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Nutritional metabolomics: Recent developments and future needs 营养代谢组学：最近的发展和未来的需求。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-05 DOI: 10.1016/j.cbpa.2023.102400
Maaria Kortesniemi , Stefania Noerman , Anna Kårlund , Jasmin Raita , Topi Meuronen , Ville Koistinen , Rikard Landberg , Kati Hanhineva
{"title":"Nutritional metabolomics: Recent developments and future needs","authors":"Maaria Kortesniemi ,&nbsp;Stefania Noerman ,&nbsp;Anna Kårlund ,&nbsp;Jasmin Raita ,&nbsp;Topi Meuronen ,&nbsp;Ville Koistinen ,&nbsp;Rikard Landberg ,&nbsp;Kati Hanhineva","doi":"10.1016/j.cbpa.2023.102400","DOIUrl":"10.1016/j.cbpa.2023.102400","url":null,"abstract":"<div><p>Metabolomics has rapidly been adopted as one of the key methods in nutrition research. This review focuses on the recent developments and updates in the field, including the analytical methodologies that encompass improved instrument sensitivity, sampling techniques and data integration (multiomics). Metabolomics has advanced the discovery and validation of dietary biomarkers and their implementation in health research. Metabolomics has come to play an important role in the understanding of the role of small molecules resulting from the diet–microbiota interactions when gut microbiota research has shifted towards improving the understanding of the activity and functionality of gut microbiota rather than composition alone. Currently, metabolomics plays an emerging role in precision nutrition and the recent developments therein are discussed.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593123001382/pdfft?md5=33562aa62ac2d1bfb266abf797b6c74d&pid=1-s2.0-S1367593123001382-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41093544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Immunomodulatory roles of PARPs: Shaping the tumor microenvironment, one ADP-ribose at a time PARPs的免疫调节作用：塑造肿瘤微环境，一次一个ADP核糖。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-04 DOI: 10.1016/j.cbpa.2023.102402
Deja M. Brooks , Sudarshan Anand , Michael S. Cohen
{"title":"Immunomodulatory roles of PARPs: Shaping the tumor microenvironment, one ADP-ribose at a time","authors":"Deja M. Brooks ,&nbsp;Sudarshan Anand ,&nbsp;Michael S. Cohen","doi":"10.1016/j.cbpa.2023.102402","DOIUrl":"10.1016/j.cbpa.2023.102402","url":null,"abstract":"<div><p><span><span><span><span>PARPs encompass a small yet pervasive group of 17 </span>enzymes<span> that catalyze a post-translational modification known as ADP-ribosylation. PARP1, the founding member, has received considerable focus; however, in recent years, the spotlight has shifted to other members within the PARP family. In this opinion piece, we first discuss surprising findings that some FDA-approved PARP1 inhibitors activate innate immune signaling in cancer cells that harbor mutations in the </span></span>DNA<span> repair pathway. We then discuss hot-off-the-press genetic and pharmacological studies that reveal roles for PARP7, PARP11, and PARP14 in immune signaling in both tumor cells and tumor-associated </span></span>immune cells<span>. We conclude with thoughts on tuning PARP1-inhibitor-mediated innate immune activation and explore the unrealized potential for small molecule </span></span>modulators of other PARP family members as next-generation immuno-oncology drugs.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41093133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Global approaches for protein thiol redox state detection 蛋白质硫醇氧化还原状态检测的全局方法。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-03 DOI: 10.1016/j.cbpa.2023.102390
Lisa R. Knoke, Lars I. Leichert
{"title":"Global approaches for protein thiol redox state detection","authors":"Lisa R. Knoke,&nbsp;Lars I. Leichert","doi":"10.1016/j.cbpa.2023.102390","DOIUrl":"10.1016/j.cbpa.2023.102390","url":null,"abstract":"<div><p>Due to its nucleophilicity, the thiol group of cysteine is chemically very versatile. Hence, cysteine often has important functions in a protein, be it as the active site or, in extracellular proteins, as part of a structural disulfide. Within the cytosol, cysteines are typically reduced. But the nucleophilicity of its thiol group makes it also particularly prone to post-translational oxidative modifications. These modifications often lead to an alteration of the function of the affected protein and are reversible <em>in vivo</em>, e.g. by the thioredoxin and glutaredoxin system. The <em>in vivo</em>-reversible nature of these modifications and their genesis in the presence of localized high oxidant levels led to the paradigm of thiol-based redox regulation, the adaptation, and modulation of the cellular metabolism in response to oxidative stimuli by thiol oxidation in regulative proteins. Consequently, the proteomic study of these oxidative posttranslational modifications of cysteine plays an indispensable role in redox biology.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S136759312300128X/pdfft?md5=e75a8a002ddc62edd7f90ea17b27ea9e&pid=1-s2.0-S136759312300128X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41095483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Editorial overview: Imaging metal ions in biological systems 编辑综述：生物系统中的金属离子成像。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102388
