Biophysics reviews最新文献_第4页

Emerging methods to model cardiac ion channel and myocyte electrophysiology. 心脏离子通道和心肌细胞电生理模型的新方法。

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-03-30 DOI: 10.1063/5.0127713

Jonathan D Moreno, Jonathan R Silva

引用次数: 0

Recent progress in polymeric gene vectors: Delivery mechanisms, molecular designs, and applications. 高分子基因载体的最新进展:传递机制、分子设计及应用。

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-03-28 DOI: 10.1063/5.0123664

Kemao Xiu, Jifeng Zhang, Jie Xu, Y Eugene Chen, Peter X Ma

{"title":"Recent progress in polymeric gene vectors: Delivery mechanisms, molecular designs, and applications.","authors":"Kemao Xiu, Jifeng Zhang, Jie Xu, Y Eugene Chen, Peter X Ma","doi":"10.1063/5.0123664","DOIUrl":"10.1063/5.0123664","url":null,"abstract":"Gene therapy and gene delivery have drawn extensive attention in recent years especially when the COVID-19 mRNA vaccines were developed to prevent severe symptoms caused by the corona virus. Delivering genes, such as DNA and RNA into cells, is the crucial step for successful gene therapy and remains a bottleneck. To address this issue, vehicles (vectors) that can load and deliver genes into cells are developed, including viral and non-viral vectors. Although viral gene vectors have considerable transfection efficiency and lipid-based gene vectors become popular since the application of COVID-19 vaccines, their potential issues including immunologic and biological safety concerns limited their applications. Alternatively, polymeric gene vectors are safer, cheaper, and more versatile compared to viral and lipid-based vectors. In recent years, various polymeric gene vectors with well-designed molecules were developed, achieving either high transfection efficiency or showing advantages in certain applications. In this review, we summarize the recent progress in polymeric gene vectors including the transfection mechanisms, molecular designs, and biomedical applications. Commercially available polymeric gene vectors/reagents are also introduced. Researchers in this field have never stopped seeking safe and efficient polymeric gene vectors via rational molecular designs and biomedical evaluations. The achievements in recent years have significantly accelerated the progress of polymeric gene vectors toward clinical applications.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 1","pages":"011313"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10062053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9296631","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}

引用次数: 0

Realizations of vascularized tissues: From in vitro platforms to in vivo grafts. 血管化组织的实现:从体外平台到体内移植。

Biophysics reviews Pub Date : 2023-03-01 Epub Date: 2023-03-13 DOI: 10.1063/5.0131972

Bing Ren, Zhihua Jiang, Walter Lee Murfee, Adam J Katz, Dietmar Siemann, Yong Huang

{"title":"Realizations of vascularized tissues: From in vitro platforms to in vivo grafts.","authors":"Bing Ren, Zhihua Jiang, Walter Lee Murfee, Adam J Katz, Dietmar Siemann, Yong Huang","doi":"10.1063/5.0131972","DOIUrl":"10.1063/5.0131972","url":null,"abstract":"Vascularization is essential for realizing thick and functional tissue constructs that can be utilized for in vitro study platforms and in vivo grafts. The vasculature enables the transport of nutrients, oxygen, and wastes and is also indispensable to organ functional units such as the nephron filtration unit, the blood-air barrier, and the blood-brain barrier. This review aims to discuss the latest progress of organ-like vascularized constructs with specific functionalities and realizations even though they are not yet ready to be used as organ substitutes. First, the human vascular system is briefly introduced and related design considerations for engineering vascularized tissues are discussed. Second, up-to-date creation technologies for vascularized tissues are summarized and classified into the engineering and cellular self-assembly approaches. Third, recent applications ranging from in vitro tissue models, including generic vessel models, tumor models, and different human organ models such as heart, kidneys, liver, lungs, and brain, to prevascularized in vivo grafts for implantation and anastomosis are discussed in detail. The specific design considerations for the aforementioned applications are summarized and future perspectives regarding future clinical applications and commercialization are provided.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"4 1","pages":"011308"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10015415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9621060","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}

