New tools for recombinant protein production in Escherichia coli: A 5‐year update

The production of proteins in sufficient amounts is key for their study or use as biotherapeutic agents. Escherichia coli is the host of choice for recombinant protein production given its fast growth, easy manipulation, and cost‐effectiveness. As such, its protein production capabilities are continuously being improved. Also, the associated tools (such as plasmids and cultivation conditions) are subject of ongoing research to optimize product yield. In this work, we review the latest advances in recombinant protein production in E. coli.     

转基因植物疫苗的研究进展

利用转基因植物作为生物反应器生产疫苗是一个新兴的技术领域,它具有生产简便、成本低廉,不需要冷藏和低温运输,安全性好,无外源性病原污染等优点。概述当前转基因植物疫苗的研究进展,并就转基因植物疫苗的作用机理及原理方法进行了介绍。     

New concept of contaminant removal from swine wastewater by a biological treatment process

Pollution from concentrated animal feeding operations (CAFOs) are the most serious pollution source in China now, and swine wastewater contains high concentrations of nutrients such as chemical oxygen demand (COD), biochemical oxygen demand 5 (BOD₅), ammonium, and emergent contaminants related to public health. Biological processes are the most popular treatment methods for COD and ammonium removal. Considering the low operation cost, easy maintenance and high removal rate of contaminants in recent years, nitrogen removal via nitrite and real-time control processes using oxidation-reduction potential (ORP) and/or pH as parameters to control the aerobic and anaerobic cycles of a system has received much attention for animal wastewater treatment. During the biological treatment process, the emergent contaminants such as estrogen, antibiotics, and disinfection reagents have been the focus of research recently, and degradation bacteria and resistance bacteria have also been extracted from activated sludge. The microbial analysis technique is also advancement in the field of biodegradation bacteria and resistance bacteria. All of these advancements in research serve to improve wastewater treatment and decrease environmental hazards, especially for using manure as a fertilizer source for crop production.     

Archivierung von Genomdaten

In view of the increasing amount of data arising from genome research, efficient research data management is becoming increasingly important in this domain. The third, and last, article of the series on “Research data management for genome data” describes the general lifecycle of research data—from their planning via the selection and inclusion into storage facilities to preservation measures and final user access. Archives play an important role in nearly all phases of this life cycle, which renders them an important component of genome data processing. Three exemplary public archives for genome data are introduced: the European Molecular Biology Laboratory (EMBL) databank, the Sequence Read Archive, and the Trace Archive. Owing to the high level of specialization of these institutions, however, additional archives are required that allow more generic data storage or, alternatively, easy extension to other genome data types. A generic concept for such archives will be described and recommendations given for their practical implementation.     

The National Climate Laboratory-an Unappreciated Tool for Ecological Research

[First paragraph(s)...]“A freezing chamber offers an easy place for such [frost] experiments... and ... valuable data as to the cold-resisting powers of our plants might be arrived at” (Cockayne, 1897). The National Climate Laboratory was opened in 1970 and has been operating for the past 25 years (recently celebrating its anniversary) for both national and international scientists carrying out environmental research on plants and animals (Halligan, 1995). The facilities have been used by a wide range of plant and animal based researchers from the pastoral, horticultural, and forestry sectors involving a range of disciplines from agronomy, pathology, entomology, physiology, plant breeding and zoology. New Zealand ecologists have been conspicuously absent (in spite of the potential in controlled environment research seen by pioneering ecologists—see above quotation) and yet there has been a range of activities that are complementary to this discipline.     

Bacillus subtilis as potential producer for polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by microbes to overcome environmental stress. Commercial production of PHAs is limited by the high cost of production compared to conventional plastics. Another hindrance is the brittle nature and low strength of polyhydroxybutyrate (PHB), the most widely studied PHA. The needs are to produce PHAs, which have better elastomeric properties suitable for biomedical applications, preferably from inexpensive renewable sources to reduce cost. Certain unique properties of Bacillus subtilis such as lack of the toxic lipo-polysaccharides, expression of self-lysing genes on completion of PHA biosynthetic process – for easy and timely recovery, usage of biowastes as feed enable it to compete as potential candidate for commercial production of PHA.     

Dunaliella as an attractive candidate for molecular farming

Pharmaceutical recombinant proteins are widely used in human healthcare. At present, several protein expression systems are available to generate therapeutic proteins. These conventional systems have distinct advantages and disadvantages in protein yielding; in terms of ease of manipulation, the time required from gene transformation to protein purification, cost of production and scaling-up capitalization, proper folding and stability of active proteins. Depending on the research goal and priorities, a special system may be selected for protein expression. However, considering the limited variety of organisms currently used and their usage restrictions, there are still much more pharmaceutical proteins waiting to be economically and efficiently produced. Distinguished biological and technical features of microalgae Dunaliella such as inexpensive medium requirement, fast growth rate, the ease of manipulation, easy scaling up procedure, facility of milking in bioreactors and the ability of post-translational modifications make this microorganism an attractive candidate for molecular farming.     

