Frontiers in Molecular Biosciences最新文献_第7页

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-11 DOI: 10.3389/fmolb.2024.1348091

Hansotto Reiber

{"title":"Disease-related data patterns in cerebrospinal fluid diagnostics: medical quality versus analytical quantity","authors":"Hansotto Reiber","doi":"10.3389/fmolb.2024.1348091","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1348091","url":null,"abstract":"Cerebrospinal fluid (CSF) diagnostics is characterized by the biologically relevant combination of analytes in order to obtain disease-related data patterns that enable medically relevant interpretations. The necessary change in knowledge bases such as barrier function as a diffusion/CSF flow model and immunological networks of B-cell clones and pleiotropic cytokines is considered. The biophysical and biological principles for data combination are demonstrated using examples from neuroimmunological and dementia diagnostics. In contrast to current developments in clinical chemistry and laboratory medicine, CSF diagnostics is moving away from mega-automated systems with a constantly growing number of individual analyses toward a CSF report that integrates all patient data. Medical training in data sample interpretation in the inter-laboratory test systems (“EQA schemes”) has become increasingly important. However, the results for CSF diagnostics (EQAS from INSTAND) indicate a crucially misguided trend. The separate analysis of CSF and serum in different, non-matched assays and extreme batch variations systematically lead to misinterpretations, which are the responsibility of the test providers. The questionable role of expensive accreditation procedures and the associated false quality expectations are discussed. New concepts that reintegrate the medical expertise of the clinical chemist must be emphasized along with the positive side effect of reducing costs in the healthcare system.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"38 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Non-coding RNA and its network in the pathogenesis of Myasthenia Gravis 肌无力发病机制中的非编码 RNA 及其网络

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-10 DOI: 10.3389/fmolb.2024.1388476

Fuqiang Wang, Xiaoli Mei, Yunhao Yang, Hanlu Zhang, Zhiyang Li, Lei Zhu, Senyi Deng, Yun Wang

引用次数: 0

Pathogenic role of PFKFB3 in endothelial inflammatory diseases PFKFB3 在内皮炎症性疾病中的致病作用

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-10 DOI: 10.3389/fmolb.2024.1454456

Ling Zhou, Juan Li, Juanjuan Wang, Xuping Niu, Junqin Li, Kaiming Zhang

引用次数: 0

From in vitro to in silico: a pipeline for generating virtual tissue simulations from real image data 从体外到硅学：从真实图像数据生成虚拟组织模拟的管道

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-10 DOI: 10.3389/fmolb.2024.1467366

Elina Nürnberg, Mario Vitacolonna, Roman Bruch, Markus Reischl, Rüdiger Rudolf, Simeon Sauer

{"title":"From in vitro to in silico: a pipeline for generating virtual tissue simulations from real image data","authors":"Elina Nürnberg, Mario Vitacolonna, Roman Bruch, Markus Reischl, Rüdiger Rudolf, Simeon Sauer","doi":"10.3389/fmolb.2024.1467366","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1467366","url":null,"abstract":"3D cell culture models replicate tissue complexity and aim to study cellular interactions and responses in a more physiologically relevant environment compared to traditional 2D cultures. However, the spherical structure of these models makes it difficult to extract meaningful data, necessitating advanced techniques for proper analysis. In silico simulations enhance research by predicting cellular behaviors and therapeutic responses, providing a powerful tool to complement experimental approaches. Despite their potential, these simulations often require advanced computational skills and significant resources, which creates a barrier for many researchers. To address these challenges, we developed an accessible pipeline using open-source software to facilitate virtual tissue simulations. Our approach employs the Cellular Potts Model, a versatile framework for simulating cellular behaviors in tissues. The simulations are constructed from real world 3D image stacks of cancer spheroids, ensuring that the virtual models are rooted in experimental data. By introducing a new metric for parameter optimization, we enable the creation of realistic simulations without requiring extensive computational expertise. This pipeline benefits researchers wanting to incorporate computational biology into their methods, even if they do not possess extensive expertise in this area. By reducing the technical barriers associated with advanced computational modeling, our pipeline enables more researchers to utilize these powerful tools. Our approach aims to foster a broader use of in silico methods in disease research, contributing to a deeper understanding of disease biology and the refinement of therapeutic interventions.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"290 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolomic changes in tear fluid following zinc biofortification in the BiZiFED nutritional study: a feasibility study BiZiFED营养研究中锌生物强化后泪液中代谢组的变化：一项可行性研究