引用次数: 0

Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing 空间转录组学中的深度学习:从下一代测序中学习

Biophysics reviews Pub Date : 2023-02-07 DOI: 10.1063/5.0091135

A. Ali Heydari, Suzanne S. Sindi

{"title":"Deep learning in spatial transcriptomics: Learning from the next next-generation sequencing","authors":"A. Ali Heydari, Suzanne S. Sindi","doi":"10.1063/5.0091135","DOIUrl":"https://doi.org/10.1063/5.0091135","url":null,"abstract":"Spatial transcriptomics (ST) technologies are rapidly becoming the extension of single-cell RNA sequencing (scRNAseq), holding the potential of profiling gene expression at a single-cell resolution while maintaining cellular compositions within a tissue. Having both expression profiles and tissue organization enables researchers to better understand cellular interactions and heterogeneity, providing insight into complex biological processes that would not be possible with traditional sequencing technologies. Data generated by ST technologies are inherently noisy, high-dimensional, sparse, and multi-modal (including histological images, count matrices, etc.), thus requiring specialized computational tools for accurate and robust analysis. However, many ST studies currently utilize traditional scRNAseq tools, which are inadequate for analyzing complex ST datasets. On the other hand, many of the existing ST-specific methods are built upon traditional statistical or machine learning frameworks, which have shown to be sub-optimal in many applications due to the scale, multi-modality, and limitations of spatially resolved data (such as spatial resolution, sensitivity, and gene coverage). Given these intricacies, researchers have developed deep learning (DL)-based models to alleviate ST-specific challenges. These methods include new state-of-the-art models in alignment, spatial reconstruction, and spatial clustering, among others. However, DL models for ST analysis are nascent and remain largely underexplored. In this review, we provide an overview of existing state-of-the-art tools for analyzing spatially resolved transcriptomics while delving deeper into the DL-based approaches. We discuss the new frontiers and the open questions in this field and highlight domains in which we anticipate transformational DL applications.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"107 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136181299","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}

引用次数: 4

A comprehensive review of computational and image analysis techniques for quantitative evaluation of striated muscle tissue architecture. 横纹肌组织结构定量评估的计算和图像分析技术的综合综述。

IF 2.9

Biophysics reviews Pub Date : 2022-12-01 Epub Date: 2022-11-04 DOI: 10.1063/5.0057434

Tessa Altair Morris, Sarah Eldeen, Richard Duc Hien Tran, Anna Grosberg

{"title":"A comprehensive review of computational and image analysis techniques for quantitative evaluation of striated muscle tissue architecture.","authors":"Tessa Altair Morris, Sarah Eldeen, Richard Duc Hien Tran, Anna Grosberg","doi":"10.1063/5.0057434","DOIUrl":"10.1063/5.0057434","url":null,"abstract":"Unbiased evaluation of morphology is crucial to understanding development, mechanics, and pathology of striated muscle tissues. Indeed, the ability of striated muscles to contract and the strength of their contraction is dependent on their tissue-, cellular-, and cytoskeletal-level organization. Accordingly, the study of striated muscles often requires imaging and assessing aspects of their architecture at multiple different spatial scales. While an expert may be able to qualitatively appraise tissues, it is imperative to have robust, repeatable tools to quantify striated myocyte morphology and behavior that can be used to compare across different labs and experiments. There has been a recent effort to define the criteria used by experts to evaluate striated myocyte architecture. In this review, we will describe metrics that have been developed to summarize distinct aspects of striated muscle architecture in multiple different tissues, imaged with various modalities. Additionally, we will provide an overview of metrics and image processing software that needs to be developed. Importantly to any lab working on striated muscle platforms, characterization of striated myocyte morphology using the image processing pipelines discussed in this review can be used to quantitatively evaluate striated muscle tissues and contribute to a robust understanding of the development and mechanics of striated muscles.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 4","pages":"041302"},"PeriodicalIF":2.9,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9667907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40699167","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}

