Informatic tools for proteome profiling

In recent years, the practice of proteomics research has experienced a dramatic shift within the pharmaceutical and biotechnology industry with the widespread implementation of novel applications. The areas of interest extend all the way from discovery of novel drug, vaccine, and diagnostic targets, characterization of protein-based products, toxicology, and identification of surrogate markers of activity in clinical research, to the ability to provide information on the mechanisms of drug action. The power of two-dimensional gel electrophoresis as well as advances in mass spectrometric techniques combined with sequence database correlation have enabled speed and accuracy in identification of proteins in complex mixtures. This article surveys currently available software and informatic tools related to these methods for proteome profiling. The broad acceptance of these technologies, however, has not been accompanied by significant advances in the informatics and software tools necessary to support the analysis and management of the massive amounts of data generated in the process. In this context, this article also discusses the importance of relational databases for protein identification data management.     

High-throughput screening: update on practices and success

High-throughput screening (HTS) has become an important part of drug discovery at most pharmaceutical and many biotechnology companies worldwide, and use of HTS technologies is expanding into new areas. Target validation, assay development, secondary screening, ADME/Tox, and lead optimization are among the areas in which there is an increasing use of HTS technologies. It is becoming fully integrated within drug discovery, both upstream and downstream, which includes increasing use of cell-based assays and high-content screening (HCS) technologies to achieve more physiologically relevant results and to find higher quality leads. In addition, HTS laboratories are continually evaluating new technologies as they struggle to increase their success rate for finding drug candidates. The material in this article is based on a 900-page HTS industry report involving 54 HTS directors representing 58 HTS laboratories and 34 suppliers.     

Escherichia coli--a model system that benefits from and contributes to the evolution of proteomics

The large body of knowledge about Escherichia coli makes it a useful model organism for the expression of heterologous proteins. Proteomic studies have helped to elucidate the complex cellular responses of E. coli and facilitated its use in a variety of biotechnology applications. Knowledge of basic cellular processes provides the means for better control of heterologous protein expression. Beyond such important applications, E. coli is an ideal organism for testing new analytical technologies because of the extensive knowledge base available about the organism. For example, improved technology for characterization of unknown proteins using mass spectrometry has made two-dimensional electrophoresis (2DE) studies more useful and more rewarding, and much of the initial testing of novel protocols is based on well-studied samples derived from E. coli. These techniques have facilitated the construction of more accurate 2DE maps. In this review, we present work that led to the 2DE databases, including a new map based on tandem time-of-flight (TOF) mass spectrometry (MS); describe cellular responses relevant to biotechnology applications; and discuss some emerging proteomic techniques.     

Next‐generation bioproduction systems: Cell‐free conversion concepts for industrial biotechnology

Within the last decade, biotechnology gained pace in substituting petro‐based products for the chemical industries. This is visible with the appearance of bio‐based products in the market, from biosurfactants to bio‐based polymers like polylactic acid to bio‐ethylene. These technologies are mainly based on established fermentation technologies fostered by the use of renewable resources, culminating in the establishment of biorefineries that may be connected directly to the existing chemical infrastructure. Besides these large‐scale technologies, the combination of molecular technologies, microfluidic devices, and enzymatic and cell‐free conversions are currently developed to create new bioproduction systems enabling the production of compounds that may not be produced within a cell. This article summarizes some of the current ideas that are currently in development paving the way for a next generation of biotechnology.     

工业生物技术的前沿科技

随着石化资源逐步消耗,气候问题日益凸显,工业生物技术被认为是解决能源和资源供给、应对气候变化、实现绿色可持续发展的重要方向。得益于理论突破、技术变革和学科交叉,工业生物技术主要经历了由生命科学突破性成就、多学科技术理念交汇融合和产业应用导向推动的3个阶段。本文回顾总结了工业生物技术的发展历程及近年来取得的重要突破,并展望了其未来发展方向。     

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

Driven by advancements in high-throughput biological technologies and the growing number of sequenced genomes, the construction of in silico models at the genome scale has provided powerful tools to investigate a vast array of biological systems and applications. Here, we review comprehensively the uses of such models in industrial and medical biotechnology, including biofuel generation, food production, and drug development. While the use of in silico models is still in its early stages for delivering to industry, significant initial successes have been achieved. For the cases presented here, genome-scale models predict engineering strategies to enhance properties of interest in an organism or to inhibit harmful mechanisms of pathogens. Going forward, genome-scale in silico models promise to extend their application and analysis scope to become a transformative tool in biotechnology.     

