepsis workups. The incorporation of PCT testing could significantly reduce the financial burden, antibiotic usage, and mortality rates in sepsis cases.
{"title":"PCT testing in sepsis protocols","authors":"Luke Valencia","doi":"10.3389/frans.2023.1229003","DOIUrl":"https://doi.org/10.3389/frans.2023.1229003","url":null,"abstract":"Septicemia is a prominent disease with a mortality rate of over 20%, making it one of the most expensive illnesses for hospitals in the United States. Many cells throughout the body release procalcitonin (PCT) in response to severe bacterial infection. This literature review attempts to assess PCT testing as a potential addition to sepsis protocols and to identify recommendations when implementing PCT testing into sepsis workups. The incorporation of PCT testing could significantly reduce the financial burden, antibiotic usage, and mortality rates in sepsis cases.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42963389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-29DOI: 10.3389/frans.2023.1234943
J. Grant
Many techniques have been developed since the 1960s to study the surfaces of materials. Some of them provide information on the chemical composition of surfaces and three have achieved widespread application. These three are X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and secondary ion mass spectrometry (SIMS). XPS is also referred to as electron spectroscopy for chemical analysis (ESCA), and photoemission spectroscopy (PES). Histories and the backgrounds of XPS (Briggs and Grant, 2003; Kelly, 2004), AES (Burhop, 1952; Briggs and Grant, 2003) and SIMS (Benninghoven et al., 1987; Benninghoven, 2001) have been written, and these techniques continue to be developed today, providing increased sensitivity, spatial resolution, and automation. XPS and AES measure the kinetic energies of electrons leaving the surface from incident X-rays (XPS) or incident electrons (AES). Auger electrons can also be produced by other means such as X-rays, positrons (Ohdaira and Suzuki, 2013), and even ions (Grant, 2003). SIMS measures the mass spectrum (actually the mass-to-charge ratio) of positively or negatively charged ions ejected from the surface of a material following impact by energetic ions. A variation of SIMS, sputtered neutral mass spectrometry (SNMS), measures the mass spectrum of the neutral species emitted. In SNMS, ionization of the neutral species is made after they leave the surface. Other surface analysis techniques include ion scattering spectroscopy (ISS) and Rutherford backscattering spectrometry (RBS), and these have been compared with the other techniques mentioned above (Powell et al., 1991). The most commonly used technique for surface analysis is XPS as it provides the simplest spectrum and is the easiest to quantify. XPS instruments also have a much lower cost than AES, SIMS, etc., so when groups are financially constrained, they tend towards XPS. In most cases, XPS also provides excellent information on the chemical state of surface atoms. AES can sometimes provide superior chemical information, such as the chemical state of carbon onmetal surfaces (Haas et al., 1972; Hooker and Grant, 1977).While XPS and AES do not directly detect hydrogen and helium in materials, the effect of hydrogen on other elements in the surface can sometimes be observed with XPS (Smentkowski et al., 1995) and AES (Bevolo, 1985). On the other hand, SIMS can detect all elements as well as distinguish isotopes; spectra can be quite complex as large molecular fragments from the material are also formed. Isotope detection can be very useful when an oxygen beam is used for analysis, where oxygen from the surface of the material can be distinguished from the oxygen in the beam. The number of papers published each year in AES and SIMS has been fairly constant for the past 20 years, whereas those published in XPS continue to increase. This is illustrated in Figure 1, which is plotted on a logarithmic scale to better show their growth since the
自20世纪60年代以来，已经开发了许多研究材料表面的技术。其中一些提供了有关表面化学成分的信息，三个已经得到了广泛应用。这三种是X射线光电子能谱（XPS）、俄歇电子能谱（AES）和二次离子质谱（SIMS）。XPS也被称为用于化学分析的电子光谱（ESCA）和光发射光谱（PES）。XPS（Briggs和Grant，2003；Kelly，2004）、AES（Burhop，1952；Briggs和格兰特，2003）和SIMS（Benninghoven et al.，1987；Benninghoen，2001）的历史和背景已经被编写出来，这些技术今天仍在不断发展，提供了更高的灵敏度、空间分辨率和自动化。XPS和AES测量从入射X射线（XPS）或入射电子（AES）离开表面的电子的动能。俄歇电子也可以通过其他方式产生，如X射线、正电子（Ohdaira和Suzuki，2013），甚至离子（Grant，2003）。SIMS测量高能离子撞击后从材料表面喷出的带正电或带负电离子的质谱（实际上是质荷比）。SIMS的一种变体，溅射中性质谱法（SNMS），测量发射的中性物质的质谱。在SNMS中，中性物质的电离是在它们离开表面后进行的。其他表面分析技术包括离子散射光谱法（ISS）和卢瑟福背散射光谱法，并且这些技术已经与上述其他技术进行了比较（Powell等人，1991）。表面分析最常用的技术是XPS，因为它提供了最简单的光谱，也最容易量化。XPS仪器的成本也比AES、SIMS等低得多，因此当集团经济拮据时，他们倾向于使用XPS。在大多数情况下，XPS还提供了关于表面原子化学状态的极好信息。AES有时可以提供优越的化学信息，例如金属表面碳的化学状态（Haas等人，1972；Hooker和Grant，1977年）。虽然XPS和AES不能直接检测材料中的氢和氦，但有时可以用XPS（Smentkowski等人，1995）和AES（Bevolo，1985）观察到氢对表面其他元素的影响。另一方面，SIMS可以检测所有元素并区分同位素；光谱可能相当复杂，因为还形成了来自材料的大分子片段。当使用氧束进行分析时，同位素检测可能非常有用，其中可以将材料表面的氧与束中的氧区分开来。在过去的20年里，每年以AES和SIMS发表的论文数量一直保持不变，而以XPS发表的论文则在继续增加。这一点如图1所示，图1以对数刻度绘制，以更好地显示它们自早年以来的增长情况。使用术语ESCA、PES、HAXPES、NAP-XPS、ARXPS（角度分辨XPS）和ARPES（角度分辨PES）的出版物与使用XPS的出版物一起被包括在内，以与其他技术进行比较。图2说明了XPS的不同术语的使用，并显示ESCA是20世纪60年代和70年代的首选术语，但在20世纪80年代被XPS取代，并保持主导地位。术语PES通常用于开放访问