引用次数: 0

In vitro skeletal muscle models for type 2 diabetes. 2 型糖尿病的体外骨骼肌模型。

Biophysics reviews Pub Date : 2022-09-01 Epub Date: 2022-09-13 DOI: 10.1063/5.0096420

Christina Y Sheng, Young Hoon Son, Jeongin Jang, Sung-Jin Park

{"title":"In vitro skeletal muscle models for type 2 diabetes.","authors":"Christina Y Sheng, Young Hoon Son, Jeongin Jang, Sung-Jin Park","doi":"10.1063/5.0096420","DOIUrl":"10.1063/5.0096420","url":null,"abstract":"Type 2 diabetes mellitus, a metabolic disorder characterized by abnormally elevated blood sugar, poses a growing social, economic, and medical burden worldwide. The skeletal muscle is the largest metabolic organ responsible for glucose homeostasis in the body, and its inability to properly uptake sugar often precedes type 2 diabetes. Although exercise is known to have preventative and therapeutic effects on type 2 diabetes, the underlying mechanism of these beneficial effects is largely unknown. Animal studies have been conducted to better understand the pathophysiology of type 2 diabetes and the positive effects of exercise on type 2 diabetes. However, the complexity of in vivo systems and the inability of animal models to fully capture human type 2 diabetes genetics and pathophysiology are two major limitations in these animal studies. Fortunately, in vitro models capable of recapitulating human genetics and physiology provide promising avenues to overcome these obstacles. This review summarizes current in vitro type 2 diabetes models with focuses on the skeletal muscle, interorgan crosstalk, and exercise. We discuss diabetes, its pathophysiology, common in vitro type 2 diabetes skeletal muscle models, interorgan crosstalk type 2 diabetes models, exercise benefits on type 2 diabetes, and in vitro type 2 diabetes models with exercise.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 3","pages":"031306"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9478902/pdf/BRIEIM-000003-031306_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10632609","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}

引用次数: 0

Myocardial infarction from a tissue engineering and regenerative medicine point of view: A comprehensive review on models and treatments. 组织工程和再生医学视角下的心肌梗死:模型和治疗方法综述。

Biophysics reviews Pub Date : 2022-09-01 DOI: 10.1063/5.0093399

Gozde Basara, Gokhan Bahcecioglu, S Gulberk Ozcebe, Bradley W Ellis, George Ronan, Pinar Zorlutuna

{"title":"Myocardial infarction from a tissue engineering and regenerative medicine point of view: A comprehensive review on models and treatments.","authors":"Gozde Basara, Gokhan Bahcecioglu, S Gulberk Ozcebe, Bradley W Ellis, George Ronan, Pinar Zorlutuna","doi":"10.1063/5.0093399","DOIUrl":"https://doi.org/10.1063/5.0093399","url":null,"abstract":"In the modern world, myocardial infarction is one of the most common cardiovascular diseases, which are responsible for around 18 million deaths every year or almost 32% of all deaths. Due to the detrimental effects of COVID-19 on the cardiovascular system, this rate is expected to increase in the coming years. Although there has been some progress in myocardial infarction treatment, translating pre-clinical findings to the clinic remains a major challenge. One reason for this is the lack of reliable and human representative healthy and fibrotic cardiac tissue models that can be used to understand the fundamentals of ischemic/reperfusion injury caused by myocardial infarction and to test new drugs and therapeutic strategies. In this review, we first present an overview of the anatomy of the heart and the pathophysiology of myocardial infarction, and then discuss the recent developments on pre-clinical infarct models, focusing mainly on the engineered three-dimensional cardiac ischemic/reperfusion injury and fibrosis models developed using different engineering methods such as organoids, microfluidic devices, and bioprinted constructs. We also present the benefits and limitations of emerging and promising regenerative therapy treatments for myocardial infarction such as cell therapies, extracellular vesicles, and cardiac patches. This review aims to overview recent advances in three-dimensional engineered infarct models and current regenerative therapeutic options, which can be used as a guide for developing new models and treatment strategies.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 3","pages":"031305"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9447372/pdf/BRIEIM-000003-031305_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10166535","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}

