Single molecule localization microscopy (SMLM) recently became more and more popular for studying the synaptic architecture, providing substantial advances in modern neuroscience. Recently developed methods based on DNA origami calibration transformed SML into an effective quantitative tool able to estimate the oligomeric states of macromolecular complexes. In this work, we apply a recently developed quantitative method based on stochastic optical reconstruction microscopy (qSTORM) to study the distribution of the synaptic proteins Homer in hippocampal neurons. Our experiments prove qSTORM as a suitable tool for novel quantitative insights into the nanoscale organization of excitatory synapses.
{"title":"Quantitative Super-resolution of Synaptic Proteins","authors":"F. C. Zanacchi","doi":"10.22580/iscinotej7.7.1","DOIUrl":"https://doi.org/10.22580/iscinotej7.7.1","url":null,"abstract":"Single molecule localization microscopy (SMLM) recently became more and more popular for studying the synaptic architecture, providing substantial advances in modern neuroscience. Recently developed methods based on DNA origami calibration transformed SML into an effective quantitative tool able to estimate the oligomeric states of macromolecular complexes. In this work, we apply a recently developed quantitative method based on stochastic optical reconstruction microscopy (qSTORM) to study the distribution of the synaptic proteins Homer in hippocampal neurons. Our experiments prove qSTORM as a suitable tool for novel quantitative insights into the nanoscale organization of excitatory synapses.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41443941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In spite of research over the past decades, robust, replicable, and clinically translatable markers to objectively diagnose psychiatric disorders are yet to be ascertained. Several factors such as biological heterogeneity (partly due to the complex genetic basis that is further compounded by environmental interactions), the potential mismatch between contemporary diagnostic criteria / clinical symptom scores and findings that emanate from cutting-edge neuroscience observations, and similar others have made the identification of biomarkers a daunting challenge. This challenge becomes much harder to solve in the context of disorders of childhood onset such as, autism spectrum disorders (ASD) especially because of the additional complexity of examining the developing brain.
{"title":"Machine Learning-based Diagnosis of Autism Spectrum Disorder Using Brain Imaging","authors":"G. Venkatasubramanian","doi":"10.22580/iscinotej7.7.4","DOIUrl":"https://doi.org/10.22580/iscinotej7.7.4","url":null,"abstract":"In spite of research over the past decades, robust, replicable, and clinically translatable markers to objectively diagnose psychiatric disorders are yet to be ascertained. Several factors such as biological heterogeneity (partly due to the complex genetic basis that is further compounded by environmental interactions), the potential mismatch between contemporary diagnostic criteria / clinical symptom scores and findings that emanate from cutting-edge neuroscience observations, and similar others have made the identification of biomarkers a daunting challenge. This challenge becomes much harder to solve in the context of disorders of childhood onset such as, autism spectrum disorders (ASD) especially because of the additional complexity of examining the developing brain.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45337637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Although the origin of disease and drug targets are primarily at intracellular space, such targeting is not achievable in currently available drugs. We and others recently show that molecular drugs can be transformed into nanodrug for better subcellular targeting with the enhanced therapeutic performance. This can be achieved via appropriate size and surface chemistry of colloidal nanodrug to control or bypass the endocytic uptake and intracellular trafficking processes. This approach can be adapted for enhanced drug performance with lower side effects.
{"title":"Subcellular Targeting-Based Advanced Therapy Via Chemically Designed Nanodrug","authors":"A. Sarkar, N. Jana","doi":"10.22580/iscinotej7.7.3","DOIUrl":"https://doi.org/10.22580/iscinotej7.7.3","url":null,"abstract":"Although the origin of disease and drug targets are primarily at intracellular space, such targeting is not achievable in currently available drugs. We and others recently show that molecular drugs can be transformed into nanodrug for better subcellular targeting with the enhanced therapeutic performance. This can be achieved via appropriate size and surface chemistry of colloidal nanodrug to control or bypass the endocytic uptake and intracellular trafficking processes. This approach can be adapted for enhanced drug performance with lower side effects.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47168224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Deep learning models have advanced many branches of science. However, these models have not been adequately developed for neuroimaging applications mainly because of the non-availability of large labelled datasets. In this study, we present an explainable deep learning approach to investigate the neurobiology of the autism spectrum disorder (ASD), which is one of the most prevalent neurodevelopmental disorders. Our approach achieved state of the art classification accuracy and identified brain features in discriminating ASDs from the typical subjects and finally identified features that predicted the severity of the symptoms.
