Metabolic engineering

Metabolic engineering has developed as a very powerful approach to optimising industrial fermentation processes through the introduction of directed genetic changes using recombinant DNA technology. Successful metabolic engineering starts with a careful analysis of cellular function; based on the results of this analysis, an improved strain is designed and subsequently constructed by genetic engineering. In recent years some very powerful tools have been developed, both for analysing cellular function and for introducing directed genetic changes. In this paper, some of these tools are reviewed and many examples of metabolic engineering are presented to illustrate the power of the technology. The examples are categorised according to the approach taken or the aim: (1) heterologous protein production, (2) extension of substrate range, (3) pathways leading to new products, (4) pathways for degradation of xenobiotics, (5) improvement of overall cellular physiology, (6) elimination or reduction of by-product formation, and (7) improvement of yield or productivity.     

Microlitre/millilitre shaken bioreactors in fermentative and biotransformation processes – a review

The use of small-scale vessels (below 100?mL) as tools for the characterization of fermentative and biotransformation processes is an emergent approach, which may provide a wide array of data with significant time and cost savings. These result from the reduced reagent requirements and the possibility of simultaneously carrying out the evaluation of multiple operational parameters and assessing their individual or combined effect in the process. Furthermore, it is envisaged that such data will provide the basis for a rational scale-up of the systems evaluated. This requires an engineering approach, which has been integrated with the development of microscale technology. This review comprises recent findings related to the use and characterization of Erlenmeyer type flasks, test tubes and microtiter plates as bioreactors.     

Microlitre/millilitre shaken bioreactors in fermentative and biotransformation processes - a review

The use of small-scale vessels (below 100 mL) as tools for the characterization of fermentative and biotransformation processes is an emergent approach, which may provide a wide array of data with significant time and cost savings. These result from the reduced reagent requirements and the possibility of simultaneously carrying out the evaluation of multiple operational parameters and assessing their individual or combined effect in the process. Furthermore, it is envisaged that such data will provide the basis for a rational scale-up of the systems evaluated. This requires an engineering approach, which has been integrated with the development of microscale technology. This review comprises recent findings related to the use and characterization of Erlenmeyer type flasks, test tubes and microtiter plates as bioreactors.     

Towards a systems level analysis of health and nutrition

Although theoretical systems analysis has been available for over half a century, the recent advent of omic high-throughput analytical platforms along with the integration of individual tools and technologies has given rise to the field of modern systems biology. Coupled with information technology, bioinformatics, knowledge management and powerful mathematical models, systems biology has opened up new vistas in our understanding of complex biological systems. Currently there are two distinct approaches that include the inductively driven computational systems biology (bottom-up approach) and the deductive data-driven top-down analysis. Such approaches offer enormous potential in the elucidation of disease as well as defining key pathways and networks involved in optimal human health and nutrition. The tools and technologies now available in systems biology analyses offer exciting opportunities to develop the emerging areas of personalized medicine and individual nutritional profiling.     

Emerging novel functions of RNAs, and binary phenotype?

Loss-of-function technology has been one of the most popular knockout tools for the study of gene function in cell and developmental biology. This technology employs two basic approaches for elimination of the protein of interest. The morpholino antisense oligonucleotides approach relies on inhibiting translation of the given protein without degrading the cognate mRNA. The antisense deoxynucleotides and siRNA approach acts via removal of the mRNA template, which then prevents protein translation. In the latest approach, as well as in these genetic knockout approaches that eliminate or alter the level of mRNA transcribed from the gene of interest, the assumption is and always has been that the only relevant function of mRNA is to make a protein, and, thus, the effect of removing mRNA equals the effect of removing its protein function. However, the most recent studies of different biological systems point to completely novel and unexpected functions of the subpopulation of localized RNAs and suggest that, at least in some cases, the normal cell or embryo phenotype is in fact binary i.e. depends not only on the function of the protein but also on the autonomous function of its mRNA.     

