Pub Date : 2024-06-20DOI: 10.1021/cbmi.4c0002610.1021/cbmi.4c00026
Michael C. Hart, Ritesh K. Isuri, Drew Ramos, Sofya A. Osharovich, Andrea E. Rodriguez, Stefan Harmsen, Grace C. Dudek, Jennifer L. Huck, David E. Holt, Anatoliy V. Popov, Sunil Singhal and Edward J. Delikatny*,
Lung cancer, the most common cause of cancer-related death in the United States, requires advanced intraoperative detection methods to improve evaluation of surgical margins. In this study we employed DDAO-arachidonate (DDAO-A), a phospholipase A2 (PLA2) activatable fluorophore, designed for the specific optical identification of lung cancers in real-time during surgery. The in vitro fluorescence activation of DDAO-A by porcine sPLA2 was tested in various liposomal formulations, with 100 nm extruded EggPC showing the best overall characteristics. Extruded EggPC liposomes containing DDAO-A were tested for their stability under various storage conditions, demonstrating excellent stability for up to 4 weeks when stored at −20 °C or below. Cell studies using KLN 205 and LLC1 lung cancer cell lines showed DDAO-A activation was proportional to cell number. DDAO-A showed preferential activation by human recombinant cPLA2, an isoform highly specific to arachidonic acid-containing lipids, when compared to a control probe, DDAO palmitate (DDAO-P). In vivo studies with DBA/2 mice bearing KLN 205 lung tumors recapitulated these results, with preferential activation of DDAO-A relative to DDAO-P following intratumoral injection. Topical application of DDAO-A-containing liposomes to human (n = 10) and canine (n = 3) lung cancers ex vivo demonstrated the preferential activation of DDAO-A in tumor tissue relative to adjacent normal lung tissue, with fluorescent tumor-to-normal ratios (TNR) of up to 5.2:1. The combined results highlight DDAO-A as a promising candidate for clinical applications, showcasing its potential utility in intraoperative and back-table imaging and topical administration during lung cancer surgeries. By addressing the challenge of residual microscopic disease at resection margins and offering stability in liposomal formulations, DDAO-A emerges as a potentially valuable tool for advancing precision lung cancer surgery and improving curative resection rates.
{"title":"Non-Small Cell Lung Cancer Imaging Using a Phospholipase A2 Activatable Fluorophore","authors":"Michael C. Hart, Ritesh K. Isuri, Drew Ramos, Sofya A. Osharovich, Andrea E. Rodriguez, Stefan Harmsen, Grace C. Dudek, Jennifer L. Huck, David E. Holt, Anatoliy V. Popov, Sunil Singhal and Edward J. Delikatny*, ","doi":"10.1021/cbmi.4c0002610.1021/cbmi.4c00026","DOIUrl":"https://doi.org/10.1021/cbmi.4c00026https://doi.org/10.1021/cbmi.4c00026","url":null,"abstract":"<p >Lung cancer, the most common cause of cancer-related death in the United States, requires advanced intraoperative detection methods to improve evaluation of surgical margins. In this study we employed DDAO-arachidonate (DDAO-A), a phospholipase A2 (PLA2) activatable fluorophore, designed for the specific optical identification of lung cancers in real-time during surgery. The <i>in vitro</i> fluorescence activation of DDAO-A by porcine sPLA2 was tested in various liposomal formulations, with 100 nm extruded EggPC showing the best overall characteristics. Extruded EggPC liposomes containing DDAO-A were tested for their stability under various storage conditions, demonstrating excellent stability for up to 4 weeks when stored at −20 °C or below. Cell studies using KLN 205 and LLC1 lung cancer cell lines showed DDAO-A activation was proportional to cell number. DDAO-A showed