Daniela Buccella, Christoph J. Fahrni
{"title":"Editorial overview: Imaging metal ions in biological systems","authors":"Daniela Buccella,&nbsp;Christoph J. Fahrni","doi":"10.1016/j.cbpa.2023.102388","DOIUrl":"10.1016/j.cbpa.2023.102388","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41096004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Peptide-based molecules for the disruption of bacterial Hsp70 chaperones 用于破坏细菌Hsp70伴侣蛋白的肽基分子。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102373
Aweon Richards, Tania J. Lupoli
{"title":"Peptide-based molecules for the disruption of bacterial Hsp70 chaperones","authors":"Aweon Richards,&nbsp;Tania J. Lupoli","doi":"10.1016/j.cbpa.2023.102373","DOIUrl":"10.1016/j.cbpa.2023.102373","url":null,"abstract":"<div><p><span>DnaK is a chaperone that aids in nascent protein folding and the maintenance of </span>proteome<span><span> stability across bacteria. Due to the importance of DnaK in cellular proteostasis<span><span>, there have been efforts to generate molecules that modulate its function. In nature, both protein substrates and antimicrobial peptides interact with DnaK. However, many of these ligands interact with other cellular machinery as well. Recent work has sought to modify these peptide scaffolds to create DnaK-selective and species-specific probes. Others have reported </span>protein domain mimics of interaction partners to disrupt cellular DnaK function and high-throughput screening approaches to discover clinically-relevant </span></span>peptidomimetics that inhibit DnaK. The described work provides a foundation for the design of new assays and molecules to regulate DnaK activity.</span></p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9889259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Luminescent lanthanide probes for cations and anions: Promises, compromises, and caveats 阳离子和阴离子的发光镧系元素探针：承诺、妥协和注意事项。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102374
Thibaut L.M. Martinon, Valérie C. Pierre
{"title":"Luminescent lanthanide probes for cations and anions: Promises, compromises, and caveats","authors":"Thibaut L.M. Martinon,&nbsp;Valérie C. Pierre","doi":"10.1016/j.cbpa.2023.102374","DOIUrl":"10.1016/j.cbpa.2023.102374","url":null,"abstract":"<div><p><span>The long luminescence lifetimes and sharp emission bands of </span>luminescent<span><span> lanthanide complexes have long been recognized as invaluable strengths for sensing and imaging in complex aqueous biological or environmental media. Herein we discuss the recent developments of these probes for sensing </span>metal ions<span> and, increasingly, anions. Underappreciated in the field, buffers and metal hydrolysis influence the response of many responsive lanthanide probes. The inherent complexities arising from these interactions are further discussed.</span></span></p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9894504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Multimodal and multiscale correlative elemental imaging: From whole tissues down to organelles 多模式和多尺度相关元素成像：从整个组织到细胞器。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102372
Stéphane Roudeau, Asuncion Carmona, Richard Ortega
{"title":"Multimodal and multiscale correlative elemental imaging: From whole tissues down to organelles","authors":"Stéphane Roudeau,&nbsp;Asuncion Carmona,&nbsp;Richard Ortega","doi":"10.1016/j.cbpa.2023.102372","DOIUrl":"10.1016/j.cbpa.2023.102372","url":null,"abstract":"<div><p><span>Chemical elements, especially metals, play very specific roles in the life sciences. The implementation of correlative imaging methods, of elements on the one hand and of molecules or biological structures on the other hand, is the subject of recent developments. The most commonly used spectro-imaging techniques for metals are synchrotron-induced X-ray fluorescence, mass spectrometry and fluorescence imaging of metal molecular sensors. These imaging methods can be correlated with a wide variety of other analytical techniques used for structural imaging (e.g., electron microscopy), small molecule imaging (e.g., molecular mass spectrometry) or protein imaging (e.g., fluorescence microscopy). The resulting correlative imaging is developed at different scales, from biological tissue to the subcellular level. The fields of application are varied, with some major research topics, the role of metals in the aetiology of </span>neurodegenerative diseases and the use of metals for medical imaging or cancer treatment.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9856490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 advances in Zn2+ imaging: From organelles to in vivo applications Zn2+成像的最新进展:从细胞器到体内应用