Phytoremediation: an overview of metallic ion decontamination from soil

In recent years, phytoremediation has emerged as a promising ecoremediation technology, particularly for soil and water cleanup of large volumes of contaminated sites. The exploitation of plants to remediate soils contaminated with trace elements could provide a cheap and sustainable technology for bioremediation. Many modern tools and analytical devices have provided insight into the selection and optimization of the remediation process by plant species. This review describes certain factors for the phytoremediation of metal ion decontamination and various aspects of plant metabolism during metallic decontamination. Metal-hyperaccumulating plants, desirable for heavily polluted environments, can be developed by the introduction of novel traits into high biomass plants in a transgenic approach, which is a promising strategy for the development of effective phytoremediation technology. The genetic manipulation of a phytoremediator plant needs a number of optimization processes, including mobilization of trace elements/metal ions, their uptake into the root, stem and other viable parts of the plant and their detoxification and allocation within the plant. This upcoming science is expanding as technology continues to offer new, low-cost remediation options.     

Infectious disease in the Pleistocene: Old friends or old foes?

The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.     

A whole-genome shotgun optical map of Yersinia pestis strain KIM

Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.     

条件转基因技术研究的新进展

转基因技术是近20年发展起来的在体内研究基因功能的分子生物学方法之一,近年来在原有技术的基础上,取得了许多新进展。综述条件转基因技术研究的新进展。阐明转基因的诱导表达系统争条件基因剔除系统的原理、操作过程以及这两系统各自的优缺点。     

禽流感病毒跨种属感染人的机制研究进展

禽流感病毒(avian influenza virus,简称AIV)不仅引起禽类感染和流行,而且可以打破种属屏障(speciesbarrier)、引起人或其他哺乳动物感染和传播。近年来对人呼吸道抗禽流感病毒感染的非特异屏障机制、禽流感病毒对人感染的机制研究不断取得新的进展。     

Quantifying Traces of Tool Use: A Novel Morphometric Analysis of Damage Patterns on Percussive Tools

Percussive technology continues to play an increasingly important role in understanding the evolution of tool use. Comparing the archaeological record with extractive foraging behaviors in nonhuman primates has focused on percussive implements as a key to investigating the origins of lithic technology. Despite this, archaeological approaches towards percussive tools have been obscured by a lack of standardized methodologies. Central to this issue have been the use of qualitative, non-diagnostic techniques to identify percussive tools from archaeological contexts. Here we describe a new morphometric method for distinguishing anthropogenically-generated damage patterns on percussive tools from naturally damaged river cobbles. We employ a geomatic approach through the use of three-dimensional scanning and geographical information systems software to statistically quantify the identification process in percussive technology research. This will strengthen current technological analyses of percussive tools in archaeological frameworks and open new avenues for translating behavioral inferences of early hominins from percussive damage patterns.     

Mechanistic modelling of the three waves of the 1918 influenza pandemic

Influenza pandemics through history have shown very different patterns of incidence, morbidity and mortality. In particular, pandemics in different times and places have shown anywhere from one to three “waves” of incidence. Understanding the factors that underlie variability in temporal patterns, as well as patterns of morbidity and mortality, is important for public health planning. We use a likelihood-based approach to explore different potential explanations for the three waves of incidence and mortality seen in the 1918 influenza pandemic in London, England. Our analysis suggests that temporal variation in transmission rate provides the best proximate explanation and that the variation in transmission required to generate these three epidemic waves is within biologically plausible values.     

Artificial antigen-presenting cells as a tool to exploit the immune 'synapse'

Recent progress in molecular medicine has provided important tools to identify antigen-specific T cells. In most cases, the approach is based on oligomeric combinations of recombinant major histocompatibility complex-peptide complexes fixed to various rigid supports available for binding by the T-cell receptor. These tools have greatly increased our insight into mechanisms of immune responses mediated by CD8+ T cells. Examples of the diverse fields of application for this technology include immunization, viral infections and oral tolerance induction.     