preferential activation by human recombinant cPLA2, an isoform highly specific to arachidonic acid-containing lipids, when compared to a control probe, DDAO palmitate (DDAO-P). <i>In vivo</i> studies with DBA/2 mice bearing KLN 205 lung tumors recapitulated these results, with preferential activation of DDAO-A relative to DDAO-P following intratumoral injection. Topical application of DDAO-A-containing liposomes to human (n = 10) and canine (n = 3) lung cancers <i>ex vivo</i> demonstrated the preferential activation of DDAO-A in tumor tissue relative to adjacent normal lung tissue, with fluorescent tumor-to-normal ratios (TNR) of up to 5.2:1. The combined results highlight DDAO-A as a promising candidate for clinical applications, showcasing its potential utility in intraoperative and back-table imaging and topical administration during lung cancer surgeries. By addressing the challenge of residual microscopic disease at resection margins and offering stability in liposomal formulations, DDAO-A emerges as a potentially valuable tool for advancing precision lung cancer surgery and improving curative resection rates.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 7","pages":"490–500 490–500"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/cbmi.4c00026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141959230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-20eCollection Date: 2024-07-22DOI: 10.1021/cbmi.4c00026
Michael C Hart, Ritesh K Isuri, Drew Ramos, Sofya A Osharovich, Andrea E Rodriguez, Stefan Harmsen, Grace C Dudek, Jennifer L Huck, David E Holt, Anatoliy V Popov, Sunil Singhal, Edward J Delikatny
Lung cancer, the most common cause of cancer-related death in the United States, requires advanced intraoperative detection methods to improve evaluation of surgical margins. In this study we employed DDAO-arachidonate (DDAO-A), a phospholipase A2 (PLA2) activatable fluorophore, designed for the specific optical identification of lung cancers in real-time during surgery. The in vitro fluorescence activation of DDAO-A by porcine sPLA2 was tested in various liposomal formulations, with 100 nm extruded EggPC showing the best overall characteristics. Extruded EggPC liposomes containing DDAO-A were tested for their stability under various storage conditions, demonstrating excellent stability for up to 4 weeks when stored at -20 °C or below. Cell studies using KLN 205 and LLC1 lung cancer cell lines showed DDAO-A activation was proportional to cell number. DDAO-A showed preferential activation by human recombinant cPLA2, an isoform highly specific to arachidonic acid-containing lipids, when compared to a control probe, DDAO palmitate (DDAO-P). In vivo studies with DBA/2 mice bearing KLN 205 lung tumors recapitulated these results, with preferential activation of DDAO-A relative to DDAO-P following intratumoral injection. Topical application of DDAO-A-containing liposomes to human (n = 10) and canine (n = 3) lung cancers ex vivo demonstrated the preferential activation of DDAO-A in tumor tissue relative to adjacent normal lung tissue, with fluorescent tumor-to-normal ratios (TNR) of up to 5.2:1. The combined results highlight DDAO-A as a promising candidate for clinical applications, showcasing its potential utility in intraoperative and back-table imaging and topical administration during lung cancer surgeries. By addressing the challenge of residual microscopic disease at resection margins and offering stability in liposomal formulations, DDAO-A emerges as a potentially valuable tool for advancing precision lung cancer surgery and improving curative resection rates.
