红霉素生物合成的分子生物学

近年来,国外对大环内酯类抗生素生物合成和基因工程的研究非常迅速,不仅认识了许多抗生素生物合成的过程,而且利用基因工程技术改造抗生素生物合成基因,合成了100多种非天然的“天然”抗生素。抗生素生物合成的分子生物学是抗生素基因工程的基础。本全面介绍了五厌内酯类抗生素的代表－红霉素生物合成分子生物学的历史、现状及发展趋势。     

Modelling ethanol production from cellulose: separate hydrolysis and fermentation versus simultaneous saccharification and fermentation

In ethanol production from cellulose, enzymatic hydrolysis, and fermentative conversion may be performed sequentially (separate hydrolysis and fermentation, SHF) or in a single reaction vessel (simultaneous saccharification and fermentation, SSF). Opting for either is essentially a trade-off between optimal temperatures and inhibitory glucose concentrations on the one hand (SHF) vs. sub-optimal temperatures and ethanol-inhibited cellulolysis on the other (SSF). Although the impact of ethanol on cellobiose hydrolysis was found to be negligible, formation of glucose and cellobiose from cellulose were found to be significantly inhibited by ethanol. A previous model for the kinetics of enzymatic cellulose hydrolysis was, therefore, extended with enzyme inhibition by ethanol, thus allowing a rational evaluation of SSF and SHF. The model predicted SSF processing to be superior. The superiority of SSF over SHF (separate hydrolysis and fermentation) was confirmed experimentally, both with respect to ethanol yield on glucose (0.41 g g^?1 for SSF vs. 0.35 g g^?1 for SHF) and ethanol production rate, being 30% higher for an SSF type process. High conversion rates were found to be difficult to achieve since at a conversion rate of 52% in a SSF process the reaction rate dropped to 5% of its initial value. The model, extended with the impact of ethanol on the cellulase complex proved to predict reaction progress accurately.     

鱼类生殖细胞移植的研究进展

生殖细胞移植在生物学、畜牧学及兴起的鱼类生物工程上都有很多用途。目前,采用基于基因组的育种方法已选育出多种带有所需遗传性状的鱼类新品系;但由于缺乏鱼卵与胚胎的低温保存技术,尚未找到长期保存其种质资源的方法。就鱼类生殖细胞移植的最新研究进展进行综述,同时针对鱼类生殖细胞移植及其低温保存技术研究中存在的问题进行讨论,并提出了鱼类生殖细胞移植的应用前景,以期能积极推动鱼类生物工程的研究,加速鱼类生殖细胞移植在产业中的应用。     

用氨基葡萄糖含量的测定值间接表示红曲菌固态发酵过程中生物量的研究

【目的】为准确快速地了解紫色红曲菌固态发酵中生物量的变化,【方法】采用理化方法测定菌体量和氨基葡萄糖含量,研究了不同培养时间、培养基组成、培养方式下菌体量与氨基葡萄糖含量的关系,建立生物量和氨基葡萄糖含量的换算关系式;构建关联该菌固态培养物近红外光谱数据与实测氨基葡萄糖含量的PLS模型。【结果】建立了可通过近红外光谱法测定氨基葡萄糖来快速预测固态发酵生物量的方法,其中最优近红外模型的校正集内部交叉验证均方根误差(RMSECV)为0.209 4,预测集相关系数(Rp)和均方根误差(RMSEP)分别为0.993 4和0.217 3;同时利用所建的换算关系式也大大提高了生物量计算的准确性。【结论】基于所建立的生物量和氨基葡萄糖的换算关系式,利用近红外光谱法可以快速并且较准确地测定紫色红曲菌固态发酵过程中生物量的变化。     

Solid-state fermentation--are there any biotechnological advantages?

Solid-state fermentation (SSF) has developed in eastern countries over many centuries, and has enjoyed broad application in these regions to date. By contrast, in western countries the technique had to compete with classical submerged fermentation and, because of the increasing pressure of rationalisation and standardisation, it has been widely superseded by classical submerged fermentation since the 1940s. This is mainly because of problems in engineering that appear when scaling up this technique. However, there are several advantages of SSF, for example high productivities, extended stability of products and low production costs, which say much about such an intensive biotechnological application. With increasing progress and application of rational methods in engineering, SSF will achieve higher levels in standardisation and reproducibility in the future. This can make SSF the preferred technique for special fields of application such as the production of enzymes and food.     

