Wiley Interdisciplinary Reviews-Systems Biology and Medicine最新文献_第9页

Systems biology of cellular membranes: a convergence with biophysics. 细胞膜的系统生物学:与生物物理学的融合。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-09-01 Epub Date: 2017-05-05 DOI: 10.1002/wsbm.1386

Morgan Chabanon, Jeanne C Stachowiak, Padmini Rangamani

{"title":"Systems biology of cellular membranes: a convergence with biophysics.","authors":"Morgan Chabanon, Jeanne C Stachowiak, Padmini Rangamani","doi":"10.1002/wsbm.1386","DOIUrl":"10.1002/wsbm.1386","url":null,"abstract":"Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 5","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561455/pdf/nihms858717.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34969682","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

Biomechanics of the human uterus. 人类子宫的生物力学。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-09-01 Epub Date: 2017-05-12 DOI: 10.1002/wsbm.1388

Kristin M Myers, David Elad

{"title":"Biomechanics of the human uterus.","authors":"Kristin M Myers, David Elad","doi":"10.1002/wsbm.1388","DOIUrl":"https://doi.org/10.1002/wsbm.1388","url":null,"abstract":"The appropriate biomechanical function of the uterus is required for the execution of human reproduction. These functions range from aiding the transport of the embryo to the implantation site, to remodeling its tissue walls to host the placenta, to protecting the fetus during gestation, to contracting forcefully for a safe parturition and postpartum, to remodeling back to its nonpregnant condition to renew the cycle of menstruation. To serve these remarkably diverse functions, the uterus is optimally geared with evolving and contractile muscle and tissue layers that are cued by chemical, hormonal, electrical, and mechanical signals. The relationship between these highly active biological signaling mechanisms and uterine biomechanical function is not completely understood for normal reproductive processes and pathological conditions such as adenomyosis, endometriosis, infertility and preterm labor. Animal studies have illuminated the rich structural function of the uterus, particularly in pregnancy. In humans, medical imaging techniques in ultrasound and magnetic resonance have been combined with computational engineering techniques to characterize the uterus in vivo, and advanced experimental techniques have explored uterine function using ex vivo tissue samples. The collective evidence presented in this review gives an overall perspective on uterine biomechanics related to both its nonpregnant and pregnant function, highlighting open research topics in the field. Additionally, uterine disease and infertility are discussed in the context of tissue injury and repair processes and the role of computational modeling in uncovering etiologies of disease. WIREs Syst Biol Med 2017, 9:e1388. doi: 10.1002/wsbm.1388 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 5","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1388","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34991432","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: 57

Therapeutic genome engineering via CRISPR‐Cas systems 利用CRISPR‐Cas系统进行治疗性基因组工程

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-07-01 DOI: 10.1002/wsbm.1380

Ana M. Moreno, P. Mali

引用次数: 23

Virtual endovascular treatment of intracranial aneurysms: models and uncertainty. 颅内动脉瘤的虚拟血管内治疗:模型和不确定性。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-07-01 Epub Date: 2017-05-10 DOI: 10.1002/wsbm.1385

Ali Sarrami-Foroushani, Toni Lassila, Alejandro F Frangi

{"title":"Virtual endovascular treatment of intracranial aneurysms: models and uncertainty.","authors":"Ali Sarrami-Foroushani, Toni Lassila, Alejandro F Frangi","doi":"10.1002/wsbm.1385","DOIUrl":"https://doi.org/10.1002/wsbm.1385","url":null,"abstract":"Virtual endovascular treatment models (VETMs) have been developed with the view to aid interventional neuroradiologists and neurosurgeons to pre-operatively analyze the comparative efficacy and safety of endovascular treatments for intracranial aneurysms. Based on the current state of VETMs in aneurysm rupture risk stratification and in patient-specific prediction of treatment outcomes, we argue there is a need to go beyond personalized biomechanical flow modeling assuming deterministic parameters and error-free measurements. The mechanobiological effects associated with blood clot formation are important factors in therapeutic decision making and models of post-treatment intra-aneurysmal biology and biochemistry should be linked to the purely hemodynamic models to improve the predictive power of current VETMs. The influence of model and parameter uncertainties associated to each component of a VETM is, where feasible, quantified via a random-effects meta-analysis of the literature. This allows estimating the pooled effect size of these uncertainties on aneurysmal wall shear stress. From such meta-analyses, two main sources of uncertainty emerge where research efforts have so far been limited: (1) vascular wall distensibility, and (2) intra/intersubject systemic flow variations. In the future, we suggest that current deterministic computational simulations need to be extended with strategies for uncertainty mitigation, uncertainty exploration, and sensitivity reduction techniques. WIREs Syst Biol Med 2017, 9:e1385. doi: 10.1002/wsbm.1385 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 4","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1385","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34982948","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: 13

Recent lab‐on‐chip developments for novel drug discovery 新药物研发的最新芯片实验室进展

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-07-01 DOI: 10.1002/wsbm.1381