{"title":"Non-Small Cell Lung Cancer Imaging Using a Phospholipase A2 Activatable Fluorophore.","authors":"Michael C Hart, Ritesh K Isuri, Drew Ramos, Sofya A Osharovich, Andrea E Rodriguez, Stefan Harmsen, Grace C Dudek, Jennifer L Huck, David E Holt, Anatoliy V Popov, Sunil Singhal, Edward J Delikatny","doi":"10.1021/cbmi.4c00026","DOIUrl":"10.1021/cbmi.4c00026","url":null,"abstract":"<p><p>Lung cancer, the most common cause of cancer-related death in the United States, requires advanced intraoperative detection methods to improve evaluation of surgical margins. In this study we employed DDAO-arachidonate (DDAO-A), a phospholipase A2 (PLA2) activatable fluorophore, designed for the specific optical identification of lung cancers in real-time during surgery. The <i>in vitro</i> fluorescence activation of DDAO-A by porcine sPLA2 was tested in various liposomal formulations, with 100 nm extruded EggPC showing the best overall characteristics. Extruded EggPC liposomes containing DDAO-A were tested for their stability under various storage conditions, demonstrating excellent stability for up to 4 weeks when stored at -20 °C or below. Cell studies using KLN 205 and LLC1 lung cancer cell lines showed DDAO-A activation was proportional to cell number. DDAO-A showed preferential activation by human recombinant cPLA2, an isoform highly specific to arachidonic acid-containing lipids, when compared to a control probe, DDAO palmitate (DDAO-P). <i>In vivo</i> studies with DBA/2 mice bearing KLN 205 lung tumors recapitulated these results, with preferential activation of DDAO-A relative to DDAO-P following intratumoral injection. Topical application of DDAO-A-containing liposomes to human (n = 10) and canine (n = 3) lung cancers <i>ex vivo</i> demonstrated the preferential activation of DDAO-A in tumor tissue relative to adjacent normal lung tissue, with fluorescent tumor-to-normal ratios (TNR) of up to 5.2:1. The combined results highlight DDAO-A as a promising candidate for clinical applications, showcasing its potential utility in intraoperative and back-table imaging and topical administration during lung cancer surgeries. By addressing the challenge of residual microscopic disease at resection margins and offering stability in liposomal formulations, DDAO-A emerges as a potentially valuable tool for advancing precision lung cancer surgery and improving curative resection rates.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 7","pages":"490-500"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11267604/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/cbmi.4c0002110.1021/cbmi.4c00021
Nancy Sharma, Walaa Mohammad, Xavier Le Guével* and Asifkhan Shanavas*,
In the realm of nanomaterials, atomically precise quasi-molecular gold nanoclusters (AuNCs) play a prime role due to their unique, stable, and highly tunable optical properties. They are extensively structure-engineered for modulation of surface electronic states toward long wavelength photoluminescence, particularly in the NIR-II (1000 to 1700 nm) window. Contrast agents with NIR-II emission can potentially transform optical imaging in terms of higher spatial resolution, deeper tissue penetration, and reduced tissue autofluorescence. These advantages allow real-time imaging in living organisms for observing disease progression and treatment response. In this short review, we discuss origin of NIR-II emission in rationally designed AuNCs and their application toward high resolution imaging of vasculatures and hard and soft tissue structures for identification of pathological conditions such as stroke and injury. Further, recent employment of these AuNCs in the rapidly growing field of tumor theranostics is also summarized. Final remarks are provided on the scope for improvement in their optical properties and persisting challenges for clinical translation.