{"title":"Challenges in surface analysis","authors":"J. Grant","doi":"10.3389/frans.2023.1234943","DOIUrl":"https://doi.org/10.3389/frans.2023.1234943","url":null,"abstract":"Many techniques have been developed since the 1960s to study the surfaces of materials. Some of them provide information on the chemical composition of surfaces and three have achieved widespread application. These three are X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and secondary ion mass spectrometry (SIMS). XPS is also referred to as electron spectroscopy for chemical analysis (ESCA), and photoemission spectroscopy (PES). Histories and the backgrounds of XPS (Briggs and Grant, 2003; Kelly, 2004), AES (Burhop, 1952; Briggs and Grant, 2003) and SIMS (Benninghoven et al., 1987; Benninghoven, 2001) have been written, and these techniques continue to be developed today, providing increased sensitivity, spatial resolution, and automation. XPS and AES measure the kinetic energies of electrons leaving the surface from incident X-rays (XPS) or incident electrons (AES). Auger electrons can also be produced by other means such as X-rays, positrons (Ohdaira and Suzuki, 2013), and even ions (Grant, 2003). SIMS measures the mass spectrum (actually the mass-to-charge ratio) of positively or negatively charged ions ejected from the surface of a material following impact by energetic ions. A variation of SIMS, sputtered neutral mass spectrometry (SNMS), measures the mass spectrum of the neutral species emitted. In SNMS, ionization of the neutral species is made after they leave the surface. Other surface analysis techniques include ion scattering spectroscopy (ISS) and Rutherford backscattering spectrometry (RBS), and these have been compared with the other techniques mentioned above (Powell et al., 1991). The most commonly used technique for surface analysis is XPS as it provides the simplest spectrum and is the easiest to quantify. XPS instruments also have a much lower cost than AES, SIMS, etc., so when groups are financially constrained, they tend towards XPS. In most cases, XPS also provides excellent information on the chemical state of surface atoms. AES can sometimes provide superior chemical information, such as the chemical state of carbon onmetal surfaces (Haas et al., 1972; Hooker and Grant, 1977).While XPS and AES do not directly detect hydrogen and helium in materials, the effect of hydrogen on other elements in the surface can sometimes be observed with XPS (Smentkowski et al., 1995) and AES (Bevolo, 1985). On the other hand, SIMS can detect all elements as well as distinguish isotopes; spectra can be quite complex as large molecular fragments from the material are also formed. Isotope detection can be very useful when an oxygen beam is used for analysis, where oxygen from the surface of the material can be distinguished from the oxygen in the beam. The number of papers published each year in AES and SIMS has been fairly constant for the past 20 years, whereas those published in XPS continue to increase. This is illustrated in Figure 1, which is plotted on a logarithmic scale to better show their growth since the ","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44024819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-07DOI: 10.3389/frans.2023.1073540
Federico Saba, Julien Mariethoz, F. Lisacek
Introduction: One of the main challenges in bioinformatics has been and still is, the comparison of entities through the development of algorithms for similarity scoring and data clustering according to biologically relevant aspects. Glycoinformatics also faces this challenge, in particular regarding the automated comparison of protein and/or tissue glycomes, that remains a relatively uncharted territory. Methods: Low and high throughput experimental glycomic and glycoproteomic results were collected, revealing a bias toward N-linked glycomes. Then, N-glycomes were considered and represented as networks of related glycan compositions as opposed to lists of glycans. They were processed and compared through a java application generating graphs and another producing a similarity matrix based on graph content. Several scoring schemes (e.g., Jaccard index or cosine) were tested and evaluated using the Matthews Correlation Coefficient, in order to capture a meaningful protein