N. Khalid, I. Kobayashi, M. Nakajima

{"title":"Recent lab‐on‐chip developments for novel drug discovery","authors":"N. Khalid, I. Kobayashi, M. Nakajima","doi":"10.1002/wsbm.1381","DOIUrl":"https://doi.org/10.1002/wsbm.1381","url":null,"abstract":"Microelectromechanical systems (MEMS) and micro total analysis systems (μTAS) revolutionized the biochemical and electronic industries, and this miniaturization process became a key driver for many markets. Now, it is a driving force for innovations in life sciences, diagnostics, analytical sciences, and chemistry, which are called ‘lab‐on‐a‐chip, (LOC)’ devices. The use of these devices allows the development of fast, portable, and easy‐to‐use systems with a high level of functional integration for applications such as point‐of‐care diagnostics, forensics, the analysis of biomolecules, environmental or food analysis, and drug development. In this review, we report on the latest developments in fabrication methods and production methodologies to tailor LOC devices. A brief overview of scale‐up strategies is also presented together with their potential applications in drug delivery and discovery. The impact of LOC devices on drug development and discovery has been extensively reviewed in the past. The current research focuses on fast and accurate detection of genomics, cell mutations and analysis, drug delivery, and discovery. The current research also differentiates the LOC devices into new terminology of microengineering, like organ‐on‐a‐chip, stem cells‐on‐a‐chip, human‐on‐a‐chip, and body‐on‐a‐chip. Key challenges will be the transfer of fabricated LOC devices from lab‐scale to industrial large‐scale production. Moreover, extensive toxicological studies are needed to justify the use of microfabricated drug delivery vehicles in biological systems. It will also be challenging to transfer the in vitro findings to suitable and promising in vivo models. WIREs Syst Biol Med 2017, 9:e1381. doi: 10.1002/wsbm.1381","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"54 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82231151","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: 60

Understanding the mTOR signaling pathway via mathematical modeling. 通过数学建模了解mTOR信号通路。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-07-01 Epub Date: 2017-02-10 DOI: 10.1002/wsbm.1379

Nurgazy Sulaimanov, Martin Klose, Hauke Busch, Melanie Boerries

{"title":"Understanding the mTOR signaling pathway via mathematical modeling.","authors":"Nurgazy Sulaimanov, Martin Klose, Hauke Busch, Melanie Boerries","doi":"10.1002/wsbm.1379","DOIUrl":"https://doi.org/10.1002/wsbm.1379","url":null,"abstract":"The mechanistic target of rapamycin (mTOR) is a central regulatory pathway that integrates a variety of environmental cues to control cellular growth and homeostasis by intricate molecular feedbacks. In spite of extensive knowledge about its components, the molecular understanding of how these function together in space and time remains poor and there is a need for Systems Biology approaches to perform systematic analyses. In this work, we review the recent progress how the combined efforts of mathematical models and quantitative experiments shed new light on our understanding of the mTOR signaling pathway. In particular, we discuss the modeling concepts applied in mTOR signaling, the role of multiple feedbacks and the crosstalk mechanisms of mTOR with other signaling pathways. We also discuss the contribution of principles from information and network theory that have been successfully applied in dissecting design principles of the mTOR signaling network. We finally propose to classify the mTOR models in terms of the time scale and network complexity, and outline the importance of the classification toward the development of highly comprehensive and predictive models. WIREs Syst Biol Med 2017, 9:e1379. doi: 10.1002/wsbm.1379 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 4","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1379","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720149","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: 36

Multiscale modeling methods in biomechanics. 生物力学中的多尺度建模方法。

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-05-01 Epub Date: 2017-01-19 DOI: 10.1002/wsbm.1375

Pinaki Bhattacharya, Marco Viceconti

{"title":"Multiscale modeling methods in biomechanics.","authors":"Pinaki Bhattacharya, Marco Viceconti","doi":"10.1002/wsbm.1375","DOIUrl":"https://doi.org/10.1002/wsbm.1375","url":null,"abstract":"More and more frequently, computational biomechanics deals with problems where the portion of physical reality to be modeled spans over such a large range of spatial and temporal dimensions, that it is impossible to represent it as a single space-time continuum. We are forced to consider multiple space-time continua, each representing the phenomenon of interest at a characteristic space-time scale. Multiscale models describe a complex process across multiple scales, and account for how quantities transform as we move from one scale to another. This review offers a set of definitions for this emerging field, and provides a brief summary of the most recent developments on multiscale modeling in biomechanics. Of all possible perspectives, we chose that of the modeling intent, which vastly affect the nature and the structure of each research activity. To the purpose we organized all papers reviewed in three categories: 'causal confirmation,' where multiscale models are used as materializations of the causation theories; 'predictive accuracy,' where multiscale modeling is aimed to improve the predictive accuracy; and 'determination of effect,' where multiscale modeling is used to model how a change at one scale manifests in an effect at another radically different space-time scale. Consistent with how the volume of computational biomechanics research is distributed across application targets, we extensively reviewed papers targeting the musculoskeletal and the cardiovascular systems, and covered only a few exemplary papers targeting other organ systems. The review shows a research subdomain still in its infancy, where causal confirmation papers remain the most common. WIREs Syst Biol Med 2017, 9:e1375. doi: 10.1002/wsbm.1375 For further resources related to this article, please visit the WIREs website.","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"9 3","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/wsbm.1375","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89720148","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: 22