{"title":"Gold Nanoclusters as High Resolution NIR-II Theranostic Agents","authors":"Nancy Sharma, Walaa Mohammad, Xavier Le Guével* and Asifkhan Shanavas*, ","doi":"10.1021/cbmi.4c0002110.1021/cbmi.4c00021","DOIUrl":"https://doi.org/10.1021/cbmi.4c00021https://doi.org/10.1021/cbmi.4c00021","url":null,"abstract":"<p >In the realm of nanomaterials, atomically precise quasi-molecular gold nanoclusters (AuNCs) play a prime role due to their unique, stable, and highly tunable optical properties. They are extensively structure-engineered for modulation of surface electronic states toward long wavelength photoluminescence, particularly in the NIR-II (1000 to 1700 nm) window. Contrast agents with NIR-II emission can potentially transform optical imaging in terms of higher spatial resolution, deeper tissue penetration, and reduced tissue autofluorescence. These advantages allow real-time imaging in living organisms for observing disease progression and treatment response. In this short review, we discuss origin of NIR-II emission in rationally designed AuNCs and their application toward high resolution imaging of vasculatures and hard and soft tissue structures for identification of pathological conditions such as stroke and injury. Further, recent employment of these AuNCs in the rapidly growing field of tumor theranostics is also summarized. Final remarks are provided on the scope for improvement in their optical properties and persisting challenges for clinical translation.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 7","pages":"462–480 462–480"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/cbmi.4c00021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141959070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/cbmi.4c0003710.1021/cbmi.4c00037
Nischal Sharma, Antoine M. van Oijen, Lisanne M. Spenkelink* and Stefan H. Mueller*,
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
基因组维护包括一组复杂而相互关联的过程,对保存和保护所有生物体内的遗传信息至关重要。基因组维护的关键环节包括 DNA 复制、转录、重组和修复。对这些过程的不当调控会导致基因变化,从而可能导致细菌群体产生抗生素耐药性。由于这些过程的复杂性,集合平均研究可能无法提供捕捉每个生物分子的分子行为和动态所需的全部细节。因此,研究人员越来越多地转向单分子方法,因为这些技术可以直接观察和操纵单个生物分子,并提供传统集合方法无法提供的详细程度。在这篇综述中,我们将概述最近用于研究原核生物基因组维护复杂过程的体外和体内单分子成像方法。我们将首先重点介绍成像技术的原理,如主要用于体外研究的全内反射荧光显微镜和原子力显微镜,以及主要用于体内研究的高倾斜和层叠光学薄片和超分辨率显微镜。然后,我们将展示如何应用这些单分子技术实现对复制、转录、DNA 修复和重组等生物过程的实时直接可视化。最后,我们将展示超分辨率显微镜方法所取得的成果,这些成果为了解细菌生物体内不同生物分子的空间组织提供了前所未有的见解。
{"title":"Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance","authors":"Nischal Sharma, Antoine M. van Oijen, Lisanne M. Spenkelink* and Stefan H. Mueller*, ","doi":"10.1021/cbmi.4c0003710.1021/cbmi.4c00037","DOIUrl":"https://doi.org/10.1021/cbmi.4c00037https://doi.org/10.1021/cbmi.4c00037","url":null,"abstract":"<p >Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 9","pages":"595–614 595–614"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/cbmi.4c00037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18eCollection Date: 2024-08-26DOI: 10.1021/cbmi.4c00027
Alison J Hobro, Takatoshi Sakaguchi, Shizuo Akira, Nicholas I Smith
Raman imaging has the capability to provide unlabeled, spatially aware analysis of chemical components, with no a priori assumptions. Several lifestyle diseases such as nonalcoholic steatohepatitis (NASH) can appear in the liver as changes in the nature, abundance, and distribution of lipids, proteins, and other biomolecules and are detectable by Raman imaging. In order to identify which of these liver-associated changes occur as a direct result of the diet and which are secondary effects, we developed correlative imaging and analysis of diet and liver samples. Oleic acid was found to be a direct contributor to NASH liver composition, whereas protein and collagen distributions were found to be affected in a manner consistent with early fibrotic transformation, as a secondary consequence of the high-fat diet.