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-10 DOI: 10.3389/fmolb.2024.1421699

Connor N. Brown, Babar Shahzad, Mukhtiar Zaman, Xiaobei Pan, Brian D. Green, Nicola M. Lowe, Imre Lengyel

{"title":"Metabolomic changes in tear fluid following zinc biofortification in the BiZiFED nutritional study: a feasibility study","authors":"Connor N. Brown, Babar Shahzad, Mukhtiar Zaman, Xiaobei Pan, Brian D. Green, Nicola M. Lowe, Imre Lengyel","doi":"10.3389/fmolb.2024.1421699","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1421699","url":null,"abstract":"BackgroundBiofortified Zinc Flour to Eliminate Deficiency in Pakistan (BiZiFED) is a nutritional research program that evaluates the impact of consuming zinc biofortified wheat flour on zinc status and associated health outcomes of vulnerable communities in northwest Pakistan. Measuring zinc status from blood samples is fraught with problems. This feasibility study evaluated whether metabolite changes in tear biofluids could be used to understand zinc status.MethodsZinc deficiency is particularly prevalent amongst the female population in Pakistan. Therefore, a crossover trial was developed in which 25 women of reproductive age received standard, wheat flour, and another 25 received zinc-biofortified wheat flour for 8 weeks. At the end of this period, the nutritional intervention was switched between the groups for another 8 weeks. Tear biofluid was collected using Schirmer strips at baseline and after 8 and 16 weeks. Metabolomic analysis was conducted using the MxP® Quant 500 kit on the tear biofluid from a subset of the study participants.ResultsTwo metabolites had a significantly negative correlation with plasma zinc concentration: tiglylcarnitine and valine. Compared to baseline metabolite concentrations, acetylcarnitine, glutamine, two lysophosphatidylcholines (lysoPC a C16:0 and lysoPC a C18:1), and four sphingomyelins (SM (OH) C16:1, SM C16:0, SM C16:1, and SM C24:0) were all significantly decreased post-zinc intervention, whilst a ceramide (Cer(d18:1/18:0) was significantly increased.ConclusionThese results highlight the potential of using tear biofluids as an alternative source for metabolomic biomarkers, both for the assessment of the zinc status of individuals enrolled in nutritional studies and for indicating physiological changes that arise from nutritional supplementation.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"18 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring metabolic anomalies in COVID-19 and post-COVID-19: a machine learning approach with explainable artificial intelligence 探索 COVID-19 和后 COVID-19 的代谢异常：采用可解释人工智能的机器学习方法

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-09 DOI: 10.3389/fmolb.2024.1429281

Juan José Oropeza-Valdez, Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Xavier Soberon, Osbaldo Resendis-Antonio

{"title":"Exploring metabolic anomalies in COVID-19 and post-COVID-19: a machine learning approach with explainable artificial intelligence","authors":"Juan José Oropeza-Valdez, Cristian Padron-Manrique, Aarón Vázquez-Jiménez, Xavier Soberon, Osbaldo Resendis-Antonio","doi":"10.3389/fmolb.2024.1429281","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1429281","url":null,"abstract":"The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant challenges worldwide, including diverse clinical outcomes and prolonged post-recovery symptoms known as Long COVID or Post-COVID-19 syndrome. Emerging evidence suggests a crucial role of metabolic reprogramming in the infection’s long-term consequences. This study employs a novel approach utilizing machine learning (ML) and explainable artificial intelligence (XAI) to analyze metabolic alterations in COVID-19 and Post-COVID-19 patients. Samples were taken from a cohort of 142 COVID-19, 48 Post-COVID-19, and 38 control patients, comprising 111 identified metabolites. Traditional analysis methods, like PCA and PLS-DA, were compared with ML techniques, particularly eXtreme Gradient Boosting (XGBoost) enhanced by SHAP (SHapley Additive exPlanations) values for explainability. XGBoost, combined with SHAP, outperformed traditional methods, demonstrating superior predictive performance and providing new insights into the metabolic basis of the disease’s progression and aftermath. The analysis revealed metabolomic subgroups within the COVID-19 and Post-COVID-19 conditions, suggesting heterogeneous metabolic responses to the infection and its long-term impacts. Key metabolic signatures in Post-COVID-19 include taurine, glutamine, alpha-Ketoglutaric acid, and LysoPC a C16:0. This study highlights the potential of integrating ML and XAI for a fine-grained description in metabolomics research, offering a more detailed understanding of metabolic anomalies in COVID-19 and Post-COVID-19 conditions.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"31 1 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Applicability of metabolomics to improve sustainable grapevine production 代谢组学在提高葡萄可持续生产中的应用