Trends in high‐throughput and functional neuroimaging in Caenorhabditis elegans 秀丽隐杆线虫的高通量和功能性神经成像趋势

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-05-01 DOI: 10.1002/wsbm.1376

Yongmin Cho, Charles L. Zhao, Hang Lu

{"title":"Trends in high‐throughput and functional neuroimaging in Caenorhabditis elegans","authors":"Yongmin Cho, Charles L. Zhao, Hang Lu","doi":"10.1002/wsbm.1376","DOIUrl":"https://doi.org/10.1002/wsbm.1376","url":null,"abstract":"The nervous system of Caenorhabditis elegans is an important model system for understanding the development and function of larger, more complex nervous systems. It is prized for its ease of handling, rapid life cycle, and stereotyped, well‐cataloged development, with the development of all 302 neurons mapped all the way from zygote to adult. The combination of easy genetic manipulation and optical transparency of the worm allows for the direct imaging of its interior with fluorescent microscopy, without physically compromising the normal physiology of the animal itself. By expressing fluorescent markers, biologists study many developmental and cell biology questions in vivo; by expressing genetically encoded fluorescent calcium indicators within neurons, it is also possible to monitor their dynamic activity, answering questions about the structure and function of neural microcircuitry in the worm. However, to successfully image the worm it is necessary to overcome a number of experimental challenges. It is necessary to hold worms within the field of view, collect images efficiently and rapidly, and robustly analyze the data obtained. In recent years, a trend has developed toward imaging a large number of worms or neurons simultaneously, directly exploiting the unique properties of C. elegans to acquire data on a scale, which is not possible in other organisms. Doing this has required the development of new experimental tools, techniques, and data analytic approaches, all of which come together to open new perspectives on the field of neurobiology in C. elegans, and neuroscience in general. WIREs Syst Biol Med 2017, 9:e1376. doi: 10.1002/wsbm.1376","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"37 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76559402","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: 18

Integrated precision medicine: the role of electronic health records in delivering personalized treatment 综合精准医疗:电子健康记录在提供个性化治疗中的作用

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-05-01 DOI: 10.1002/wsbm.1378

Amy M. Sitapati, Hyeon-Wui Kim, B. Berkovich, R. Marmor, Siddharth Singh, R. El-Kareh, B. Clay, L. Ohno-Machado

{"title":"Integrated precision medicine: the role of electronic health records in delivering personalized treatment","authors":"Amy M. Sitapati, Hyeon-Wui Kim, B. Berkovich, R. Marmor, Siddharth Singh, R. El-Kareh, B. Clay, L. Ohno-Machado","doi":"10.1002/wsbm.1378","DOIUrl":"https://doi.org/10.1002/wsbm.1378","url":null,"abstract":"Precision Medicine involves the delivery of a targeted, personalized treatment for a given patient. By harnessing the power of electronic health records (EHRs), we are increasingly able to practice precision medicine to improve patient outcomes. In this article, we introduce the scientific community at large to important building blocks for personalized treatment, such as terminology standards that are the foundation of the EHR and allow for exchange of health information across systems. We briefly review different types of clinical decision support (CDS) and present the current state of CDS, which is already improving the care patients receive with genetic profile‐based tailored recommendations regarding diagnostic and treatment plans. We also report on limitations of current systems, which are slowly beginning to integrate new genomic data into patient records but still present many challenges. Finally, we discuss future directions and how the EHR can evolve to increase the capacity of the healthcare system in delivering Precision Medicine at the point of care. WIREs Syst Biol Med 2017, 9:e1378. doi: 10.1002/wsbm.1378","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"28 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88931106","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: 49

Traditional and novel tools to probe the mitochondrial metabolism in health and disease 探索线粒体代谢在健康和疾病中的传统和新型工具

IF 7.9

Wiley Interdisciplinary Reviews-Systems Biology and Medicine Pub Date : 2017-03-01 DOI: 10.1002/wsbm.1373

Yanfei Zhang, J. Avalos

{"title":"Traditional and novel tools to probe the mitochondrial metabolism in health and disease","authors":"Yanfei Zhang, J. Avalos","doi":"10.1002/wsbm.1373","DOIUrl":"https://doi.org/10.1002/wsbm.1373","url":null,"abstract":"Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α‐ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl‐CoA, iron‐sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans‐omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373","PeriodicalId":49254,"journal":{"name":"Wiley Interdisciplinary Reviews-Systems Biology and Medicine","volume":"21 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2017-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84300915","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: 11