{"title":"Correlative Quantitative Raman Chemical Imaging and MCR-ALS in Mouse NASH Model Reveals Direct Relationships between Diet and Resultant Liver Pathology.","authors":"Alison J Hobro, Takatoshi Sakaguchi, Shizuo Akira, Nicholas I Smith","doi":"10.1021/cbmi.4c00027","DOIUrl":"https://doi.org/10.1021/cbmi.4c00027","url":null,"abstract":"<p><p>Raman imaging has the capability to provide unlabeled, spatially aware analysis of chemical components, with no <i>a priori</i> assumptions. Several lifestyle diseases such as nonalcoholic steatohepatitis (NASH) can appear in the liver as changes in the nature, abundance, and distribution of lipids, proteins, and other biomolecules and are detectable by Raman imaging. In order to identify which of these liver-associated changes occur as a direct result of the diet and which are secondary effects, we developed correlative imaging and analysis of diet and liver samples. Oleic acid was found to be a direct contributor to NASH liver composition, whereas protein and collagen distributions were found to be affected in a manner consistent with early fibrotic transformation, as a secondary consequence of the high-fat diet.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 8","pages":"577-583"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18eCollection Date: 2024-09-23DOI: 10.1021/cbmi.4c00037
Nischal Sharma, Antoine M van Oijen, Lisanne M Spenkelink, Stefan H Mueller
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
基因组维护包括一组复杂而相互关联的过程,对保存和保护所有生物体内的遗传信息至关重要。基因组维护的关键环节包括 DNA 复制、转录、重组和修复。对这些过程的不当调控会导致基因变化,从而可能导致细菌群体产生抗生素耐药性。由于这些过程的复杂性,集合平均研究可能无法提供捕捉每个生物分子的分子行为和动态所需的全部细节。因此,研究人员越来越多地转向单分子方法,因为这些技术可以直接观察和操纵单个生物分子,并提供传统集合方法无法提供的详细程度。在这篇综述中,我们将概述最近用于研究原核生物基因组维护复杂过程的体外和体内单分子成像方法。我们将首先重点介绍成像技术的原理,如主要用于体外研究的全内反射荧光显微镜和原子力显微镜,以及主要用于体内研究的高倾斜和层叠光学薄片和超分辨率显微镜。然后,我们将展示如何应用这些单分子技术实现对复制、转录、DNA 修复和重组等生物过程的实时直接可视化。最后,我们将展示超分辨率显微镜方法所取得的成果,这些成果为了解细菌生物体内不同生物分子的空间组织提供了前所未有的见解。
{"title":"Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance.","authors":"Nischal Sharma, Antoine M van Oijen, Lisanne M Spenkelink, Stefan H Mueller","doi":"10.1021/cbmi.4c00037","DOIUrl":"https://doi.org/10.1021/cbmi.4c00037","url":null,"abstract":"<p><p>Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 9","pages":"595-614"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/cbmi.4c0001310.1021/cbmi.4c00013
Yawen Zhang, Weiyue Wu, Hongdou Shen, Juan Xu, Qing Jiang*, Xiaodong Han* and Pingqiang Cai*,
The quest for high spatial resolution in molecular identification is critical across various domains, including physiology, pathology, and pharmaceutical research. Super-resolution microscopy has made strides by surpassing the Abbe diffraction limit, but it relies on sophisticated equipment and is limited by the sample size to handle. Expansion microscopy, an emerging technique, has broadened the scope of subdiffraction imaging. It chemically preserves tissues at a large scale and physically enlarges them 4–20 times linearly, enabling super-resolution observation. This review begins by exploring the foundational concepts of tissue clearing and the latest methodologies in the field. It then delves into the core tenets of expansion microscopy, covering a range of protocols. The review spotlights advancements in enhancing resolution, improving labeling efficiency, and ensuring isotropic tissue expansion. Finally, the review offers insights into the prospective evolution of expansion microscopy. It emphasizes the potential role of machine learning in refining image quality and in the autonomous extraction of data, which could revolutionize the way we visualize and understand biological tissues.