and tissue N-glycome similarity. Results: Assuming that a glycome corresponds to a well-connected graph of glycan compositions, graph comparison has revealed gaps that can be interpreted as inconsistencies. The outcome of systematic graph comparison is both formal and practical. In principle, it is shown that the idiosyncrasy of current glycome data limits the definition of appropriate estimates for systematically comparing N-glycomes. Yet, several potentially interesting criteria could be identified in a series of use cases detailed in the study. Discussion: Differentially expressed glycomes are usually compared manually, but the resulting work tends to remain in publications due to the lack of dedicated tools. Even manually, cross-comparison is challenging mostly because different sets of features are used from one study to the other. The work presented here enables laying down guidelines for developing a software tool comparing glycomes based on appropriate definitions of similarity and suitable methods for its evaluation and implementation.
{"title":"What is a consistent glycan composition dataset?","authors":"Federico Saba, Julien Mariethoz, F. Lisacek","doi":"10.3389/frans.2023.1073540","DOIUrl":"https://doi.org/10.3389/frans.2023.1073540","url":null,"abstract":"Introduction: One of the main challenges in bioinformatics has been and still is, the comparison of entities through the development of algorithms for similarity scoring and data clustering according to biologically relevant aspects. Glycoinformatics also faces this challenge, in particular regarding the automated comparison of protein and/or tissue glycomes, that remains a relatively uncharted territory. Methods: Low and high throughput experimental glycomic and glycoproteomic results were collected, revealing a bias toward N-linked glycomes. Then, N-glycomes were considered and represented as networks of related glycan compositions as opposed to lists of glycans. They were processed and compared through a java application generating graphs and another producing a similarity matrix based on graph content. Several scoring schemes (e.g., Jaccard index or cosine) were tested and evaluated using the Matthews Correlation Coefficient, in order to capture a meaningful protein and tissue N-glycome similarity. Results: Assuming that a glycome corresponds to a well-connected graph of glycan compositions, graph comparison has revealed gaps that can be interpreted as inconsistencies. The outcome of systematic graph comparison is both formal and practical. In principle, it is shown that the idiosyncrasy of current glycome data limits the definition of appropriate estimates for systematically comparing N-glycomes. Yet, several potentially interesting criteria could be identified in a series of use cases detailed in the study. Discussion: Differentially expressed glycomes are usually compared manually, but the resulting work tends to remain in publications due to the lack of dedicated tools. Even manually, cross-comparison is challenging mostly because different sets of features are used from one study to the other. The work presented here enables laying down guidelines for developing a software tool comparing glycomes based on appropriate definitions of similarity and suitable methods for its evaluation and implementation.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47840289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-05-12DOI: 10.3389/frans.2023.1154391
G. P. Szekeres, E. Hanozin, Robyn Diehn, Jan Horlebein, Lukasz Polewski, Andreas Zappe, D. Lauster, K. Pagel
The increasing antibiotic resistance in bacteria is an alarming phenomenon all around the world. Certain strains have developed resistance against multiple antimicrobial molecules, in which cases, the final option is to use a last-resort drug. These drugs, however, are last-resort for a reason: they can pose serious risk on vital organ functions in the patient. To mitigate the risk of severe side-effects and to reduce the rate of bacterial mutation, co-administration with other molecules that increase their efficacy seems to be the only suitable option. This leads to a reduced dose while maintaining the same level of antibiotic activity within the body. In this study, the effect of heparin derivatives on the antibiotic activity of colistin and their interactions were studied by ion mobility, mass spectrometry, and bacterium growth assays. The results show that during the association of colistin and heparin, they retain their structure while higher-stoichiometry complexes can form. When long-chain heparin is co-administered, multiple colistin molecules can associate with it, which increases the antibiotic activity by ∼40% relative to the sole administration of colistin.