Exosomes derived from uMSCs promote hair regrowth in alopecia areata through accelerating human hair follicular keratinocyte proliferation and migration

Alopecia areata (AA) is a complex genetic disease that results in hair loss due to an autoimmune-mediated attack on the hair follicle. Mesenchymal stem cells (MSCs) have great potential to induce hair regeneration due to their strong secretion ability and multidirectional differentiation. Recent studies have revealed that the therapeutic potential of MSCs comes from their secretion ability, which can produce large amounts of bioactive substances and regulate the key physiological functions of subjects. The secretion products of MSCs, such as vesicles, exosomes, and conditioned media, have significant advantages in preparing of biological products derived from stem cells. Human umbilical cord mesenchymal stem cells (uMSCs) are the best choice for exosome production. uMSCs are obtained from the human umbilical cord. The umbilical cord is easy to obtain, and the efficiency of uMSCs isolation and culture higher than that of obtaining MSCs from bone marrow or adipose tissue. In this study, we investigated the effects of exosomes released from uMSCs in AA mice. In summary, due to easy isolation and cultivation, simple preparation, and convenient storage, it is possible to obtain uMSCs, or uMSCs exosomes for research and clinical treatment.     

海藻酸分解菌研究进展

海藻酸分解菌是一类能够自身合成海藻酸裂解酶,能够降解并同化海藻酸的微生物。海藻酸分解菌是海藻酸裂解酶的重要来源,其产生的海藻酸裂解酶具有种类多、反应条件温和、酶活高和易于大规模生产等优点,并且在生物、医疗、化工等领域有重要的应用价值。在过去的几十年里,海藻酸分解菌一直作为海藻酸裂解酶生产者的角色被研究和应用。但随着近年来能源危机的加剧,以海藻酸等海藻生物质为原料转化生物能源成为解决能源危机的潜在途径,因此,海藻酸分解菌又有了崭新的研究领域,即海藻酸分解菌利用海藻酸发酵生产生物能源。本文从海藻酸分解菌及其海藻酸裂解酶的种类和特性、海藻酸分解菌的代谢以及海藻酸分解菌基因工程等方面,介绍海藻酸分解菌的研究现状,并展望未来的发展趋势。     

The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications

Background

Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms.

Methodology/Principal Findings

We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins. The network includes the core circuit of Oct4 (Pou5f1), Sox2 and Nanog, its periphery (such as Stat3, Klf4, Esrrb, and c-Myc), connections to upstream signaling pathways (such as Activin, WNT, FGF, BMP, Insulin, Notch and LIF), and epigenetic regulators as well as some other relevant genes/proteins, such as proteins involved in nuclear import/export. We describe the general properties of the network, as well as a Gene Ontology analysis of the genes included. We use several expression data sets to condense the network to a set of network links that are affected in the course of an experiment, yielding hypotheses about the underlying mechanisms.

Conclusions/Significance

We have initiated an electronic data repository that will be useful to understand pluripotency and to facilitate the interpretation of high-throughput data. To keep up with the growth of knowledge on the fundamental processes of pluripotency and reprogramming, we suggest to combine Wiki and social networking software towards a community curation system that is easy to use and flexible, and tailored to provide a benefit for the scientist, and to improve communication and exchange of research results. A PluriNetWork tutorial is available at http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork/.     

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

Background

The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data.

Results

Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research.

Conclusions

The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.     

Developments in Wood and Packaging Materials Life Cycle Inventories in ecoinvent (9 pp)