{"title":"Subdiffraction Imaging of Cleared and Expanded Large-Scale Tissues","authors":"Yawen Zhang, Weiyue Wu, Hongdou Shen, Juan Xu, Qing Jiang*, Xiaodong Han* and Pingqiang Cai*, ","doi":"10.1021/cbmi.4c0001310.1021/cbmi.4c00013","DOIUrl":"https://doi.org/10.1021/cbmi.4c00013https://doi.org/10.1021/cbmi.4c00013","url":null,"abstract":"<p >The quest for high spatial resolution in molecular identification is critical across various domains, including physiology, pathology, and pharmaceutical research. Super-resolution microscopy has made strides by surpassing the Abbe diffraction limit, but it relies on sophisticated equipment and is limited by the sample size to handle. Expansion microscopy, an emerging technique, has broadened the scope of subdiffraction imaging. It chemically preserves tissues at a large scale and physically enlarges them 4–20 times linearly, enabling super-resolution observation. This review begins by exploring the foundational concepts of tissue clearing and the latest methodologies in the field. It then delves into the core tenets of expansion microscopy, covering a range of protocols. The review spotlights advancements in enhancing resolution, improving labeling efficiency, and ensuring isotropic tissue expansion. Finally, the review offers insights into the prospective evolution of expansion microscopy. It emphasizes the potential role of machine learning in refining image quality and in the autonomous extraction of data, which could revolutionize the way we visualize and understand biological tissues.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 8","pages":"542–559 542–559"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/cbmi.4c00013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142075685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18DOI: 10.1021/cbmi.4c0002710.1021/cbmi.4c00027
Alison J. Hobro*, Takatoshi Sakaguchi, Shizuo Akira and Nicholas I. Smith*,
Raman imaging has the capability to provide unlabeled, spatially aware analysis of chemical components, with no a priori assumptions. Several lifestyle diseases such as nonalcoholic steatohepatitis (NASH) can appear in the liver as changes in the nature, abundance, and distribution of lipids, proteins, and other biomolecules and are detectable by Raman imaging. In order to identify which of these liver-associated changes occur as a direct result of the diet and which are secondary effects, we developed correlative imaging and analysis of diet and liver samples. Oleic acid was found to be a direct contributor to NASH liver composition, whereas protein and collagen distributions were found to be affected in a manner consistent with early fibrotic transformation, as a secondary consequence of the high-fat diet.
{"title":"Correlative Quantitative Raman Chemical Imaging and MCR–ALS in Mouse NASH Model Reveals Direct Relationships between Diet and Resultant Liver Pathology","authors":"Alison J. Hobro*, Takatoshi Sakaguchi, Shizuo Akira and Nicholas I. Smith*, ","doi":"10.1021/cbmi.4c0002710.1021/cbmi.4c00027","DOIUrl":"https://doi.org/10.1021/cbmi.4c00027https://doi.org/10.1021/cbmi.4c00027","url":null,"abstract":"<p >Raman imaging has the capability to provide unlabeled, spatially aware analysis of chemical components, with no <i>a priori</i> assumptions. Several lifestyle diseases such as nonalcoholic steatohepatitis (NASH) can appear in the liver as changes in the nature, abundance, and distribution of lipids, proteins, and other biomolecules and are detectable by Raman imaging. In order to identify which of these liver-associated changes occur as a direct result of the diet and which are secondary effects, we developed correlative imaging and analysis of diet and liver samples. Oleic acid was found to be a direct contributor to NASH liver composition, whereas protein and collagen distributions were found to be affected in a manner consistent with early fibrotic transformation, as a secondary consequence of the high-fat diet.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 8","pages":"577–583 577–583"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/cbmi.4c00027","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142075684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18eCollection Date: 2024-08-26DOI: 10.1021/cbmi.4c00013
Yawen Zhang, Weiyue Wu, Hongdou Shen, Juan Xu, Qing Jiang, Xiaodong Han, Pingqiang Cai
The quest for high spatial resolution in molecular identification is critical across various domains, including physiology, pathology, and pharmaceutical research. Super-resolution microscopy has made strides by surpassing the Abbe diffraction limit, but it relies on sophisticated equipment and is limited by the sample size to handle. Expansion microscopy, an emerging technique, has broadened the scope of subdiffraction imaging. It chemically preserves tissues at a large scale and physically enlarges them 4-20 times linearly, enabling super-resolution observation. This review begins by exploring the foundational concepts of tissue clearing and the latest methodologies in the field. It then delves into the core tenets of expansion microscopy, covering a range of protocols. The review spotlights advancements in enhancing resolution, improving labeling efficiency, and ensuring isotropic tissue expansion. Finally, the review offers insights into the prospective evolution of expansion microscopy. It emphasizes the potential role of machine learning in refining image quality and in the autonomous extraction of data, which could revolutionize the way we visualize and understand biological tissues.