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-06 DOI: 10.3389/fmolb.2024.1395677

Catarina Estêvão, Lénia Rodrigues, Ana Elisa Rato, Raquel Garcia, Hélia Cardoso, Catarina Campos

{"title":"Applicability of metabolomics to improve sustainable grapevine production","authors":"Catarina Estêvão, Lénia Rodrigues, Ana Elisa Rato, Raquel Garcia, Hélia Cardoso, Catarina Campos","doi":"10.3389/fmolb.2024.1395677","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1395677","url":null,"abstract":"Metabolites represent the end product of gene expression, protein interaction and other regulatory mechanisms. The metabolome reflects a biological system’s response to genetic and environmental changes, providing a more accurate description of plants’ phenotype than the transcriptome or the proteome. Grapevine (Vitis vinifera L.), established for the production of wine grapes, table grapes, and raisins, holds immense agronomical and economic significance not only in the Mediterranean region but worldwide. As all plants, grapevines face the adverse impact of biotic and abiotic stresses that negatively affect multiple stages of grape and wine industry, including plant and berry development pre- and post-harvest, fresh grapes processing and consequently wine quality. In the present review we highlight the applicability of metabolome analysis in the understanding of the mechanisms involved in grapevine response and acclimatization upon the main biotic and abiotic constrains. The metabolome of induced morphogenic processes such as adventitious rooting and somatic embryogenesis is also explored, as it adds knowledge on the physiological and molecular phenomena occurring in the explants used, and on the successfully propagation of grapevines with desired traits. Finally, the microbiome-induced metabolites in grapevine are discussed in view of beneficial applications derived from the plant symbioses.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"29 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis 通过蜕变态分析发现一种潜在的 SARS-CoV-2 主要蛋白酶（Mpro）异位抑制剂

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-06 DOI: 10.3389/fmolb.2024.1451280

Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed, Kabir H. Biswas

{"title":"A potential allosteric inhibitor of SARS-CoV-2 main protease (Mpro) identified through metastable state analysis","authors":"Asma Fatima, Anupriya M. Geethakumari, Wesam S. Ahmed, Kabir H. Biswas","doi":"10.3389/fmolb.2024.1451280","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1451280","url":null,"abstract":"Anti-COVID19 drugs, such as nirmatrelvir, have been developed targeting the SARS-CoV-2 main protease, Mpro, based on the critical requirement of its proteolytic processing of the viral polyproteins into functional proteins essential for viral replication. However, the emergence of SARS-CoV-2 variants with Mpro mutations has raised the possibility of developing resistance against these drugs, likely due to therapeutic targeting of the Mpro catalytic site. An alternative to these drugs is the development of drugs that target an allosteric site distant from the catalytic site in the protein that may reduce the chance of the emergence of resistant mutants. Here, we combine computational analysis with in vitro assay and report the discovery of a potential allosteric site and an allosteric inhibitor of SARS-CoV-2 Mpro. Specifically, we identified an Mpro metastable state with a deformed catalytic site harboring potential allosteric sites, raising the possibility that stabilization of this metastable state through ligand binding can lead to the inhibition of Mpro activity. We then performed a computational screening of a library (∼4.2 million) of drug-like compounds from the ZINC database and identified several candidate molecules with high predicted binding affinity. MD simulations showed stable binding of the three top-ranking compounds to the putative allosteric sites in the protein. Finally, we tested the three compounds in vitro using a BRET-based Mpro biosensor and found that one of the compounds (ZINC4497834) inhibited the Mpro activity. We envisage that the identification of a potential allosteric inhibitor of Mpro will aid in developing improved anti-COVID-19 therapy.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"182 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization LncSTPred：lncRNA亚细胞定位的预测模型和影响定位的生物决定因素的破译

