我国淡水养殖鱼类育种的实践和思考

用于鱼类育种的传统方法 ,如引种驯化、选种和杂交 ,虽然有其自身的局限性 ,但都是行之有效的 .自本世纪 70年代以来兴起的生物工程技术 ,已应用于鱼类育种 ,如细胞工程中的雌核发育、多倍体形成和性别控制等方面都取得了较好的成效 .80年代以来 ,基因工程技术也已用之于鱼类育种的研究中 ,并取得了一些成效 .实践证明 ,基因工程育种离生产尚有一定距离 .根据当前的实际 ,鱼类育种仍然离不开传统方法 ,应该是细胞工程和传统方法相结合 ,或是细胞工程和基因工程相结合 ,或是传统方法、细胞工程和基因工程相结合的综合技术育种     

Reverse engineering of metabolic networks, a critical assessment

Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.     

Protein engineering for metabolic engineering: Current and next-generation tools

Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. We review advances in selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use; produce non-natural amino acids, alcohols, and carboxylic acids; and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes.     

Genome‐scale engineering for systems and synthetic biology

Genome‐modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre‐defined locations across the genome. The handful of methods capable of targeted gene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome‐scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.     

Advances in directed protein evolution by recursive genetic recombination: applications to therapeutic proteins

Recent developments in directed evolution technologies combined with innovations in robotics and screening methods have revolutionized protein engineering. These methods are being applied broadly to many fields of biotechnology, including chemical engineering, agriculture and human therapeutics. More specifically, DNA shuffling and other methods of genetic recombination and mutation have resulted in the improvement of proteins of therapeutic interest. Optimizing genetic diversity and fitness through iterative directed evolution will accelerate improvements in engineered protein therapeutics.     

Non-canonical amino acids in protein engineering

Methods for engineering proteins that contain non-canonical amino acids have advanced rapidly in the past few years. Novel amino acids can be introduced into recombinant proteins in either a residue-specific or site-specific fashion. The methods are complementary: residue-specific incorporation allows engineering of the overall physical and chemical behavior of proteins and protein-like macromolecules, whereas site-specific methods allow mechanistic questions to be probed in atomistic detail. Challenges remain in the engineering of the translational apparatus and in the design of schemes that can be used to encode both canonical and non-canonical amino acids.     

Ecological engineering methods for soil and water conservation in Taiwan

This paper describes the development of Taiwan's localized ecological engineering methods to make the mitigation works more effective. To strengthen the soil and water conservation and protection of the ecological environment, comprehensive mitigation planning is necessary with considerations that include balancing the safety, ecology, and landscape, and treating the whole watershed as a unit. To demonstrate the achievement of the promotion of the ecological engineering methods in Taiwan, this paper illustrates two complete mitigation examples for a debris flow torrent and a stream. Most of the mitigation works have survived and are still stable (with some minor damages) after the two strong typhoons of 2004. We show that the developed ecological engineering methods are very suitable in mitigation and worthwhile for further promotion for Taiwan's ecological environment.     

Systems Metabolic Engineering Meets Machine Learning: A New Era for Data‐Driven Metabolic Engineering

The recent increase in high‐throughput capacity of ‘omics datasets combined with advances and interest in machine learning (ML) have created great opportunities for systems metabolic engineering. In this regard, data‐driven modeling methods have become increasingly valuable to metabolic strain design. In this review, the nature of ‘omics is discussed and a broad introduction to the ML algorithms combining these datasets into predictive models of metabolism and metabolic rewiring is provided. Next, this review highlights recent work in the literature that utilizes such data‐driven methods to inform various metabolic engineering efforts for different classes of application including product maximization, understanding and profiling phenotypes, de novo metabolic pathway design, and creation of robust system‐scale models for biotechnology. Overall, this review aims to highlight the potential and promise of using ML algorithms with metabolic engineering and systems biology related datasets.     

Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Taking the example of computer systems engineering for the analysis of biological cell systems

In this paper, we discuss the potential for the use of engineering methods that were originally developed for the design of embedded computer systems, to analyse biological cell systems. For embedded systems as well as for biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. In contrast to the biology domain, the computer engineering domain has the opportunity to quickly evaluate design options and consequences of its systems by methods for computer aided design and in particular design space exploration. We argue that there are enough concrete similarities between the two systems to assume that the engineering methodology from the computer systems domain, and in particular that related to embedded systems, can be applied to the domain of cellular systems. This will help to understand the myriad of different design options cellular systems have. First we compare computer systems with cellular systems. Then, we discuss exactly what features of engineering methods could aid researchers with the analysis of cellular systems, and what benefits could be gained.     

Phage display for engineering and analyzing protein interaction interfaces

Phage display is the longest-standing platform among molecular display technologies. Recent developments have extended its utility to proteins that were previously recalcitrant to phage display. The technique has played a dominant role in forming the field of synthetic binding protein engineering, where novel interfaces have been generated from libraries built using antibody fragment frameworks and also alternative scaffolds. Combinatorial methods have also been developed for the rapid analysis of binding energetics across protein interfaces. The ability to rapidly select and analyze binding interfaces, and compatibility with high-throughput methods under diverse conditions, makes it likely that the combination of phage display and synthetic combinatorial libraries will prove to be the method of choice for synthetic binding protein engineering for broad applications.     