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102378
Hongbao Fang , Yaheng Li , Xiuzhi Yang , Yuncong Chen , Zijian Guo , Weijiang He
{"title":"Recent advances in Zn2+ imaging: From organelles to in vivo applications","authors":"Hongbao Fang ,&nbsp;Yaheng Li ,&nbsp;Xiuzhi Yang ,&nbsp;Yuncong Chen ,&nbsp;Zijian Guo ,&nbsp;Weijiang He","doi":"10.1016/j.cbpa.2023.102378","DOIUrl":"https://doi.org/10.1016/j.cbpa.2023.102378","url":null,"abstract":"<div><p>Zn<sup>2+</sup> is involved in various physiological and pathological processes in living systems. Monitoring the dynamic spatiotemporal changes of Zn<sup>2+</sup> levels in organelles, cells, and in vivo is of great importance for the investigation of the physiological and pathological functions of Zn<sup>2+</sup>. However, this task is quite challenging since Zn<sup>2+</sup><span> in living systems is present at low concentrations and undergoes rapid dynamic changes. In this review, we summarize the design and application of fluorescent probes for Zn</span><sup>2+</sup> imaging in organelles, cells, and live organisms reported over the past two years. We aim to provide inspiration for the design of novel Zn<sup>2+</sup> probes for multi-level monitoring and deepen the understanding of Zn<sup>2+</sup> biology.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91588683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Virus-assisted directed evolution of biomolecules 病毒辅助生物分子的定向进化。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102375
Delilah Jewel , Quan Pham , Abhishek Chatterjee
{"title":"Virus-assisted directed evolution of biomolecules","authors":"Delilah Jewel ,&nbsp;Quan Pham ,&nbsp;Abhishek Chatterjee","doi":"10.1016/j.cbpa.2023.102375","DOIUrl":"10.1016/j.cbpa.2023.102375","url":null,"abstract":"<div><p>Directed evolution is a powerful technique that uses principles of natural evolution to enable the development of biomolecules with novel functions. However, the slow pace of natural evolution does not support the demand for rapidly generating new biomolecular functions in the laboratory. Viruses offer a unique path to design fast laboratory evolution experiments, owing to their innate ability to evolve much more rapidly than most living organisms, facilitated by a smaller genome size that tolerate a high frequency of mutations, as well as a fast rate of replication. These attributes offer a great opportunity to evolve various biomolecules by linking their activity to the replication of a suitable virus. This review highlights the recent advances in the application of virus-assisted directed evolution of designer biomolecules in both prokaryotic and eukaryotic cells.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9994988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Advanced imaging techniques for studying protein phase separation in living cells and at single-molecule level 用于研究活细胞中蛋白质相分离和单分子水平的先进成像技术。
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2023-10-01 DOI: 10.1016/j.cbpa.2023.102371
Gemechu Mekonnen , Nathalie Djaja , Xincheng Yuan , Sua Myong
{"title":"Advanced imaging techniques for studying protein phase separation in living cells and at single-molecule level","authors":"Gemechu Mekonnen ,&nbsp;Nathalie Djaja ,&nbsp;Xincheng Yuan ,&nbsp;Sua Myong","doi":"10.1016/j.cbpa.2023.102371","DOIUrl":"10.1016/j.cbpa.2023.102371","url":null,"abstract":"<div><p><span>Protein-protein and protein-RNA interactions are essential for cell function and survival. These interactions facilitate the formation of ribonucleoprotein<span> complexes and biomolecular condensates via phase separation. Such assembly is involved in transcription, splicing, translation and stress response. When dysregulated, proteins and RNA can undergo irreversible aggregation which can be cytotoxic and pathogenic. Despite technical advances in investigating biomolecular condensates, achieving the necessary spatiotemporal resolution to deduce the parameters that govern their assembly and behavior has been challenging. Many laboratories have applied advanced </span></span>microscopy<span><span> methods for imaging condensates. For example, single molecule imaging<span> methods have enabled the detection of RNA-protein interaction, protein-protein interaction, protein conformational dynamics, and diffusional motion of molecules that report on the intrinsic molecular interactions<span> underlying liquid-liquid phase separation. This review will outline advances in both microscopy and spectroscopy techniques which allow </span></span></span>single molecule detection and imaging, and how these techniques can be used to probe unique aspects of biomolecular condensates.</span></p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10038502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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