Why is it crucial to reintegrate pathology into cancer research?

The integration of pathology with molecular biology is vital if we are to enhance the translational value of cancer research. Pathology represents a bridge between medicine and basic biology, it remains the gold standard for cancer diagnosis, and it plays an important role in discovery studies. In the past, pathology and cancer research were closely associated; however, the molecular biology revolution has shifted the focus of investigators toward the molecular alterations of tumors. The reductionist approach taken in molecular studies is producing great insight into the inner workings of neoplasia, but it can also minimize the importance of histopathology and of understanding the disease as a whole. In turn, pathologists can underestimate the role of molecular studies in developing new ancillary techniques for clinical diagnosis. A multidisciplinary approach that integrates pathology and molecular biology within a translational research system is needed. This process will require overcoming cultural barriers and can be achieved through education, a more effective incorporation of pathology into biological research, and conversely an integration of biological research into the pathology laboratory.     

系统生物学研究及其在医学中的应用

目前,系统生物学研究已初显端倪。生物学正从分子生物学走向系统生物学,由精细的分解研究转向系统的整体研究,由还原论的研究方法过渡到系统论的研究方法。简要论述了系统生物学的产生背景、结构和内容、研究思路和方法、与医学的关系等,重点介绍系统生物学的内容和研究方法,以及在疾病治疗和药物开发中的研究进展。     

基于机制的生理药动- 药效学模型研究进展

生理药动- 药效学模型通过对生物学过程的描述,可预测体内药物的吸收、分布、代谢、排泄以及进一步的生理生化反应。这类模型是通过已知的生化/ 生理基础来构建,采用了一种“自下而上”的建模方法,并利用数学方法对生理过程及药物的作用机制作出准确的描述。其中药效学部分,根据预测目的和药物作用的复杂性,可进一步分为基于经验的和基于机制的效应模型,这两种模型均可与基于机制的生理药动学模型相连接,最终预测药物的体内处置和效应。基于机制的生理药动- 药效学模型的优势在于：可外推性、新的影响因素的可纳入性以及可用于未知领域的预测等。随着实验技术的不断革新,药物作用机制的逐渐明确,这类模型越来越多的被成功应用于药物研发及风险评估中。综述生理药动- 药效学模型的构建策略与分类以及在药物研发和风险评估中的应用研究。     

系统生物学与细胞发生系统动力学

系统生物学是系统理论和实验生物技术、计算机数学模型等方法整合的生物系统研究,系统遗传学研究基因组的稳态与进化、功能基因组和生物性状等复杂系统的结构、动态与发生演变等。合成生物学是系统生物学的工程应用,采用工程学方法、基因工程和计算机辅助设计等研究人工生物系统的生物技术。系统与合成生物学的结构理论,序列标志片段显示分析与微流控生物芯片,广泛用于研究细胞代谢、繁殖和应激的自组织进化、生物体形态发生等细胞分子生物系统原理等。     

Psychiatric research: psychoproteomics,degradomics and systems biology

While proteomics has excelled in several disciplines in biology (cancer, injury and aging), neuroscience and psychiatryproteomic studies are still in their infancy. Several proteomic studies have been conducted in different areas of psychiatric disorders, including drug abuse (morphine, alcohol and methamphetamine) and other psychiatric disorders (depression, schizophrenia and psychosis). However, the exact cellular and molecular mechanisms underlying these conditions have not been fully investigated. Thus, one of the primary objectives of this review is to discuss psychoproteomic application in the area of psychiatric disorders, with special focus on substance- and drug-abuse research. In addition, we illustrate the potential role of degradomic utility in the area of psychiatric research and its application in establishing and identifying biomarkers relevant to neurotoxicity as a consequence of drug abuse. Finally, we will discuss the emerging role of systems biology and its current use in the field of neuroscience and its integral role in establishing a comprehensive understanding of specific brain disorders and brain function in general.     

人工细胞在合成生物学中的应用

人工细胞作为一种模拟天然细胞结构和功能的人工系统,在多个领域的研究中发挥着重要作用。基于人工细胞构建策略可分为“自上而下”的人工细胞和“自下而上”的人工细胞。这与以构建或模拟天然生物细胞中存在的复杂路径为目标的“自下而上”的合成生物学思想不谋而合。利用合成生物学“自下而上”的逻辑属性,可以工程化设计人工细胞,并应用于生物工程、医药和疾病治疗等领域。本文重点介绍了人工细胞在合成生物学和医学领域中的应用,尤其是基于人工细胞构建的药物递送系统以及人工细胞在组织工程和再生医学中的应用。同时探讨了如何运用新的工程方法提高人工细胞的活性和稳定性,从而缩小人工细胞与天然细胞之间的差距。本文可为加速和推进多功能人工细胞的研究,将人工细胞的应用范围扩展到生物技术、医学和靶向药物治疗等诸多领域提供参考,为人类社会的可持续性发展提供更多可能性。     

Modeling and simulation of biological systems from image data

This essay provides an introduction to the terminology, concepts, methods, and challenges of image‐based modeling in biology. Image‐based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image‐based systems biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum.     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

Application of an integrated physical and functional screening approach to identify inhibitors of the Wnt pathway

Large‐scale proteomic approaches have been used to study signaling pathways. However, identification of biologically relevant hits from a single screen remains challenging due to limitations inherent in each individual approach. To overcome these limitations, we implemented an integrated, multi‐dimensional approach and used it to identify Wnt pathway modulators. The LUMIER protein–protein interaction mapping method was used in conjunction with two functional screens that examined the effect of overexpression and siRNA‐mediated gene knockdown on Wnt signaling. Meta‐analysis of the three data sets yielded a combined pathway score (CPS) for each tested component, a value reflecting the likelihood that an individual protein is a Wnt pathway regulator. We characterized the role of two proteins with high CPSs, Ube2m and Nkd1. We show that Ube2m interacts with and modulates β‐catenin stability, and that the antagonistic effect of Nkd1 on Wnt signaling requires interaction with Axin, itself a negative pathway regulator. Thus, integrated physical and functional mapping in mammalian cells can identify signaling components with high confidence and provides unanticipated insights into pathway regulators.     

Vaccinology in the era of high-throughput biology

Vaccination has been tremendously successful saving lives and preventing infections. However, the development of vaccines against global pandemics such as HIV, malaria and tuberculosis has been obstructed by several challenges. A major challenge is the lack of knowledge about the correlates and mechanisms of protective immunity. Recent advances in the application of systems biological approaches to analyse immune responses to vaccination in humans are beginning to yield new insights about mechanisms of vaccine immunity, and to define molecular signatures, induced rapidly after vaccination, that correlate with and predict vaccine induced immunity. Here, we review these advances and discuss the potential of this systems vaccinology approach in defining novel correlates of protection in clinical trials, and in infection-induced ‘experimental challenge models'' in humans.