Production of high-value compounds: carotenoids and vitamin E

The unraveling in recent years of the pathways and genes that are responsible for biosynthesis of vitamins and carotenoids in plants has provided new molecular tools that can be utilized to genetically modify the content and composition of these compounds in vivo. There have been recent examples of successful manipulation of carotenoid composition and vitamin E activity in plants using gene-transfer technology.     

Reassortment Patterns in Swine Influenza Viruses

Three human influenza pandemics occurred in the twentieth century, in 1918, 1957, and 1968. Influenza pandemic strains are the results of emerging viruses from non-human reservoirs to which humans have little or no immunity. At least two of these pandemic strains, in 1957 and in 1968, were the results of reassortments between human and avian viruses. Also, many cases of swine influenza viruses have reportedly infected humans, in particular, the recent H1N1 influenza virus of swine origin, isolated in Mexico and the United States. Pigs are documented to allow productive replication of human, avian, and swine influenza viruses. Thus it has been conjectured that pigs are the “mixing vessel” that create the avian-human reassortant strains, causing the human pandemics. Hence, studying the process and patterns of viral reassortment, especially in pigs, is a key to better understanding of human influenza pandemics. In the last few years, databases containing sequences of influenza A viruses, including swine viruses, collected since 1918 from diverse geographical locations, have been developed and made publicly available. In this paper, we study an ensemble of swine influenza viruses to analyze the reassortment phenomena through several statistical techniques. The reassortment patterns in swine viruses prove to be similar to the previous results found in human viruses, both in vitro and in vivo, that the surface glycoprotein coding segments reassort most often. Moreover, we find that one of the polymerase segments (PB1), reassorted in the strains responsible for the last two human pandemics, also reassorts frequently.     

Extracting haplotypes from diploid organisms

Each diploid organism has two alleles at every gene locus. In sexual organisms such as most plants, animals and fungi, the two alleles in an individual may be genetically very different from each other. DNA sequence data from individual alleles (called a haplotype) can provide powerful information to address a variety of biological questions and guide many practical applications. The advancement in molecular technology and computational tools in the last decade has made obtaining large-scale haplotypes feasible. This review summarizes the two basic approaches for obtaining haplotypes and discusses the associated techniques and methods. The first approach is to experimentally obtain diploid sequence information and then use computer algorithms to infer haplotypes. The second approach is to obtain haplotype sequences directly through experimentation. The advantages and disadvantages of each approach are discussed. I then discussed a specific example on how the direct approach was used to obtain haplotype information to address several fundamental biological questions of a pathogenic yeast. With increasing sophistication in both bioinformatics tools and high-throughput molecular techniques, haplotype analysis is becoming an integrated component in biomedical research.     

Implementation of quality by design toward processing of food products

Quality by design (QbD) is a systematic approach that begins with predefined objectives and emphasizes product and process understanding and process control. It is an approach based on principles of sound science and quality risk management. As the food processing industry continues to embrace the idea of in-line, online, and/or at-line sensors and real-time characterization for process monitoring and control, the existing gaps with regard to our ability to monitor multiple parameters/variables associated with the manufacturing process will be alleviated over time. Investments made for development of tools and approaches that facilitate high-throughput analytical and process development, process analytical technology, design of experiments, risk analysis, knowledge management, and enhancement of process/product understanding would pave way for operational and economic benefits later in the commercialization process and across other product pipelines. This article aims to achieve two major objectives. First, to review the progress that has been made in the recent years on the topic of QbD implementation in processing of food products and second, present a case study that illustrates benefits of such QbD implementation.     

An integrative approach for the identification of quantitative trait loci

The genetic dissection of complex traits is one of the most difficult and most important challenges facing science today. We discuss here an integrative approach to quantitative trait loci (QTL) mapping in mice. This approach makes use of the wealth of genetic tools available in mice, as well as the recent advances in genome sequence data already available for a number of inbred mouse strains. We have developed mapping strategies that allow a stepwise narrowing of a QTL mapping interval, prioritizing candidate genes for further analysis with the potential of identifying the most probable candidate gene for the given trait. This approach integrates traditional mapping tools, fine mapping tools, sequence-based analysis, bioinformatics and gene expression.