{"title":"Heparin increases the antibiotic efficacy of colistin","authors":"G. P. Szekeres, E. Hanozin, Robyn Diehn, Jan Horlebein, Lukasz Polewski, Andreas Zappe, D. Lauster, K. Pagel","doi":"10.3389/frans.2023.1154391","DOIUrl":"https://doi.org/10.3389/frans.2023.1154391","url":null,"abstract":"The increasing antibiotic resistance in bacteria is an alarming phenomenon all around the world. Certain strains have developed resistance against multiple antimicrobial molecules, in which cases, the final option is to use a last-resort drug. These drugs, however, are last-resort for a reason: they can pose serious risk on vital organ functions in the patient. To mitigate the risk of severe side-effects and to reduce the rate of bacterial mutation, co-administration with other molecules that increase their efficacy seems to be the only suitable option. This leads to a reduced dose while maintaining the same level of antibiotic activity within the body. In this study, the effect of heparin derivatives on the antibiotic activity of colistin and their interactions were studied by ion mobility, mass spectrometry, and bacterium growth assays. The results show that during the association of colistin and heparin, they retain their structure while higher-stoichiometry complexes can form. When long-chain heparin is co-administered, multiple colistin molecules can associate with it, which increases the antibiotic activity by ∼40% relative to the sole administration of colistin.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47891727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-19DOI: 10.3389/frans.2023.1069678
T. C. Davies
Mercury (Hg) pollution is of global concern. Despite the prolificity of research in the past two decades or so, there are still several uncertainties and variabilities in our knowledge of both the element’s exposure dynamics and its health effects. Understanding the intricacies of the element’s emissions-to-impact path, for instance, is rendered intractable by its varied environmental fate and the overarching influence of environmental, geochemical, biological and socioeconomic drivers. In this paper, an updated synopsis of the relevant and more important geomedical characteristics of Hg is considered to constitute part of the provision of high-quality input data needed in Hg simulation modelling studies, and other applications such as the provision of long-term data necessary for evaluating the effectiveness of regulatory measures at various scales. A critical overview is presented on the importance of data quality in parameterisation, and validation of Hg simulation models and other related applications. In this connection, the dearth of modern measurements of Hg abundance in crustal rocks and other Earth materials which needs to be set prior to simulation as well as in modelling source to sink transfers in the Hg cycle, is highlighted. An improved input data quality would also foster the production of model outcomes that are accurate enough for applications in design of better exposure-limiting strategies; and in providing insights on how the course of diagnosis and treatment currently proffered by physicians for Hg-induced maladies, can be revised or expanded. Model results derived from high-quality input datasets also have a high potential for providing forecasting capabilities to inform policy.
{"title":"An updated review of the salient geomedical aspects of mercury for enhancement of data quality in simulation modelling and other prognostic applications: Africa case descriptions","authors":"T. C. Davies","doi":"10.3389/frans.2023.1069678","DOIUrl":"https://doi.org/10.3389/frans.2023.1069678","url":null,"abstract":"Mercury (Hg) pollution is of global concern. Despite the prolificity of research in the past two decades or so, there are still several uncertainties and variabilities in our knowledge of both the element’s exposure dynamics and its health effects. Understanding the intricacies of the element’s emissions-to-impact path, for instance, is rendered intractable by its varied environmental fate and the overarching influence of environmental, geochemical, biological and socioeconomic drivers. In this paper, an updated synopsis of the relevant and more important geomedical characteristics of Hg is considered to constitute part of the provision of high-quality input data needed in Hg simulation modelling studies, and other applications such as the provision of long-term data necessary for evaluating the effectiveness of regulatory measures at various scales. A critical overview is presented on the importance of data quality in parameterisation, and validation of Hg simulation models and other related applications. In this connection, the dearth of modern measurements of Hg abundance in crustal rocks and other Earth materials which needs to be set prior to simulation as well as in modelling source to sink transfers in the Hg cycle, is highlighted. An improved input data quality would also foster the production of model outcomes that are accurate enough for applications in design of better exposure-limiting strategies; and in providing insights on how the course of diagnosis and treatment currently proffered by physicians for Hg-induced maladies, can be revised or expanded. Model results derived from high-quality input datasets also have a high potential for providing forecasting capabilities to inform policy.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46766657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-17DOI: 10.3389/frans.2023.1125049