{"title":"Deep Learning for the Classification of Autism Using Functional Neuroimaging","authors":"S. Ryali","doi":"10.22580/iscinotej7.7.2","DOIUrl":"https://doi.org/10.22580/iscinotej7.7.2","url":null,"abstract":"Deep learning models have advanced many branches of science. However, these models have not been adequately developed for neuroimaging applications mainly because of the non-availability of large labelled datasets. In this study, we present an explainable deep learning approach to investigate the neurobiology of the autism spectrum disorder (ASD), which is one of the most prevalent neurodevelopmental disorders. Our approach achieved state of the art classification accuracy and identified brain features in discriminating ASDs from the typical subjects and finally identified features that predicted the severity of the symptoms.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44976224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In an organism, different organ systems are highly specialised for performing dedicated functions. However, it is increasingly becoming clear that the organ systems do not function in isolation but are rather extensively dependent on each other. This phenomenon is known as inter-organ communication and is a novel paradigm of exocrine signaling. In this minireview, we discuss the theoretical implications of this kind of crosstalk and the resources available for practical demonstration of the same. We focus on the fruit fly, Drosophila melanogaster, and the zebrafish, Danio rerio. Both the model organisms are amenable to genetic manipulation and have been largely used to address many pending questions in all the fields of biology using cutting-edge cellular, molecular, and imaging techniques and tools. Both the organisms also offer the advantages of having organ systems functionally equivalent to those of humans to dissect how the development and functions of organs are established in dialogue with others.
{"title":"Two to Tango: Untangling Inter-organ Communication Using Drosophila Melanogaster and Danio Rerio","authors":"Amartya Mukherjee, S. Dutta, U. Nongthomba","doi":"10.22580/iscinotej6.6.1","DOIUrl":"https://doi.org/10.22580/iscinotej6.6.1","url":null,"abstract":"In an organism, different organ systems are highly specialised for performing dedicated functions. However, it is increasingly becoming clear that the organ systems do not function in isolation but are rather extensively dependent on each other. This phenomenon is known as inter-organ communication and is a novel paradigm of exocrine signaling. In this minireview, we discuss the theoretical implications of this kind of crosstalk and the resources available for practical demonstration of the same. We focus on the fruit fly, Drosophila melanogaster, and the zebrafish, Danio rerio. Both the model organisms are amenable to genetic manipulation and have been largely used to address many pending questions in all the fields of biology using cutting-edge cellular, molecular, and imaging techniques and tools. Both the organisms also offer the advantages of having organ systems functionally equivalent to those of humans to dissect how the development and functions of organs are established in dialogue with others.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44722273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seldom, do we come across a technology that advances multiple research disciplines across science and engineering. One such technology is light sheet that promises to take scientific investigation to the next level. The existing technology, predominantly based on point-focusing has reached a saturation limit, in terms of speed, limited field-of-view and lack of biophysical parameter estimation. Moreover, current technology is complex and needs human intervention. Light sheet techniques based on sheet-illumination expand our abilities for high throughput interrogation of a large pool of live biological specimens with near diffraction-limited resolution and an order increase in field-of-view. The outlook of research community has changed dramatically over the last decade that has seen an increased use of light sheet technology. Light sheet technique has penetrated both biological and physical sciences with its impact on microscopy, cytometry, nanolithography, beam-shaping, plasma physics and optical manipulation. Eventually, the technique will influence other disciplines and may give rise to new research fields.