Goal, Scope and Background This paper gives an overview on how the wood and packaging material production is inventoried in ecoinvent. Packaging materials have been a very important topic in the area of Life Cycle Assessment for more than twenty years. Wood is the most important renewable material and regenerative fuel used worldwide, and an important raw material for paper / board. Several methodological problems arising when inventorying wood for material and energetic uses in a generic database are discussed in more detail. Within the ecoinvent project, the Swiss data base for life cycle inventory data, two reports are dedicated to these two important topics – report No. 9 for wood and report No. 11 for packaging materials. Methods The whole wood chain has been modeled in a consistent way. This allows one to use this data for LCAs of building materials, bioenergy or paper production. The data represent average technologies used in Central Europe in the year 2000. A revenue-based co-product allocation approach is used for the different outputs. Correction factors are introduced for the consistent modeling of mass-based, material inherent wood properties such as solar energy, carbon uptake and land use. For packaging materials, the datasets represent European average data for the most often used materials as well as specific datasets for the production of actual packaging boxes and containers.Results and Discussion For wood, revenue-based allocation and the use of the correction factors for mass-related wood properties are shown and explained. For packaging materials, the importance of the raw material wood to the total load is shown. Furthermore trends in the data inventories for board packaging materials over the last two decades are discussed: mainly due to the increased comprehensiveness of the data, higher cumulative emissions can be observed. Conclusion For wood, the database ecoinvent provides consistent datasets for the entire chain from forestry to intermediate products such as timber, different types of wood-based boards, chips, pellets, etc. For packaging materials, the number of datasets of basic materials has been extended. A modular concept for actual packaging container datasets allows the user an easy modeling of various types of packaging containers/boxes. In the area of paper and board, a comprehensive database for the production of various types of pulp, paper and board is provided, which is representative for the average European production situation. Outlook Since wood is only limited and representative data for Europe is therefore not included, an update in the near future would be reasonable. Possible further extensions in the future could include various, final wooden products. For the data on paper/board, different levels of quality are observed, requiring a selective up-date of these data. Future extensions could include datasets for the import of pulp from overseas – especially from South America and Canada.     

Socio-ecological biotechnology concepts for developing countries

Conclusions The two socio-ecological concepts described will work, of course, also with other microorganisms.Zymomonas mobilis can be replaced by yeast,Rhizopus could be replaced byAspergillus. However, both microorganisms which are presently used can produce by-products that are unsafe for human or animal consumption. It is therefore a microbiological challenge to find further microorganisms to expand the product formation.It should also be realized that the largest renewable resource, cellulose, has not been mentioned in the context of either concept. It is well known that cellulose must eventually be included if research and development can find ways and means to separate lignin from cellulose and convert cellulose to glucose in a similar and as easy a manner as starch (Doelle 1984).In order to be successful, fermentation processes have to be fast and efficient with a low energy input (Doelle 1986a, b; Doelle & Jones 1986). This excludes the traditional microbiological sterilization of substrates, excessive substrate or product inhibitions in any of these processes.A further omission of socio-ecological concepts lies in the fermented food production. It is encouraging to see the realization that fermented foods are mixedculture processes and that it is time to start detailed and extensive investigations into the functioning of such cultures (Doelle 1985; Steinkraus 1987; Okagbu 1988; Odunfa 1988). It is the suggestion of the author to encourage a review on mixed culture with particular emphasis on fermented food production and its waste disposal.     

蓝细菌固碳合成乳酸技术的发展与展望

乳酸是一种重要的工业化学品,被广泛应用于各个行业。近年来,随着聚乳酸(PLA)市场的兴起,乳酸原料的需求也在不断增加。糖基异养生产乳酸所带来的高昂成本与市场需求的矛盾吸引着研究人员积极寻找其他有利的解决方案。蓝细菌光合固碳生产乳酸是一种潜力巨大的新型原料供应策略,基于光合自养的细胞工厂,可以在单一平台上以太阳能为驱动力,从二氧化碳中直接生产出高光学纯度的乳酸。该方法原料廉价易得、过程简单可控、产物明确且易分离,同时达到节能减排和高附加值产品生产的双重效果,具有重要的研究与应用价值。文中回顾了蓝细菌固碳产乳酸技术的发展历程,从代谢基础、代谢工程策略、代谢动力学分析与技术应用等方面,梳理其研究进展和所遇到的技术难点,并对该技术的未来进行展望。     

脱落酸生物合成研究进展

脱落酸作为一种抑制生长的植物激素,是平衡植物内源激素和调节生长代谢的关键因子。脱落酸具有提高作物抗旱耐盐、减少果实褐变的作用,同时可降低疟疾发病率、刺激胰岛素分泌,因此在农业和医药领域有着广阔的应用前景。相较于传统的植物提取法和化学合成法,利用微生物合成脱落酸是一种经济、可持续的来源方式。目前利用天然微生物如灰葡萄孢霉菌、蔷薇色尾孢菌等合成脱落酸的研究已经取得了诸多进展,而脱落酸的异源微生物合成研究相对较少。酿酒酵母、解脂耶氏酵母、大肠杆菌等工程菌株作为天然产物异源合成的常用宿主,具有遗传背景清晰、易于操作、便于工业化生产等优势,因此利用微生物异源合成脱落酸是一种更具潜力的生产方式。本文着重从底盘细胞的选择、关键酶的筛选与表达强化、辅因子的调节、增强前体供应及促进脱落酸外排5个方面对微生物异源合成脱落酸的研究进行综述。最后,对该领域的未来发展方向进行了展望。     