Ting-Yu Huang, J. Yu
Introduction: Gas chromatography combined with mass spectrometry (GC/MS) is popular analytical instrumentation for chemical separation and identification. A novel framework for chemical forensics based on the visualization of GC/MS data and transfer learning is proposed. Methods: To evaluate the framework, 228 GC/MS data collected from two standard cannabis varieties, i.e., hemp and marijuana, were utilized. By processing the raw GC/MS data, analytical features, including retention times, mass-to-charge ratios, intensities, and summed ion mass spectra, were successfully transformed into two types of image representations. The GC/MS data transformed images were fed into a pre-trained convolutional neural network (CNN) to develop intelligent classifiers for the sample classification tasks. The effectiveness of several hyper-parameters for improving classification performance was investigated during transfer learning. Results: The proposed analytical workflow could classify hemp and marijuana with 97% accuracy. Furthermore, the transfer-learning-based classifiers were established without requiring big data sets and peak alignment. Discussion: The potential application of the new artificial intelligence (AI)-powered framework for chemical forensics using GC/MS data has been demonstrated. This framework provides unique opportunities for classifying various types of physical evidence using chromatography and mass spectrometry signals.
{"title":"Intelligent framework for cannabis classification using visualization of gas chromatography/mass spectrometry data and transfer learning","authors":"Ting-Yu Huang, J. Yu","doi":"10.3389/frans.2023.1125049","DOIUrl":"https://doi.org/10.3389/frans.2023.1125049","url":null,"abstract":"Introduction: Gas chromatography combined with mass spectrometry (GC/MS) is popular analytical instrumentation for chemical separation and identification. A novel framework for chemical forensics based on the visualization of GC/MS data and transfer learning is proposed. Methods: To evaluate the framework, 228 GC/MS data collected from two standard cannabis varieties, i.e., hemp and marijuana, were utilized. By processing the raw GC/MS data, analytical features, including retention times, mass-to-charge ratios, intensities, and summed ion mass spectra, were successfully transformed into two types of image representations. The GC/MS data transformed images were fed into a pre-trained convolutional neural network (CNN) to develop intelligent classifiers for the sample classification tasks. The effectiveness of several hyper-parameters for improving classification performance was investigated during transfer learning. Results: The proposed analytical workflow could classify hemp and marijuana with 97% accuracy. Furthermore, the transfer-learning-based classifiers were established without requiring big data sets and peak alignment. Discussion: The potential application of the new artificial intelligence (AI)-powered framework for chemical forensics using GC/MS data has been demonstrated. This framework provides unique opportunities for classifying various types of physical evidence using chromatography and mass spectrometry signals.","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42578490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-11DOI: 10.3389/frans.2023.1186952
R. Vitale, J. Roger
Centre National de la Recherche Scientifique (CNRS), LASIRE (UMR 8516), Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et I’Environnement, Université de Lille, Lille, France, Technologies et Méthodes pour les Agricultures de Demain Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (ITAP-INRAE), Institut Agro, Université de Montpellier, Montpellier, France, ChemHouse Research Group, Université de Montpellier, Montpellier, France
{"title":"Editorial: Variable selection in chemometrics","authors":"R. Vitale, J. Roger","doi":"10.3389/frans.2023.1186952","DOIUrl":"https://doi.org/10.3389/frans.2023.1186952","url":null,"abstract":"Centre National de la Recherche Scientifique (CNRS), LASIRE (UMR 8516), Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et I’Environnement, Université de Lille, Lille, France, Technologies et Méthodes pour les Agricultures de Demain Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (ITAP-INRAE), Institut Agro, Université de Montpellier, Montpellier, France, ChemHouse Research Group, Université de Montpellier, Montpellier, France","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41288958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-11DOI: 10.3389/frans.2023.1175290
M. D. de Moraes, Fernando Gonçalves de Almeida, L. Tinoco