Cell surface engineering and application in cell delivery to heart diseases

Cell-based therapy has expanded its influence in cancer immunotherapy, regenerative medicine, and tissue engineering. Due to their secretory functions, differentiation capabilities, specific homing effects through chemotaxis, distinctive therapeutic potentials, and ex vivo expandability, cells have become an attractive reagent for advanced therapeutic strategies. Therefore, the ability to modify cells and manipulate their functions according to intended therapeutic designs has been the central scientific interest in the field of biomedical research. Many innovative methods have been developed with genetic modification of cells being the most advanced cell surface engineering technique. Although genetic modification is a powerful tool, it has a limited applicability due to the permanent modifications made on cells. Alternatively, many endeavors have been made to develop surface engineering techniques that can circumvent the limitations of genetic modification. In this review, current methods of non-genetic cell surface modification, including chemical conjugations, polymeric encapsulation, hydrophobic insertion, enzymatic and metabolic addition, will be introduced. Moreover, cell surface engineering plausible for cardiac remodeling and the future prospective will be discussed at the end.     

The folding of an enzyme. V. H/2H exchange-nuclear magnetic resonance studies on the folding pathway of barnase: complementarity to and agreement with protein engineering studies.

Two major methods are currently being used to characterize transient intermediates during protein folding at the level of individual residues. Nuclear magnetic resonance (n.m.r.) measurements on the protection of peptide NH hydrogens against exchange with solvent during refolding can provide information about secondary structure formation. Protein engineering and kinetics can provide direct information about intramolecular interactions of protein side-chains and indirect evidence on secondary structure. These procedures have provided the most complete pictures so far about protein folding intermediates. Both methods have been applied to the characterization of an intermediate in the refolding of barnase. Although the two methods give complementary information, there are some regions of the protein where the methods overlap well. We show that, with one possible exception that is obscure, n.m.r. and protein engineering give identical results for those interactions that can be analysed by both methods. This suggests that these are valid approaches for the study of protein folding intermediates in the case of barnase and that the combination of the methods is a powerful analytical procedure. Information provided by n.m.r. data that is complementary to the protein engineering experiments is: (1) early formation of the C terminus of helix2; (2) early formation of helix3; (3) early formation of several beta-turns (46-49, 101-104 in loop5); and (5) partial formation of loop5. Confirmatory evidence of protein engineering data on the intermediate is: (1) helix1 is complete from residues 10 to 18; (2) the interactions between all beta-strands are present; (3) part of loop2 is not formed; (4) part of loop3 is formed; and (5) some specific tertiary interactions are not made. For some interactions the protein engineering and H/2H exchange methods overlap directly. The information obtained for direct overlap is self consistent.     

Enabling inverse metabolic engineering through genomics

Inverse metabolic engineering (IME) is a powerful framework for engineering cellular phenotypes. Progress in this field has been limited by a lack of comprehensive methods for efficiently identifying the genetic basis of relevant phenotypes. Advances in genomics technologies, including DNA microarrays and gene sequencing, have dramatically improved our ability to relate changes in phenotype with associated changes in genotype. When applied in the context of IME, these tools should enable the integration of "evolutionary" and "direct" approaches to engineering cell physiology, which should improve our understanding of the complex interactions affecting the expression, evolution and engineering of traits in natural and industrial hosts.     

Genetic engineering of filamentous fungi--progress, obstacles and future trends

Filamentous fungi are widely used in biotechnology as cell factories for the production of chemicals, pharmaceuticals and enzymes. In order to improve their productivities, genetic engineering strategies can be powerful approaches. Different transformation techniques as well as DNA- and RNA-based methods to rationally design metabolic fluxes have been developed for industrially important filamentous fungi. However, the lack of efficient genetic engineering approaches still forms an obstacle for a multitude of fungi producing new and commercially interesting metabolites. This review summarises the variety of options that have recently become available to introduce and control gene expression in filamentous fungi and discusses their advantages and disadvantages. Furthermore, important considerations that have to be taken into account to design the best engineering strategy will be discussed.     

Tissue engineering; strategies,tissues, and biomaterials

Current tissue regenerative strategies rely mainly on tissue repair by transplantation of the synthetic/natural implants. However, limitations of the existing strategies have increased the demand for tissue engineering approaches. Appropriate cell source, effective cell modification, and proper supportive matrices are three bases of tissue engineering. Selection of appropriate methods for cell stimulation, scaffold synthesis, and tissue transplantation play a definitive role in successful tissue engineering. Although the variety of the players are available, but proper combination and functional synergism determine the practical efficacy. Hence, in this review, a comprehensive view of tissue engineering and its different aspects are investigated.     

Enhanced crystallizability by protein engineering approaches: a general overview

The limiting step in macromolecular crystallography is the preparation protein crystals suitable for X-ray diffraction studies. A strong prerequisite for the success of crystallization experiments is the ability to produce monodisperse and properly folded protein samples. Since the production of most protein is usually achieved using recombinant methods, it has become possible to engineer target proteins with increased propensities to form well diffracting crystals. Recent advances in bioinformatics, which takes advantage from an enhanced information in the protein databases, are of enormous help for the design of modified proteins. Based on bioinformatics analyses, the reduction of the structural complexity of proteins or their site-specific mutagenesis has proven to have a dramatic impact on both the yield of heterologous protein expression and its crystallizability. Therefore, protein engineering represents a valid tool which supports the classical crystallization screenings with a more rational approach. This review describes key methods of protein-engineering and provides a number of examples of their successful use in crystallization. Scope of proposed topic: This Topic is focused on state-of-art protein engineering techniques to increase the propensity of proteins to form crystals with suitable X-ray diffraction properties. Protein engineering methods have proven to be of great help for the crystallization of difficult targets. We herein review molecular biology and chemical methods to help protein crystallization.