New concept of contaminant removal from swine wastewater by a biological treatment process

Pollution from concentrated animal feeding operations (CAFOs) are the most serious pollution source in China now, and swine wastewater contains high concentrations of nutrients such as chemical oxygen demand (COD), biochemical oxygen demand 5 (BOD5), ammonium, and emergent contaminants related to public health. Biological processes are the most popular treatment methods for COD and ammonium removal. Considering the low operation cost, easy maintenance and high removal rate of contaminants in recent years, nitrogen removal via nitrite and real-time control processes using oxidation-reduction potential (ORP) and/or pH as parameters to control the aerobic and anaerobic cycles of a system has received much attention for animal wastewater treatment. During the biological treatment process, the emergent contaminants such as estrogen, antibiotics, and disinfec-tion reagents have been the focus of research recently, and degradation bacteria and resistance bacteria have also been extracted from activated sludge. The microbial analysis technique is also advancement in the field of biodegrada-tion bacteria and resistance bacteria. All of these advance-ments in research serve to improve wastewater treatment and decrease environmental hazards, especially for using manure as a fertilizer source for crop production.     

Implantation of Radiotelemetry Transmitters Yielding Data on ECG, Heart Rate, Core Body Temperature and Activity in Free-moving Laboratory Mice

The laboratory mouse is the animal species of choice for most biomedical research, in both the academic sphere and the pharmaceutical industry. Mice are a manageable size and relatively easy to house. These factors, together with the availability of a wealth of spontaneous and experimentally induced mutants, make laboratory mice ideally suited to a wide variety of research areas.In cardiovascular, pharmacological and toxicological research, accurate measurement of parameters relating to the circulatory system of laboratory animals is often required. Determination of heart rate, heart rate variability, and duration of PQ and QT intervals are based on electrocardiogram (ECG) recordings. However, obtaining reliable ECG curves as well as physiological data such as core body temperature in mice can be difficult using conventional measurement techniques, which require connecting sensors and lead wires to a restrained, tethered, or even anaesthetized animal. Data obtained in this fashion must be interpreted with caution, as it is well known that restraining and anesthesia can have a major artifactual influence on physiological parameters^{1, 2}.Radiotelemetry enables data to be collected from conscious and untethered animals. Measurements can be conducted even in freely moving animals, and without requiring the investigator to be in the proximity of the animal. Thus, known sources of artifacts are avoided, and accurate and reliable measurements are assured. This methodology also reduces interanimal variability, thus reducing the number of animals used, rendering this technology the most humane method of monitoring physiological parameters in laboratory animals^{3, 4}. Constant advancements in data acquisition technology and implant miniaturization mean that it is now possible to record physiological parameters and locomotor activity continuously and in realtime over longer periods such as hours, days or even weeks^{3, 5}.Here, we describe a surgical technique for implantation of a commercially available telemetry transmitter used for continuous measurements of core body temperature, locomotor activity and biopotential (i.e. onelead ECG), from which heart rate, heart rate variability, and PQ and QT intervals can be established in freeroaming, untethered mice. We also present pre-operative procedures and protocols for post-operative intensive care and pain treatment that improve recovery, well-being and survival rates in implanted mice^{5, 6}.     

From the genetic to the computer program: the historicity of 'data' and 'computation' in the investigations on the nematode worm C. elegans (1963-1998)

This paper argues that the history of the computer, of the practice of computation and of the notions of 'data' and 'programme' are essential for a critical account of the emergence and implications of data-driven research. In order to show this, I focus on the transition that the investigations on the worm C. elegans experienced in the Laboratory of Molecular Biology of Cambridge (UK). Throughout the 1980s, this research programme evolved from a study of the genetic basis of the worm's development and behaviour to a DNA mapping and sequencing initiative. By examining the changing computing technologies which were used at the Laboratory, I demonstrate that by the time of this transition researchers shifted from modelling the worm's genetic programme on a mainframe apparatus to writing minicomputer programs aimed at providing map and sequence data which was then circulated to other groups working on the genetics of C. elegans. The shift in the worm research should thus not be simply explained in the application of computers which transformed the project from hypothesis-driven to a data-intensive endeavour. The key factor was rather a historically specific technology-in-house and easy programmable minicomputers-which redefined the way of achieving the project's long-standing goal, leading the genetic programme to co-evolve with the practices of data production and distribution.