Protein-ligand interactions are essential for the regulation of biological processes, such as signal transduction, gene regulation, cellular metabolism, and immunoreaction. The term ligand encompasses nucleic acids, cofactors, metals, other proteins, peptides, amino acids, lipids, and drugs. Protein function can be regulated by its interaction with specific ligands through different mechanisms. Protein-ligand interaction studies are crucial for understanding the regulation of the biological function of proteins, elucidating potential biological targets, as well as discovering bioactive compounds in the drug development process. Within this context, this Research Topic aims to highlight different aspects of analytical techniques as a useful tool to develop new, rapid, and reliable ligand screening assays. Two original research manuscripts, one review, and one mini-review on analytical assays for ligand screening are collected in this Research Topic, covering assays for ornithine decarboxylase inhibitor screening, on-flow enzymatic inhibitor screening through liquid chromatography methods, liquid chromatography coupled to mass spectrometry (LC-MS) method to screen human kallikrein (KLKs) inhibitors, and a study on salt concentration to improve the separation performance of biomarkers for transporter protein inhibition. In the following paragraphs, each published manuscript is presented and briefly described. The ornithine decarboxylase (ODC) enzyme belongs to the polyamine biosynthetic pathway, catalyzing the decarboxylation of ornithine to putrescine. Polyamines (putrescine, spermidine, and spermine) are essential growth factors in eukaryotic cells, but their high levels are associated with carcinogenesis (Gerner and Meyskens, 2004) and Alzheimer’s disease (Mäkitie et al., 2010). Consequently, ODC is considered a biological target for developing new drugs for the treatment of several diseases. Tinoco et al. (2022) summarized the methods based on radiolabeling, colorimetric assays using auxiliary enzymes to detect CO2 or H2O2 release, chromatographic-based methods with putrescine derivation, mass spectrometry, circular dichroism, and fluorescence techniques. The authors highlight the demand for the development of high-throughput assays for the screening of ODC inhibitors. Since ornithine and putrescine (substrate and product) cannot be directly monitored by spectroscopic techniques, derivation or conversion procedures into spectrophotometrically detectable species are mandatory, resulting in low throughput assays. OPEN ACCESS
{"title":"Editorial: The protagonism of bioanalytical methods in high-throughput drug discovery","authors":"M. D. de Moraes, Fernando Gonçalves de Almeida, L. Tinoco","doi":"10.3389/frans.2023.1175290","DOIUrl":"https://doi.org/10.3389/frans.2023.1175290","url":null,"abstract":"Protein-ligand interactions are essential for the regulation of biological processes, such as signal transduction, gene regulation, cellular metabolism, and immunoreaction. The term ligand encompasses nucleic acids, cofactors, metals, other proteins, peptides, amino acids, lipids, and drugs. Protein function can be regulated by its interaction with specific ligands through different mechanisms. Protein-ligand interaction studies are crucial for understanding the regulation of the biological function of proteins, elucidating potential biological targets, as well as discovering bioactive compounds in the drug development process. Within this context, this Research Topic aims to highlight different aspects of analytical techniques as a useful tool to develop new, rapid, and reliable ligand screening assays. Two original research manuscripts, one review, and one mini-review on analytical assays for ligand screening are collected in this Research Topic, covering assays for ornithine decarboxylase inhibitor screening, on-flow enzymatic inhibitor screening through liquid chromatography methods, liquid chromatography coupled to mass spectrometry (LC-MS) method to screen human kallikrein (KLKs) inhibitors, and a study on salt concentration to improve the separation performance of biomarkers for transporter protein inhibition. In the following paragraphs, each published manuscript is presented and briefly described. The ornithine decarboxylase (ODC) enzyme belongs to the polyamine biosynthetic pathway, catalyzing the decarboxylation of ornithine to putrescine. Polyamines (putrescine, spermidine, and spermine) are essential growth factors in eukaryotic cells, but their high levels are associated with carcinogenesis (Gerner and Meyskens, 2004) and Alzheimer’s disease (Mäkitie et al., 2010). Consequently, ODC is considered a biological target for developing new drugs for the treatment of several diseases. Tinoco et al. (2022) summarized the methods based on radiolabeling, colorimetric assays using auxiliary enzymes to detect CO2 or H2O2 release, chromatographic-based methods with putrescine derivation, mass spectrometry, circular dichroism, and fluorescence techniques. The authors highlight the demand for the development of high-throughput assays for the screening of ODC inhibitors. Since ornithine and putrescine (substrate and product) cannot be directly monitored by spectroscopic techniques, derivation or conversion procedures into spectrophotometrically detectable species are mandatory, resulting in low throughput assays. OPEN ACCESS","PeriodicalId":73063,"journal":{"name":"Frontiers in analytical science","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49241632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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