基于蛋白质组芯片的结核分枝杆菌系统生物学研究进展

近些年全球结核病疫情愈发严重,耐药性结核病使其雪上加霜。一个重要原因是结核病新药的匮乏以及结核分枝杆菌相关基础研究的不足。因此迫切需要开发新的技术以促进结核病系统生物学基础研究,并在此基础上研究新机制,发现新靶标,开发新药物。结核分枝杆菌功能蛋白质组芯片的出现旨在促进结核病相关研究工作。考虑到结核分枝杆菌高毒力、复制周期长和需要在生物安全三级实验室中开展研究等特点和难点,该工具为结核病相关研究人员提供了一个强有力的武器。目前这一技术手段的应用已经使我们对结核分枝杆菌-宿主相互作用、小分子-蛋白结合以及抗生素耐药性机制等关键生物过程有了更深入的了解。为了更好地帮助同行了解这一有效的工具,本文综述了结核分枝杆菌功能蛋白组芯片的几种主要应用,期望同行专家能更好地将其应用于结核病相关的基础研究中。     

Antibody microarrays: current status and key technological advances

Antibody-based microarrays are among the novel classes of rapidly evolving proteomic technologies that holds great promise in biomedicine. Miniaturized microarrays (< 1 cm2) can be printed with thousands of individual antibodies carrying the desired specificities, and with biological sample (e.g., an entire proteome) added, virtually any specifically bound analytes can be detected. While consuming only minute amounts (< microL scale) of reagents, ultra- sensitive assays (zeptomol range) can readily be performed in a highly multiplexed manner. The microarray patterns generated can then be transformed into proteomic maps, or detailed molecular fingerprints, revealing the composition of the proteome. Thus, protein expression profiling and global proteome analysis using this tool will offer new opportunities for drug target and biomarker discovery, disease diagnostics, and insights into disease biology. Adopting the antibody microarray technology platform, several biomedical applications, ranging from focused assays to proteome-scale analysis will be rapidly emerging in the coming years. This review will discuss the current status of the antibody microarray technology focusing on recent technological advances and key issues in the process of evolving the methodology into a high-performing proteomic research tool.     

Interactome Mapping: Using Protein Microarray Technology to Reconstruct Diverse Protein Networks

A major focus of systems biology is to characterize interactions between cellular components, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flexible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to reconstruct biological networks including protein-DNA interactions, posttranslational protein modifications (PTMs), lectin-glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological systems. We will also discuss emerging applications and future directions of protein microarray technology in the global frontier.     

Functional protein microarray: an ideal platform for investigating protein binding property

Functional protein microarray is an important tool for high-throughput and large-scale systems biology studies.Besides the progresses that have been made for protein microarray fabrication,significant ...     

Advances in the development of human protein microarrays

Introduction: High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward.

Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays.

Expert commentary: The choice of appropriate protein microarray platform depends on the specific biological application in hand, with both more focused, lower density and higher density arrays having distinct advantages. Full-length protein arrays offer advantages in biomarker discovery profiling applications, although care is required in ensuring that the protein production and array fabrication methodology is compatible with the required downstream functionality.     

Advances in cell-free protein array methods

Introduction: Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management.

Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method.

Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.     

糖芯片的制备和检测应用研究进展

近数十年来,糖芯片逐渐成为分析糖介导的识别和结合作用的强有力工具,具有样品检测用量少、特异性强和高通量等优点,可以大大提高糖生物学研究的效率。主要介绍了通过糖库的构建、共价结合和非共价吸附法等方法制备糖芯片的过程,糖芯片的检测方法及其在生物学研究和生物医学领域的应用,以期为糖芯片相关研究提供参考。     