The social, moral, ethical, legal and political implications of today's biological technologies: an Indian point of view

The last 50 years have seen an increasing emphasis on ethical, moral, social, legal, political and economic implications of science for reasons that are discussed in this article. Biotechnology has been no exception to this trend. Areas of biotechnology where the above implications have been important, are briefly described. Ethical and related issues in today's biology-based technologies are discussed with special reference to India. Examples of technological exploitation within a country, or of one country by another, using modern biology-based technologies are given. The possible implications of one new and emerging biology-based technology are discussed. It is concluded that a well-informed and knowledgeable society is the only assured insurance against possible misuse of biology-based technologies of today and tomorrow, including their use for the exploitation of people. The recent decision of the Prime Minister of India to set up a National Knowledge Commission is mentioned in this context.     

A Taxonomic Review of the Use of IoT and Blockchain in Healthcare Applications

ObjectivesWith the rapid evolution and technology advancement, the healthcare sector is evolving day by day. It is taking advantage of different technologies such as Internet of things and Blockchain. Several applications related to daily healthcare activities are adopting the use of these technologies. In this paper, we present a review in which we group different healthcare applications that integrate the Internet of things and Blockchain in their systems.Material and methodsA review study about the integration of IoT and Blockchain in healthcare systems was conducted. We searched the databases ScienceDirect, IEEE Xplore, Google Scholar and ACM Digital Library.ResultsThis review focuses on categorizing the use cases of IoT and Blockchain in the healthcare sector. The study listed 6 applications in medical services, namely, remote patient monitoring, electronic medical records management, disease prediction, patient tracking, drug traceability and fighting infectious disease especially COVID-19. The paper also investigates the challenges associated with the adoption of the Blockchain technology in healthcare IoT-based systems and some of the existing solutions. It also introduces some future research directions.ConclusionThe survey of the use cases of IoT and Blockchain in the healthcare sector will serve as a state of the art for future researches. In addition, the paper gives some directions to new possible researches that could help to revolutionize the healthcare sector by using other technologies such as artificial intelligence, big data, fog and cloud computing.     

Metabolomics for phytomedicine research and drug development

Metabolomics, including both targeted and global metabolite profiling strategies, is fast becoming the approach of choice across a broad range of sciences including systems biology, drug discovery, molecular and cell biology, and other medical and agricultural sciences. New analytical and bioinformatics technologies and techniques are continually being created or optimized, significantly increasing the crossdisciplinary capabilities of this new biology. The metabolomes of medicinal plants are particularly a valuable natural resource for the evidence-based development of new phytotherapeutics and nutraceuticals. Comparative metabolomics platforms are evolving into novel technologies for monitoring disease development, drug metabolism, and chemical toxicology. An efficient multidisciplinary marriage of these emerging metabolomics techniques with agricultural biotechnology will greatly benefit both basic and applied medical research.     

蛋白质相互作用数据库及其应用

对蛋白质相互作用及其网络的了解不仅有助于深入理解生命活动的本质和疾病发生的机制,而且可以为药物研发提供靶点.目前,通过高通量筛选、计算方法预测和文献挖掘等方法,获得了大批量的蛋白质相互作用数据,并由此构建了很多内容丰富并日益更新的蛋白质相互作用数据库.本文首先简要阐述了大规模蛋白质相互作用数据产生的3种方法,然后重点介绍了几个人类相关的蛋白质相互作用公共数据库,包括HPRD、BIND、 IntAct、MINT、 DIP 和MIPS,并概述了蛋白质相互作用数据库的整合情况以及这些数据库在蛋白质相互作用网络构建上的应用.     

国外豆科牧草生物技术研究进展——生物技术在豆科牧草遗传育种研究中的应用

豆科牧草具有重要的经济价值。本文主要从豆科牧草遗传资源鉴定、保存和利用及豆科牧草育种方法和育种策略两个大的方面阐述了生物技术在国外豆科牧草研究中的应用,并重点介绍了体细胞杂交、胚拯救和分子标记技术。     

Biological coupling process for treatment of toxic and refractory compounds in coal gasification wastewater

Coal gasification wastewater (CGW) contains a large number of toxic and refractory compounds, such as phenolic compounds and polycyclic and heterocyclic aromatic compounds. These toxic and refractory compounds are difficult to degrade if biological methods are the only ones used. In recent years, several novel biological coupling processes are used to treat CGW. In the study, this review attempts to offer a comprehensive summary regarding the biological coupling treatment technologies of CGW, including conventional biological processing arts, the combination of adsorption and biotechnology, biological enhancement technologies, co-metabolism technologies and the combination of advanced oxidation and biotechnology. Meanwhile, the treatment efficiency of different biological coupling processes was compared with each other. Co-metabolism and advanced oxidation with biotechnology are both highly effective and promising technologies for degrading toxic and refractory compounds. More research should be conducted on these two aspects in the future.     