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-05 DOI: 10.3389/fmolb.2024.1452142

Si-Le Hu, Ying-Li Chen, Lu-Qiang Zhang, Hui Bai, Jia-Hong Yang, Qian-Zhong Li

{"title":"LncSTPred: a predictive model of lncRNA subcellular localization and decipherment of the biological determinants influencing localization","authors":"Si-Le Hu, Ying-Li Chen, Lu-Qiang Zhang, Hui Bai, Jia-Hong Yang, Qian-Zhong Li","doi":"10.3389/fmolb.2024.1452142","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1452142","url":null,"abstract":"IntroductionLong non-coding RNAs (lncRNAs) play crucial roles in genetic markers, genome rearrangement, chromatin modifications, and other biological processes. Increasing evidence suggests that lncRNA functions are closely related to their subcellular localization. However, the distribution of lncRNAs in different subcellular localizations is imbalanced. The number of lncRNAs located in the nucleus is more than ten times that in the exosome.MethodsIn this study, we propose a new oversampling method to construct a predictive dataset and develop a predictive model called LncSTPred. This model improves the Adaboost algorithm for subcellular localization prediction using 3-mer, 3-RF sequence, and minimum free energy structure features.Results and DiscussionBy using our improved Adaboost algorithm, better prediction accuracy for lncRNA subcellular localization was obtained. In addition, we evaluated feature importance by using the F-score and analyzed the influence of highly relevant features on lncRNAs. Our study shows that the ANA features may be a key factor for predicting lncRNA subcellular localization, which correlates with the composition of stems and loops in the secondary structure of lncRNAs.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"290 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Recent progress of methods for cuproptosis detection 杯突检测方法的最新进展

IF 5 3区生物学

Frontiers in Molecular Biosciences Pub Date : 2024-09-04 DOI: 10.3389/fmolb.2024.1460987

Ligang Zhang, Ruiting Deng, Raoqing Guo, Yawen Jiang, Yichen Guan, Caiyue Chen, Wudi Zhao, Guobin Huang, Lian Liu, Hongli Du, Dongsheng Tang

{"title":"Recent progress of methods for cuproptosis detection","authors":"Ligang Zhang, Ruiting Deng, Raoqing Guo, Yawen Jiang, Yichen Guan, Caiyue Chen, Wudi Zhao, Guobin Huang, Lian Liu, Hongli Du, Dongsheng Tang","doi":"10.3389/fmolb.2024.1460987","DOIUrl":"https://doi.org/10.3389/fmolb.2024.1460987","url":null,"abstract":"Varying from other identified cell death pathways, cuproptosis is a new type of regulated cell death characterized by excess Cu ions, abnormal aggregation of lipoylated proteins in TCA cycle, loss of Fe-S cluster proteins, upregulation of HSP70, leading to proteotoxic and oxidative stress. Cuproptosis is highly concerned by scientific community and as the field of cuproptosis further develops, remarkable progress has been made in the verification and mechanism of cuproptosis, and methods used to detect cuproptosis have been continuously improved. According to the characteristic changes of cuproptosis, techniques based on cell death verification, Cu content, morphology, molecular biology of protein levels of cuproptosis-related molecules and biochemical pathways of cuproptosis-related enzyme activity and metabolites of oxidative stress, lipoic acid, TCA cycle, Fe-S cluster proteins, oxidative phosphorylation, cell respiration intensity have been subject to cuproptosis verification and research. In order to further deepen the understanding of detecting cuproptosis, the principle and application of common cuproptosis detection methods are reviewed and categorized in cellular phenomena and molecular mechanism in terms of cell death, Cu content, morphology, molecular biology, biochemical pathways with a flow chart. All the indicating results have been displayed in response to the markers of cuproptosis, their advantages and limitations are summaried, and comparison of cuproptosis and ferroptosis detection is performed in this study. Our collection of methods for cuproptosis detection will provide a great basis for cuproptosis verification and research in the future.","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"60 1","pages":""},"PeriodicalIF":5.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142220221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0