Applied Microscopy最新文献

{"title":"Cryo-EM as a powerful tool for drug discovery: recent structural based studies of SARS-CoV-2","authors":"Han-ul Kim,&nbsp;Hyun Suk Jung","doi":"10.1186/s42649-021-00062-x","DOIUrl":"10.1186/s42649-021-00062-x","url":null,"abstract":"<div><p>The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has arisen as a global pandemic affecting the respiratory system showing acute respiratory distress syndrome (ARDS). However, there is no targeted therapeutic agent yet and due to the growing cases of infections and the rising death tolls, discovery of the possible drug is the need of the hour. In general, the study for discovering therapeutic agent for SARS-CoV-2 is largely focused on large-scale screening with fragment-based drug discovery (FBDD). With the recent advancement in cryo-electron microscopy (Cryo-EM), it has become one of the widely used tools in structural biology. It is effective in investigating the structure of numerous proteins in high-resolution and also had an intense influence on drug discovery, determining the binding reaction and regulation of known drugs as well as leading the design and development of new drug candidates. Here, we review the application of cryo-EM in a structure-based drug design (SBDD) and in silico screening of the recently acquired FBDD in SARS-CoV-2. Such insights will help deliver better understanding in the procurement of the effective remedial solution for this pandemic.</p></div>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8464538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39448854","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}

{"title":"Multispectral intravital microscopy for simultaneous bright-field and fluorescence imaging of the microvasculature","authors":"Barry G. H. Janssen,&nbsp;Mohamadreza Najiminaini,&nbsp;Yan Min Zhang,&nbsp;Parsa Omidi,&nbsp;Jeffrey J. L. Carson","doi":"10.1186/s42649-021-00059-6","DOIUrl":"10.1186/s42649-021-00059-6","url":null,"abstract":"<div><p>Intravital video microscopy permits the observation of microcirculatory blood flow. This often requires fluorescent probes to visualize structures and dynamic processes that cannot be observed with conventional bright-field microscopy. Conventional light microscopes do not allow for simultaneous bright-field and fluorescent imaging. Moreover, in conventional microscopes, only one type of fluorescent label can be observed. This study introduces multispectral intravital video microscopy, which combines bright-field and fluorescence microscopy in a standard light microscope. The technique enables simultaneous real-time observation of fluorescently-labeled structures in relation to their direct physical surroundings. The advancement provides context for the orientation, movement, and function of labeled structures in the microcirculation.</p></div>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8310548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39216679","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}

{"title":"Capture silk scaffold production in the cribellar web spider","authors":"Yan Sun,&nbsp;Seung-Min Lee,&nbsp;Bon-Jin Ku,&nbsp;Eun-Ah Park,&nbsp;Myung-Jin Moon","doi":"10.1186/s42649-021-00061-y","DOIUrl":"https://doi.org/10.1186/s42649-021-00061-y","url":null,"abstract":"<p>Spider capture silk is a natural scaffolding material that outperforms most synthetic materials in terms of its combination of strength and elasticity. Among the various kinds of silk threads, cribellar thread is the most primitive prey-capturing type of spider web material. We analyzed the functional organization of the sieve-like cribellum spigots and specialized calamistral comb bristles for capture thread production by the titanoecid spider <i>Nurscia albofasciata</i>. The outer cribellar surface is covered with thousands of tiny spigots, and the cribellar plate produces non-sticky threads composed of thousands of fine nanofibers. <i>N. albofasciata</i> cribellar spigots are typically about 10?μm long, and each spigot appears as a long individual shaft with a pagoda-like tiered tip. The five distinct segments comprising each spigot is a defining characteristic of this spider. This segmented and flexible structure not only allows for spigots to bend individually and join with adjacent spigots, but it also enables spigots to draw the silk fibrils from their cribella with rows of calamistral leg bristles to form cribellar prey-capture threads.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00061-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4540311","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}