大数据时代的整合生物信息学

随着生物数据测量技术的不断发展,生物数据的类型、内容、复杂度不断增加,生物信息学已迈入大数据时代。面对大数据时代多模态、多层次、高维度、非线性的复杂生物数据,生物信息学需要发展相应的方法和技术进行有效整合生物信息学研究与应用。本文对大数据时代整合生物信息学所涉及的数据整合、方法整合、系统整合及相关问题进行梳理和探讨。     

Synthetic biology in society: learning from past experience?

Drawing an analogy to past debates over biotechnology, some stakeholders fear that synthetic biology (SB) could raise public concerns. Accordingly, ‘lessons from the past’ should be applied to avoid controversies. However, biotechnology in the 1990s is not the only possible comparator. The potential to become contested has been attributed to a number of other novel technologies. Looking at nanotechnology for example, controversies have not materialised to the extent predicted. The article discusses factors relevant for controversies over technologies as well as differences to the situation when modern biotechnology began to proliferate. Certain properties attributed to SB in the discussion so far indeed suggest a potential for controversies of its own, but perceptions may follow those on other aspects of biotechnology subject to local contingencies. Finally, it is questioned whether ELSI research should see its task in applying lessons from the past to ease technology introduction. Today, rather than seeing themselves being embedded in a linear model of technology development, social scientists take an interest in developments ‘upstream’ where technologies take shape.     

Advanced technologies for genetically manipulating the silkworm Bombyx mori,a model Lepidopteran insect

Genetic technologies based on transposon-mediated transgenesis along with several recently developed genome-editing technologies have become the preferred methods of choice for genetically manipulating many organisms. The silkworm, Bombyx mori, is a Lepidopteran insect of great economic importance because of its use in silk production and because it is a valuable model insect that has greatly enhanced our understanding of the biology of insects, including many agricultural pests. In the past 10 years, great advances have been achieved in the development of genetic technologies in B. mori, including transposon-based technologies that rely on piggyBac-mediated transgenesis and genome-editing technologies that rely on protein- or RNA-guided modification of chromosomes. The successful development and application of these technologies has not only facilitated a better understanding of B. mori and its use as a silk production system, but also provided valuable experiences that have contributed to the development of similar technologies in non-model insects. This review summarizes the technologies currently available for use in B. mori, their application to the study of gene function and their use in genetically modifying B. mori for biotechnology applications. The challenges, solutions and future prospects associated with the development and application of genetic technologies in B. mori are also discussed.     

Metabolomics: building on a century of biochemistry to guide human health

Medical diagnosis and treatment efficacy will improve significantly when a more personalized system for health assessment is implemented. This system will require diagnostics that provide sufficiently detailed information about the metabolic status of individuals such that assay results will be able to guide food, drug and lifestyle choices to maintain or improve distinct aspects of health without compromising others. Achieving this goal will use the new science of metabolomics – comprehensive metabolic profiling of individuals linked to the biological understanding of human integrative metabolism. Candidate technologies to accomplish this goal are largely available, yet they have not been brought into practice for this purpose. Metabolomic technologies must be sufficiently rapid, accurate and affordable to be routinely accessible to both healthy and acutely ill individuals. The use of metabolomic data to predict the health trajectories of individuals will require bioinformatic tools and quantitative reference databases. These databases containing metabolite profiles from the population must be built, stored and indexed according to metabolic and health status. Building and annotating these databases with the knowledge to predict how a specific metabolic pattern from an individual can be adjusted with diet, drugs and lifestyle to improve health represents a logical application of the biochemistry knowledge that the life sciences have produced over the past 100 years.     

Will genomics guide a greener forest biotech?

Forest biotechnology has been increasingly associated with wood production using plantation forestry, and has stressed applications that use pedigreed material and transgenic trees. Reasons for this emphasis include limitations of available technologies to conform to underlying genetic features of undomesticated forest tree populations. More recently, genomic technologies have rapidly begun to expand the scope of forest biotechnology. Genomic technologies are well suited to describe and make use of the abundant genetic variation present in undomesticated forest tree populations. Genomics thus enables new research and applications for conservation and management of natural forests, and is a primary technological driver for new research addressing the use of forests trees for carbon sequestration, biofuels feedstocks, and other 'green' applications.