DNA microarrays for functional plant genomics

DNA microarray technology is a key element in today's functional genomics toolbox. The power of the method lies in miniaturization, automation and parallelism permitting large-scale and genome-wide acquisition of quantitative biological information from multiple samples. DNA microarrays are currently fabricated and assayed by two main approaches involving either in situ synthesis of oligonucleotides (`oligonucleotide microarrays') or deposition of pre-synthesized DNA fragments (`cDNA microarrays') on solid surfaces. To date, the main applications of microarrays are in comprehensive, simultaneous gene expression monitoring and in DNA variation analyses for the identification and genotyping of mutations and polymorphisms. Already at a relatively early stage of its application in plant science, microarrays are being utilized to examine a range of biological issues including the circadian clock, plant defence, environmental stress responses, fruit ripening, phytochrome A signalling, seed development and nitrate assimilation. Novel insights are obtained into the molecular mechanisms co-ordinating metabolic pathways, regulatory and signalling networks. Exciting new information will be gained in the years to come not only from genome-wide expression analyses on a few model plant species, but also from extensive studies of less thoroughly studied species on a more limited scale. The value of microarray technology to our understanding of living processes will depend both on the amount of data to be generated and on its clever exploration and integration with other biological knowledge arising from complementary functional genomics tools for `profiling' the genome, proteome, metabolome and phenome.     

A perspective on microarrays: current applications,pitfalls, and potential uses

With advances in robotics, computational capabilities, and the fabrication of high quality glass slides coinciding with increased genomic information being available on public databases, microarray technology is increasingly being used in laboratories around the world. In fact, fields as varied as: toxicology, evolutionary biology, drug development and production, disease characterization, diagnostics development, cellular physiology and stress responses, and forensics have benefiting from its use. However, for many researchers not familiar with microarrays, current articles and reviews often address neither the fundamental principles behind the technology nor the proper designing of experiments. Although, microarray technology is relatively simple, conceptually, its practice does require careful planning and detailed understanding of the limitations inherently present. Without these considerations, it can be exceedingly difficult to ascertain valuable information from microarray data. Therefore, this text aims to outline key features in microarray technology, paying particular attention to current applications as outlined in recent publications, experimental design, statistical methods, and potential uses. Furthermore, this review is not meant to be comprehensive, but rather substantive; highlighting important concepts and detailing steps necessary to conduct and interpret microarray experiments. Collectively, the information included in this text will highlight the versatility of microarray technology and provide a glimpse of what the future may hold.     

Creation of the whole human genome microarray

Several companies have recently announced the availability of products that enable a scientist to probe gene expression from the entire human genome on a single DNA microarray. This review will focus on the underlying technological trends that have made this achievement possible, the particular methodologies which are employed to create such microarrays and the implications of the whole human genome microarray for future biological studies. The single genome array represents an important milestone on the path to unraveling the complexity of the cellular networks that control living processes. The microarrays being designed today may, however, become distant ancestors to the whole human genome arrays of the future as our understanding of the functioning of the human genome increases.     

Microarrays: technologies overview and data analysis

DNA microarrays are a powerful tool to investigate differential gene expression for thousands of genes simultaneously. In this review, recent advances in DNA microarray technologies and their applications are examined. Various DNA microarray platforms are described along with their methods for fabrication and their use. In addition some algorithms and tools for the analysis of microarray expression data, including clustering methods, partitioning and machine learning methods are discussed.     

Mass Spectrometry and Proteomics 2018: the Mass Spectrometry Society of Japan,Japanese Proteomics Society,and Asia-Oceania Human Proteome Organization

ABSTRACT

Introduction: The mass spectrometry society of Japan, Japanese proteomics society, and Asia–Oceania human proteome organization held the conference ‘Mass Spectrometry and Proteomics 2018’ in Osaka, Japan, on May 15–18, 2018. This international conference focused on cutting edge technologies and their applications in a variety of research fields such as agriculture, material science, environmental factors, and clinical applications. An overview of the conference and a summary of the major lectures are reported here.

Expert commentary: The meeting will facilitate the development of fundamental technologies and the multi-disciplinary applications of proteomics.     

Nanoproteomics comes of age

ABSTRACT

Introduction: Nanoproteomics, which is defined as quantitative proteome profiling of small populations of cells (<5000 cells), can reveal critical information related to rare cell populations, hard-to-obtain clinical specimens, and the cellular heterogeneity of pathological tissues.

Areas covered: We present a brief review of the recent technological advances in nanoproteomics. These advances include new technologies or approaches covering major areas of proteomics workflow ranging from sample isolation, sample processing, high-resolution separations, to MS instrumentation.

Expert commentary: We comment on the current state of nanoproteomics and discuss perspectives on both future technological directions and potential enabling applications.