引用次数: 3

Single molecule DNA origami nanoarrays with controlled protein orientation. 具有可控蛋白质定向的单分子 DNA 折纸纳米阵列。

IF 2.9

Biophysics reviews Pub Date : 2022-08-18 eCollection Date: 2022-09-01 DOI: 10.1063/5.0099294

K Cervantes-Salguero, M Freeley, R E A Gwyther, D D Jones, J L Chávez, M Palma

{"title":"Single molecule DNA origami nanoarrays with controlled protein orientation.","authors":"K Cervantes-Salguero, M Freeley, R E A Gwyther, D D Jones, J L Chávez, M Palma","doi":"10.1063/5.0099294","DOIUrl":"10.1063/5.0099294","url":null,"abstract":"The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 3","pages":"031401"},"PeriodicalIF":2.9,"publicationDate":"2022-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10903486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177974","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}

引用次数: 0

Integrating mechanism-based modeling with biomedical imaging to build practical digital twins for clinical oncology. 将基于机制的建模与生物医学成像相结合，为临床肿瘤学构建实用的数字孪生体。

Biophysics reviews Pub Date : 2022-06-01 Epub Date: 2022-05-17 DOI: 10.1063/5.0086789

Chengyue Wu, Guillermo Lorenzo, David A Hormuth, Ernesto A B F Lima, Kalina P Slavkova, Julie C DiCarlo, John Virostko, Caleb M Phillips, Debra Patt, Caroline Chung, Thomas E Yankeelov

{"title":"Integrating mechanism-based modeling with biomedical imaging to build practical digital twins for clinical oncology.","authors":"Chengyue Wu, Guillermo Lorenzo, David A Hormuth, Ernesto A B F Lima, Kalina P Slavkova, Julie C DiCarlo, John Virostko, Caleb M Phillips, Debra Patt, Caroline Chung, Thomas E Yankeelov","doi":"10.1063/5.0086789","DOIUrl":"10.1063/5.0086789","url":null,"abstract":"Digital twins employ mathematical and computational models to virtually represent a physical object (e.g., planes and human organs), predict the behavior of the object, and enable decision-making to optimize the future behavior of the object. While digital twins have been widely used in engineering for decades, their applications to oncology are only just emerging. Due to advances in experimental techniques quantitatively characterizing cancer, as well as advances in the mathematical and computational sciences, the notion of building and applying digital twins to understand tumor dynamics and personalize the care of cancer patients has been increasingly appreciated. In this review, we present the opportunities and challenges of applying digital twins in clinical oncology, with a particular focus on integrating medical imaging with mechanism-based, tissue-scale mathematical modeling. Specifically, we first introduce the general digital twin framework and then illustrate existing applications of image-guided digital twins in healthcare. Next, we detail both the imaging and modeling techniques that provide practical opportunities to build patient-specific digital twins for oncology. We then describe the current challenges and limitations in developing image-guided, mechanism-based digital twins for oncology along with potential solutions. We conclude by outlining five fundamental questions that can serve as a roadmap when designing and building a practical digital twin for oncology and attempt to provide answers for a specific application to brain cancer. We hope that this contribution provides motivation for the imaging science, oncology, and computational communities to develop practical digital twin technologies to improve the care of patients battling cancer.","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 2","pages":"021304"},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9119003/pdf/BRIEIM-000003-021304_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9490272","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}

引用次数: 0

Interplay of long-chain tetrazine derivatives and biomembrane components at the air-water interface. 长链四嗪衍生物与生物膜成分在空气-水界面上的相互作用。

Biophysics reviews Pub Date : 2022-04-28 eCollection Date: 2022-06-01 DOI: 10.1063/5.0083352

Hiromichi Nakahara, Masayori Hagimori, Takahiro Mukai, Osamu Shibata

引用次数: 0