{"title":"Sensitivity of quantitative symmetry measurement algorithms for convergent beam electron diffraction technique","authors":"Hyeongsub So,&nbsp;Ro Woon Lee,&nbsp;Sung Taek Hong,&nbsp;Kyou-Hyun Kim","doi":"10.1186/s42649-021-00060-z","DOIUrl":"https://doi.org/10.1186/s42649-021-00060-z","url":null,"abstract":"<p>We investigate the sensitivity of symmetry quantification algorithms based on the profile R-factor (<i>R</i>_<i>p</i>) and the normalized cross-correlation (NCC) coefficient (<i>γ</i>). A DM (Digital Micrograph^?) script embedded in the Gatan digital microscopy software is used to develop the symmetry quantification program. Using the Bloch method, a variety of CBED patterns are simulated and used to investigate the sensitivity of symmetry quantification algorithms. The quantification results show that two symmetry quantification coefficients are significantly sensitive to structural changes even for small strain values of &lt;?1%.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00060-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4126201","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}

{"title":"A brief review of non-invasive brain imaging technologies and the near-infrared optical bioimaging","authors":"Beomsue Kim,&nbsp;Hongmin Kim,&nbsp;Songhui Kim,&nbsp;Young-ran Hwang","doi":"10.1186/s42649-021-00058-7","DOIUrl":"https://doi.org/10.1186/s42649-021-00058-7","url":null,"abstract":"<p>Brain disorders seriously affect life quality. Therefore, non-invasive neuroimaging has received attention to monitoring and early diagnosing neural disorders to prevent their progress to a severe level. This short review briefly describes the current MRI and PET/CT techniques developed for non-invasive neuroimaging and the future direction of optical imaging techniques to achieve higher resolution and specificity using the second near-infrared (NIR-II) region of wavelength with organic molecules.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00058-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4971476","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}

{"title":"TEM sample preparation using micro-manipulator for in-situ MEMS experiment","authors":"Hyunjong Lee,&nbsp;Odongo Francis Ngome Okello,&nbsp;Gi-Yeop Kim,&nbsp;Kyung Song,&nbsp;Si-Young Choi","doi":"10.1186/s42649-021-00057-8","DOIUrl":"https://doi.org/10.1186/s42649-021-00057-8","url":null,"abstract":"<p>Growing demands for comprehending complicated nano-scale phenomena in atomic resolution has attracted in-situ transmission electron microscopy (TEM) techniques for understanding their dynamics. However, simple to safe TEM sample preparation for in-situ observation has been limited. Here, we suggested the optical microscopy based micro-manipulating system for transferring TEM samples. By adopting our manipulator system, several types of samples from nano-wires to plate-like thin samples were transferred on micro-electro mechanical systems (MEMS) chip in a single step. Furthermore, the control of electrostatic force between the sample and the probe tip is found to be a key role in transferring process.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00057-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4388916","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}

{"title":"Advanced atomic force microscopy-based techniques for nanoscale characterization of switching devices for emerging neuromorphic applications","authors":"Young-Min Kim,&nbsp;Jihye Lee,&nbsp;Deok-Jin Jeon,&nbsp;Si-Eun Oh,&nbsp;Jong-Souk Yeo","doi":"10.1186/s42649-021-00056-9","DOIUrl":"https://doi.org/10.1186/s42649-021-00056-9","url":null,"abstract":"<p>Neuromorphic systems require integrated structures with high-density memory and selector devices to avoid interference and recognition errors between neighboring memory cells. To improve the performance of a selector device, it is important to understand the characteristics of the switching process. As changes by switching cycle occur at local nanoscale areas, a high-resolution analysis method is needed to investigate this phenomenon. Atomic force microscopy (AFM) is used to analyze the local changes because it offers nanoscale detection with high-resolution capabilities. This review introduces various types of AFM such as conductive AFM (C-AFM), electrostatic force microscopy (EFM), and Kelvin probe force microscopy (KPFM) to study switching behaviors.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00056-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5013199","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}