Biotechnological advantages of laboratory-scale solid-state fermentation with fungi

Despite the increasing number of publications dealing with solid-state (substrate) fermentation (SSF) it is very difficult to draw general conclusion from the data presented. This is due to the lack of proper standardisation that would allow objective comparison with other processes. Research work has so far focused on the general applicability of SSF for the production of enzymes, metabolites and spores, in that many different solid substrates (agricultural waste) have been combined with many different fungi and the productivity of each fermentation reported. On a gram bench-scale SSF appears to be superior to submerged fermentation technology (SmF) in several aspects. However, SSF up-scaling, necessary for use on an industrial scale, raises severe engineering problems due to the build-up of temperature, pH, O₂, substrate and moisture gradients. Hence, most published reviews also focus on progress towards industrial engineering. The role of the physiological and genetic properties of the microorganisms used during growth on solid substrates compared with aqueous solutions has so far been all but neglected, despite the fact that it may be the microbiology that makes SSF advantageous against the SmF biotechnology. This review will focus on research work allowing comparison of the specific biological particulars of enzyme, metabolite and/or spore production in SSF and in SmF. In these respects, SSF appears to possess several biotechnological advantages, though at present on a laboratory scale only, such as higher fermentation productivity, higher end-concentration of products, higher product stability, lower catabolic repression, cultivation of microorganisms specialized for water-insoluble substrates or mixed cultivation of various fungi, and last but not least, lower demand on sterility due to the low water activity used in SSF.     

水稻抗性转基因研究进展

随着水稻遗传转化技术的发展,通过基因工程手段获得抗病虫草害及逆境水稻品种成为可能。本文综述了近年来国内外水稻抗性转基因的技术、方法和策略等研究现状、发展趋势、存在的问题及解决方法,对水稻抗性转基因在水稻育种上的应用也作了评价。     

The microbial degradation of azo dyes: minireview

The removal of dyes in wastewater treatment plants still involves physical or chemical processes. Yet numerous studies currently exist on degradation based on the use of microbes—which is a well-studied field. However progress in the use of biological methods to deal with this environmentally noxious waste is currently lacking. This review focuses on the largest dye class, that is azo dyes and their biodegradation. We summarize the bacteria identified thus far which have been implicated in dye decolorization and discuss the enzymes involved and mechanisms by which these colorants are broken down.     

A short review on SSF - an interesting process option for ethanol production from lignocellulosic feedstocks

Simultaneous saccharification and fermentation (SSF) is one process option for production of ethanol from lignocellulose. The principal benefits of performing the enzymatic hydrolysis together with the fermentation, instead of in a separate step after the hydrolysis, are the reduced end-product inhibition of the enzymatic hydrolysis, and the reduced investment costs. The principal drawbacks, on the other hand, are the need to find favorable conditions (e.g. temperature and pH) for both the enzymatic hydrolysis and the fermentation and the difficulty to recycle the fermenting organism and the enzymes. To satisfy the first requirement, the temperature is normally kept below 37 degrees C, whereas the difficulty to recycle the yeast makes it beneficial to operate with a low yeast concentration and at a high solid loading. In this review, we make a brief overview of recent experimental work and development of SSF using lignocellulosic feedstocks. Significant progress has been made with respect to increasing the substrate loading, decreasing the yeast concentration and co-fermentation of both hexoses and pentoses during SSF. Presently, an SSF process for e.g. wheat straw hydrolyzate can be expected to give final ethanol concentrations close to 40 g L-1 with a yield based on total hexoses and pentoses higher than 70%.     

Computational studies of the extraction of visual spatial information from binocular and motion cues

This paper reviews some of the contributions that work in computational vision has made to the study of biological vision systems. We concentrate on two areas where there has been strong interaction between computational and experimental studies: the use of binocular stereo to recover the distances to surfaces in space, and the recovery of the three-dimensional shape of objects from relative motion in the image. With regard to stereo, we consider models proposed for solving the stereo correspondence problem, focussing on the way in which physical properties of the world constrain possible methods of solution. We also show how critical observations regarding human stereo vision have helped to shape these models. With regard to the recovery of structure from motion, we focus on how the constraint of object rigidity has been used in computational models of this process.     