{"title":"The Expanding Horizon of Light Sheet Technology","authors":"P. Mondal","doi":"10.22580/iscinotej6.6.2","DOIUrl":"https://doi.org/10.22580/iscinotej6.6.2","url":null,"abstract":"Seldom, do we come across a technology that advances multiple research disciplines across science and engineering. One such technology is light sheet that promises to take scientific investigation to the next level. The existing technology, predominantly based on point-focusing has reached a saturation limit, in terms of speed, limited field-of-view and lack of biophysical parameter estimation. Moreover, current technology is complex and needs human intervention. Light sheet techniques based on sheet-illumination expand our abilities for high throughput interrogation of a large pool of live biological specimens with near diffraction-limited resolution and an order increase in field-of-view. The outlook of research community has changed dramatically over the last decade that has seen an increased use of light sheet technology. Light sheet technique has penetrated both biological and physical sciences with its impact on microscopy, cytometry, nanolithography, beam-shaping, plasma physics and optical manipulation. Eventually, the technique will influence other disciplines and may give rise to new research fields.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45354194","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Understanding stochastic events that control the molecular events leading to the onset of neurodegenerative diseases such as Alzheimer's Disease (AD) is not well understood. Though the bulk of the attention is attributed to the increased burden of detrimental proteoforms generated by the processing of Amyloid Precursor Protein, there lacks a clear consensus on how the molecular events that control the localization and trafficking contribute to the onset. Here, we discuss emerging evidence that indicate the role of nanoscale compositionality of the membrane and random diffusion at the millisecond time scale that contribute to the onset of AD. We believe that intuitive knowledge of nanobiology controlling the local rates of product formation holds the clue for next-generation therapeutics that might delay or halt the onset of AD.
{"title":"Does Altered Probability of Real Time Diffusional Collisions of Membrane Molecules Trigger or Delay Alzheimers Disease","authors":"Deepak Nair, Shekhar Kedia, Mini Jose","doi":"10.22580/ISCINOTEJ5.5.3","DOIUrl":"https://doi.org/10.22580/ISCINOTEJ5.5.3","url":null,"abstract":"Understanding stochastic events that control the molecular events leading to the onset of neurodegenerative diseases such as Alzheimer's Disease (AD) is not well understood. Though the bulk of the attention is attributed to the increased burden of detrimental proteoforms generated by the processing of Amyloid Precursor Protein, there lacks a clear consensus on how the molecular events that control the localization and trafficking contribute to the onset. Here, we discuss emerging evidence that indicate the role of nanoscale compositionality of the membrane and random diffusion at the millisecond time scale that contribute to the onset of AD. We believe that intuitive knowledge of nanobiology controlling the local rates of product formation holds the clue for next-generation therapeutics that might delay or halt the onset of AD.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44180946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Coronavirus Disease 19 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), a highly transmissible and pathogenic coronavirus, has spread at an alarming rate throughout the world since Dec. 2019, claiming 2.196 million deaths globally, as per 30th Jan. 2021, and the count is on. The reason behind this ongoing rapid transmission and global spread of SARS-CoV-2 is that the virus is evolving to become more transmissible as it spreads across the world due to its fast host migration. The virus is rapidly evolving to adapt to the different geo‑climate environments, diverse host immune systems, and other protective counter-measures (such as prolong host survival) by accumulating adaptive mutations, deletions, and recombination. This note focuses on those mutations and the prominent viral strains that are noteworthy for epidemiological and biological reasons.
{"title":"SARS-CoV-2 Virus is Evolving to Adapt : A Fast Check Note","authors":"S. Mandal","doi":"10.22580/ISCINOTEJ5.5.2","DOIUrl":"https://doi.org/10.22580/ISCINOTEJ5.5.2","url":null,"abstract":"Coronavirus Disease 19 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), a highly transmissible and pathogenic coronavirus, has spread at an alarming rate throughout the world since Dec. 2019, claiming 2.196 million deaths globally, as per 30th Jan. 2021, and the count is on. The reason behind this ongoing rapid transmission and global spread of SARS-CoV-2 is that the virus is evolving to become more transmissible as it spreads across the world due to its fast host migration. The virus is rapidly evolving to adapt to the different geo‑climate environments, diverse host immune systems, and other protective counter-measures (such as prolong host survival) by accumulating adaptive mutations, deletions, and recombination. This note focuses on those mutations and the prominent viral strains that are noteworthy for epidemiological and biological reasons.","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49215810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Microfluidics-based Super-resolution Imaging: A New Tool for Nanoscopic Characterization of Cellular Interaction","authors":"S. Habuchi","doi":"10.22580/iscinotej4.4.1","DOIUrl":"https://doi.org/10.22580/iscinotej4.4.1","url":null,"abstract":"","PeriodicalId":92659,"journal":{"name":"iScience notes","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41890469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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