{"title":"Fractal dimension analysis as an easy computational approach to improve breast cancer histopathological diagnosis","authors":"Lucas Glaucio da Silva,&nbsp;Waleska Rayanne Sizinia da Silva Monteiro,&nbsp;Tiago Medeiros de Aguiar Moreira,&nbsp;Maria Aparecida Esteves Rabelo,&nbsp;Emílio Augusto Campos Pereira de Assis,&nbsp;Gustavo Torres de Souza","doi":"10.1186/s42649-021-00055-w","DOIUrl":"https://doi.org/10.1186/s42649-021-00055-w","url":null,"abstract":"<p>Histopathology is a well-established standard diagnosis employed for the majority of malignancies, including breast cancer. Nevertheless, despite training and standardization, it is considered operator-dependent and errors are still a concern. Fractal dimension analysis is a computational image processing technique that allows assessing the degree of complexity in patterns. We aimed here at providing a robust and easily attainable method for introducing computer-assisted techniques to histopathology laboratories. Slides from two databases were used: A) Breast Cancer Histopathological; and B) Grand Challenge on Breast Cancer Histology. Set A contained 2480 images from 24 patients with benign alterations, and 5429 images from 58 patients with breast cancer. Set B comprised 100 images of each type: normal tissue, benign alterations, in situ carcinoma, and invasive carcinoma. All images were analyzed with the FracLac algorithm in the ImageJ computational environment to yield the box count fractal dimension (Db) results. Images on set A on 40x magnification were statistically different (<i>p</i>?=?0.0003), whereas images on 400x did not present differences in their means. On set B, the mean Db values presented promissing statistical differences when comparing. Normal and/or benign images to in situ and/or invasive carcinoma (all <i>p</i>?&lt;?0.0001). Interestingly, there was no difference when comparing normal tissue to benign alterations. These data corroborate with previous work in which fractal analysis allowed differentiating malignancies. Computer-aided diagnosis algorithms may beneficiate from using Db data; specific Db cut-off values may yield ~?99% specificity in diagnosing breast cancer. Furthermore, the fact that it allows assessing tissue complexity, this tool may be used to understand the progression of the histological alterations in cancer.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00055-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5138975","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}

{"title":"Morphology and histology of the olfactory organ of two African lungfishes, Protopterus amphibius and P. dolloi (Lepidosirenidae, Dipnoi)","authors":"Hyun Tae Kim,&nbsp;Jong Young Park","doi":"10.1186/s42649-021-00054-x","DOIUrl":"https://doi.org/10.1186/s42649-021-00054-x","url":null,"abstract":"<p>The olfactory organs of two African lungfishes, <i>Protopterus amphibius</i> and <i>P. dolloi</i>, were investigated using a stereo microscope and a compound light microscope and were described anatomically, histologically, and histochemically. Like other lungfishes, these species present the following general features: i) elongated olfactory chamber (OC), ii) anterior nostril at the ventral tip of the upper lip, iii) posterior nostril on the palate of the oral cavity, iv) lamellae with multiple cell types such as olfactory receptor neurons, supporting cells, basal cells, lymphatic cells, and mucous cells (MC), and vi) vomero-like epithelial crypt (VEC) made of glandular epithelium (GE) and crypt sensory epithelium. Some of these features exhibit differences between species: MCs are abundant in both the lamellar and inner walls of the OC in <i>P. amphibius</i> but occur only in lamellae in <i>P. dolloi</i>. On the other hand, some between feature differences are consistent across species: the GE of both <i>P. amphibius</i> and <i>P. dolloi</i> is strongly positive for Alcian blue (pH?2.5)-periodic acid Schiff (deep violet coloration), and positive with hematoxylin and eosin and with Masson’s trichrome (reddish-brown staining), unlike the MCs of the two species which stain dark red with both Alcian blue (pH?2.5)-periodic acid Schiff and Masson’s trichrome but respond faintly to hematoxylin and eosin. The differing abundance of MCs in the two lungfishes might reflect different degrees in aerial exposure of the olfactory organ, while the neutral and acid mucopolysaccharide-containing VEC, as indicated by staining properties of the MCs, is evolutionary evidence that <i>P. amphibius</i> and <i>P. dolloi</i> are the closest living relatives to tetrapods, at least in the order Dipnoi.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00054-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4669104","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}

{"title":"Automated 3D scoring of fluorescence in situ hybridization (FISH) using a confocal whole slide imaging scanner","authors":"Ziv Frankenstein,&nbsp;Naohiro Uraoka,&nbsp;Umut Aypar,&nbsp;Ruth Aryeequaye,&nbsp;Mamta Rao,&nbsp;Meera Hameed,&nbsp;Yanming Zhang,&nbsp;Yukako Yagi","doi":"10.1186/s42649-021-00053-y","DOIUrl":"https://doi.org/10.1186/s42649-021-00053-y","url":null,"abstract":"<p>Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.</p>","PeriodicalId":470,"journal":{"name":"Applied Microscopy","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s42649-021-00053-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4368631","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}