Advances on in vitro production and cryopreservation of porcine embryos

There have been intensive attempts to establish reliable in vitro production (IVP) and cryopreservation methods of embryos in pigs. Although a great deal of progress has been made, current IVP systems and cryopreservation still suffer from insufficient cytoplasmic abilities of in vitro matured oocytes, polyspermic fertilization, poor quality of in vitro produced embryos and low efficiency of embryo cryopreservation. Compared to other mammalian species, pig oocytes and embryos are characterized by large amounts of lipid content stored mainly in the form of lipid droplets in the cytoplasm. This fact has a negative influence on biotechnological applications on porcine oocytes and embryos. In this review, we will discuss recent studies about methods and techniques for modifying porcine embryo IVP system and embryo cryopreservation that produces high quality of pig blastocysts using in vitro maturation, in vitro fertilization, in vitro culture, microsurgical manipulation, addition of protein, the use of cytoskeleton stabilizing agents and various physical methods. The presented methods and techniques make it possible to modify the characteristics of oocytes and embryos and thus may become major tools in mammalian gamete and embryo agricultural or biotechnological applications in the future.     

Parameter inference for stochastic biochemical models from perturbation experiments parallelised at the single cell level

Understanding and characterising biochemical processes inside single cells requires experimental platforms that allow one to perturb and observe the dynamics of such processes as well as computational methods to build and parameterise models from the collected data. Recent progress with experimental platforms and optogenetics has made it possible to expose each cell in an experiment to an individualised input and automatically record cellular responses over days with fine time resolution. However, methods to infer parameters of stochastic kinetic models from single-cell longitudinal data have generally been developed under the assumption that experimental data is sparse and that responses of cells to at most a few different input perturbations can be observed. Here, we investigate and compare different approaches for calculating parameter likelihoods of single-cell longitudinal data based on approximations of the chemical master equation (CME) with a particular focus on coupling the linear noise approximation (LNA) or moment closure methods to a Kalman filter. We show that, as long as cells are measured sufficiently frequently, coupling the LNA to a Kalman filter allows one to accurately approximate likelihoods and to infer model parameters from data even in cases where the LNA provides poor approximations of the CME. Furthermore, the computational cost of filtering-based iterative likelihood evaluation scales advantageously in the number of measurement times and different input perturbations and is thus ideally suited for data obtained from modern experimental platforms. To demonstrate the practical usefulness of these results, we perform an experiment in which single cells, equipped with an optogenetic gene expression system, are exposed to various different light-input sequences and measured at several hundred time points and use parameter inference based on iterative likelihood evaluation to parameterise a stochastic model of the system.     

A short review on SSF – an interesting process option for ethanol production from lignocellulosic feedstocks

Simultaneous saccharification and fermentation (SSF) is one process option for production of ethanol from lignocellulose. The principal benefits of performing the enzymatic hydrolysis together with the fermentation, instead of in a separate step after the hydrolysis, are the reduced end-product inhibition of the enzymatic hydrolysis, and the reduced investment costs. The principal drawbacks, on the other hand, are the need to find favorable conditions (e.g. temperature and pH) for both the enzymatic hydrolysis and the fermentation and the difficulty to recycle the fermenting organism and the enzymes. To satisfy the first requirement, the temperature is normally kept below 37°C, whereas the difficulty to recycle the yeast makes it beneficial to operate with a low yeast concentration and at a high solid loading. In this review, we make a brief overview of recent experimental work and development of SSF using lignocellulosic feedstocks. Significant progress has been made with respect to increasing the substrate loading, decreasing the yeast concentration and co-fermentation of both hexoses and pentoses during SSF. Presently, an SSF process for e.g. wheat straw hydrolyzate can be expected to give final ethanol concentrations close to 40 g L^-1 with a yield based on total hexoses and pentoses higher than 70%.     