{"title":"Subdiffraction Imaging of Cleared and Expanded Large-Scale Tissues.","authors":"Yawen Zhang, Weiyue Wu, Hongdou Shen, Juan Xu, Qing Jiang, Xiaodong Han, Pingqiang Cai","doi":"10.1021/cbmi.4c00013","DOIUrl":"https://doi.org/10.1021/cbmi.4c00013","url":null,"abstract":"<p><p>The quest for high spatial resolution in molecular identification is critical across various domains, including physiology, pathology, and pharmaceutical research. Super-resolution microscopy has made strides by surpassing the Abbe diffraction limit, but it relies on sophisticated equipment and is limited by the sample size to handle. Expansion microscopy, an emerging technique, has broadened the scope of subdiffraction imaging. It chemically preserves tissues at a large scale and physically enlarges them 4-20 times linearly, enabling super-resolution observation. This review begins by exploring the foundational concepts of tissue clearing and the latest methodologies in the field. It then delves into the core tenets of expansion microscopy, covering a range of protocols. The review spotlights advancements in enhancing resolution, improving labeling efficiency, and ensuring isotropic tissue expansion. Finally, the review offers insights into the prospective evolution of expansion microscopy. It emphasizes the potential role of machine learning in refining image quality and in the autonomous extraction of data, which could revolutionize the way we visualize and understand biological tissues.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 8","pages":"542-559"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11504467/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-18eCollection Date: 2024-07-22DOI: 10.1021/cbmi.4c00021
Nancy Sharma, Walaa Mohammad, Xavier Le Guével, Asifkhan Shanavas
In the realm of nanomaterials, atomically precise quasi-molecular gold nanoclusters (AuNCs) play a prime role due to their unique, stable, and highly tunable optical properties. They are extensively structure-engineered for modulation of surface electronic states toward long wavelength photoluminescence, particularly in the NIR-II (1000 to 1700 nm) window. Contrast agents with NIR-II emission can potentially transform optical imaging in terms of higher spatial resolution, deeper tissue penetration, and reduced tissue autofluorescence. These advantages allow real-time imaging in living organisms for observing disease progression and treatment response. In this short review, we discuss origin of NIR-II emission in rationally designed AuNCs and their application toward high resolution imaging of vasculatures and hard and soft tissue structures for identification of pathological conditions such as stroke and injury. Further, recent employment of these AuNCs in the rapidly growing field of tumor theranostics is also summarized. Final remarks are provided on the scope for improvement in their optical properties and persisting challenges for clinical translation.
{"title":"Gold Nanoclusters as High Resolution NIR-II Theranostic Agents.","authors":"Nancy Sharma, Walaa Mohammad, Xavier Le Guével, Asifkhan Shanavas","doi":"10.1021/cbmi.4c00021","DOIUrl":"https://doi.org/10.1021/cbmi.4c00021","url":null,"abstract":"<p><p>In the realm of nanomaterials, atomically precise quasi-molecular gold nanoclusters (AuNCs) play a prime role due to their unique, stable, and highly tunable optical properties. They are extensively structure-engineered for modulation of surface electronic states toward long wavelength photoluminescence, particularly in the NIR-II (1000 to 1700 nm) window. Contrast agents with NIR-II emission can potentially transform optical imaging in terms of higher spatial resolution, deeper tissue penetration, and reduced tissue autofluorescence. These advantages allow real-time imaging in living organisms for observing disease progression and treatment response. In this short review, we discuss origin of NIR-II emission in rationally designed AuNCs and their application toward high resolution imaging of vasculatures and hard and soft tissue structures for identification of pathological conditions such as stroke and injury. Further, recent employment of these AuNCs in the rapidly growing field of tumor theranostics is also summarized. Final remarks are provided on the scope for improvement in their optical properties and persisting challenges for clinical translation.</p>","PeriodicalId":53181,"journal":{"name":"Chemical & Biomedical Imaging","volume":"2 7","pages":"462-480"},"PeriodicalIF":0.0,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11503699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142548907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}