Aspergillus oryzae in solid-state and submerged fermentations. Progress report on a multi-disciplinary project

We report the progress of a multi-disciplinary research project on solid-state fermentation (SSF) of the filamentous fungus Aspergillus oryzae. The molecular and physiological aspects of the fungus in submerged fermentation (SmF) and SSF are compared and we observe a number of differences correlated with the different growth conditions. First, the aerial hyphae which occur only in SSFs are mainly responsible for oxygen uptake. Second, SSF is characterised by gradients in temperature, water activity and nutrient concentration, and inside the hyphae different polyols are accumulating. Third, pelleted growth in SmF and mycelial growth in SSF show different gene expression and protein secretion patterns. With this approach we aim to expand our knowledge of mechanisms of fungal growth on solid substrates and to exploit the biotechnological applications.     

微生物进化工程育种技术进展与展望

进化工程是一项全基因组水平的新兴技术,它通过模拟自然进化中的变异和选择过程,实现对微生物菌株优良性状的选育。近年来,进化工程在扩大底物利用范围,提高代谢物产量及提高微生物的耐受性等方面取得了显著进展。介绍了进化工程的概念、特点及发展过程,叙述了进化工程的原理和研究方法,重点总结了进化工程方法在菌株改进方面的研究进展,最后对该技术的发展趋势和潜在应用进行了展望。     

传统与未来的碰撞：食品发酵工程技术与应用进展

随着生物技术的飞速发展,作为食品生物工程的主要组成部分,食品发酵工程技术不断升级,在传统发酵食品的菌种、发酵过程、产品品质得到改善的同时,生物制造的功能食品组分、未来食品等新型产品也应运而生。首先概述了由生物技术和信息技术的进步带来的食品发酵研究手段与生产方式的多层面变革,并重点阐释了利用食品合成生物学设计构建细胞工厂的思路和方法,以及食品生物工程在微生物分析、过程工程和分离工程方面的智能化进程。其次,介绍了现代食品生物工程技术在改善传统发酵食品品质及安全性、生产功能食品组分、添加剂和酶制剂、创制未来食品和开发新型益生食品方面的应用进展。最后,对全球和我国食品发酵产业面临的挑战和未来发展趋势进行了总结和展望,以期为食品发酵的技术革新和工业化应用提供参考。     

生物工程与生物物理

生物工程包含众多的领域如细胞工程、酶工程、膜工程、医学生物工程、基因工程、蛋白质工程等.在有限的篇幅内不可能涉及所有方面,本文仅选择遗传工程、蛋白质工程以及膜通道最新的一些进展谈一些粗浅看法,以期引起生物物理学工作者的兴趣来共同关心和促进生物工程有关领域的发展.     

Ethanol production from paper material using a simultaneous saccharification and fermentation system in a fed-batch basis

In this work, a recycled paper-derived feedstock was used to produce ethanol by the simultaneous saccharification and fermentation (SSF) process using the thermotolerant yeast Kluyveromyces marxianus CECT 10875. At standard SSF conditions, the highest yield (about 80% of theoretical) was obtained at low substrate concentration and high enzyme loading. With increasing substrate concentration, mixing difficulties appeared which prevented an adequate SSF process performance and limited ethanol production. An SSF fed-batch procedure was then used which permitted an increase in substrate concentrations while maintaining SSF yields similar to that obtained at standard SSF, thus allowing an increased final ethanol production (about 18 g/l).     

Standardization of the filter paper activity assay for solid substrate fermentation

The conditions of the filter paper activity (FPA) assay were standardized for solid substrate fermentation (SSF). The FPA is a relative measure of the overall cellulose hydrolysing capacity of microbial cellulase preparations, thus reliable and comparable data may be obtained only under standardized conditions. The standardization developed for submerged fermentation (SF) cannot be translated directly to SSF. In SSF, the FPA is strongly dependent on the extraction volume and on the dilution of the enzyme in the assay. The optimal extraction volume was substrate dependent in SSF of corn fiber, spent brewing grains and wheat straw for cellulase production by Trichoderma reesei Rut C30. Other cellulolytic enzyme assays (endoglucanase, beta-glucosidase and xylanase) were much less sensitive to the extraction volume.