Data implementation matters: Effect of software choice and LCI database evolution on a comparative LCA study of permanent magnets

Life cycle assessment (LCA) databases and software evolve. We analyzed to which extent software and evolving life cycle inventory databases affect the comparison of technology alternatives, using a comparative LCA on permanent magnets as a case study, with two selected software tools: CMLCA and Brightway LCA. We migrated the system models from the CMLCA to Brightway LCA software and alternated between the ecoinvent database versions 2.2 and 3.1 to 3.6 in the system background. When using ecoinvent v3.6 instead of v2.2, the change of the indicator results ranged from $-34\%$ to 283%. The evolution of the ecoinvent database impacted the absolute amounts of the characterized results and the relative performance between alternatives. The impact category with the highest variability was ionizing radiation, which even showed a ranking inversion with ecoinvent v3.4. In contrast, the impact of using CMLCA or Brightway was negligible because the same data and modeling assumptions caused percentage differences below 0.4%. During the semi-automated data migration to Brightway, we identified 23 environmental flows in the CMLCA model that were not paired with their corresponding characterization factors in the published study of reference. This error had led to an underestimation of 63% in the photochemical oxidation indicator of one of the alternatives. This underestimation relates to an interoperability issue regarding the nomenclature of environmental flows in software alternatives and is a matter of data implementation rather than an issue intrinsic to the selected software. Finally, we identified improvement opportunities for the transparency and reusability of LCA models. This article met the requirements for a Gold-Gold JIE data openness badge described at http://jie.click/badges .      

Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions

Knowledge discovery from the exponentially growing body of structurally characterised protein-ligand complexes as a source of information in structure-based drug design is a major challenge in contemporary drug research. Given the need for powerful data retrieval, integration and analysis tools, Relibase was developed as a database system particularly designed to handle protein-ligand related problems and tasks. Here, we describe the design and functionality of the Relibase core database system. Features of Relibase include, e.g. the detailed analysis of superimposed ligand binding sites, ligand similarity and substructure searches, and 3D searches for protein-ligand and protein-protein interaction patterns. The broad range of functions provided in Relibase and its high level of data integration, along with its flexible and intuitive interface, makes Relibase an invaluable data mining tool which can significantly enhance the drug development process. An example, illustrating a 3D query for quarternary ligand nitrogen atoms interacting with aromatic ring systems in proteins, a pattern found in pharmaceutically relevant target proteins such as, e.g. acetylcholine-esterase, is discussed.     

活植物信息数据库中的植物编码系统

本文概述了南京中山植物园活植物信息数据库中的植物编码系统,重点介绍了植物编码的生成方法。该系统通过将关系数据库ORACLE与Microsoft C所提供的完备的计算模型与关系查询语言的强功能管理手段结合起来,弥补了现行商用数据库的不足,获得了较高的时空效率。     

The design and implementation of the immune epitope database and analysis resource

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, The Immune Epitope Database and Analysis Resource. We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.     

水稻二化螟地理信息系统数据库的设计与组建

组建地理信息系统数据库是进行种群时空动态分析的前提和基础。在介绍地理信息系统数据库的概念、特点等的基础上,以ArcView GIS 3.1作为组建数据库、进行时空分析的基本软件平台,对浙江省水稻二化螟数量变化的历史资料及有关的空间和属性数据进行分类、编码、输入与编辑等, 分别建立了空间及属性数据库。其中空间库包括浙江省的政区、河流、道路、等高线、土壤类型等图层, 属性库包括气象、耕作制度、灯诱及田间数据等。并将各地地名作为主关键字,以实现空间库与属性库以及各属性库之间的关联。该数据库不仅具有基本的数据库管理功能,如数据的输入、输出、编辑和查询,更重要的是可以通过该数据库对种群动态进行时空分析。     

ProtaBank: A repository for protein design and engineering data

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user‐friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org .     

高雄山虫草生物学特性及人工驯化条件优化

高雄山虫草Cordyceps tenuipes是一种重要的珍稀野生虫草,无性型为细脚棒束孢Isaria tenuipes.对采集的野生无性型高雄山虫草生物学特性进行了研究,采用小麦和大米为栽培基质,通过添加不同营养成分进行人工驯化和栽培条件优化,对后续提高其孢梗束产量和商业化栽培具有重要意义.试验结果表明,该虫草菌丝在...     

Biological disposal of hazardous waste

Hazardous wastes pose major disposal problems for all industrialized nations and a need exists to develop effective and permanent solutions. Biological technologies can assist in this regard. Biosystems can serve to recover, separate and destroy the toxic nature of hazardous waste at the source of generation, at abandoned landfills, in surface and ground waters and at the site of spills. When applying biotechnologies there are many physical, chemical and biological factors that must be considered when engineering an environment, with the biological component improved through the use of applied microbiology and genetic engineering. Biotreatment process systems include conventional aerobic and anaerobic technologies, land treatments similar to farming operations and composting, and novel techniques to treat surface and ground waters. Emerging techniques include free and immobilized cells and enzymes in batch and continuous systems, high-rate fermentations, and coupling of biotechnologies to physical/chemical methods. To develop an effective biological disposal option, research and development is required in a wide range of areas associated with microbiology and genetic engineering, and system design and testing.     

小鼠肝脏蛋白质组数据门户

肝脏是哺乳动物体内的代谢中枢,系统性研究肝脏蛋白质组在不同的生理和病理状态下的表达情况有助于我们理解肝脏的功能机理。随着高精度质谱技术的不断发展,众多小鼠肝脏生理病理研究产生了大量蛋白质组学数据。文中系统性整理了834例小鼠肝脏的蛋白质组学实验,建立了小鼠肝脏蛋白质组数据门户(Mouse Liver Portal,http://mouseliver.com),该门户中包含了肝脏在不同生理和病理状态下的蛋白质组学数据,如不同性别、年龄、昼夜节律、细胞类型和不同时间阶段的部分肝切除、非酒精性脂肪肝等状态。该门户能够提供肝脏在不同状态下蛋白的表达变化情况、差异显著的蛋白质和它们参与的生物学过程以及潜在的信号转导和调控网络。作为目前最全面的小鼠肝脏蛋白质组数据门户,该数据库能够给肝脏生物学研究提供重要的资源和参考。     

Competing endogenous RNA database

A given mRNA can be regulated by interactions with miRNAs and in turn the availability of these miRNAs can be regulated by their interactions with alternate mRNAs. The concept of regulation of a given mRNA by alternate mRNA (competing endogenous mRNA) by virtue of interactions with miRNAs through shared miRNA response elements is poised to become a fundamental genetic regulatory mechanism. The molecular basis of the mRNA-mRNA cross talks is via miRNA response elements, which can be predicted based on both molecular interaction and evolutionary conservation. By examining the co-occurrence of miRNA response elements in the mRNAs on a genome-wide basis we predict competing endogenous RNA for specific mRNAs targeted by miRNAs. Comparison of the mRNAs predicted to regulate PTEN with recently published work, indicate that the results presented within the competing endogenous RNA database (ceRDB) have biological relevance.

Availability

http://www.oncomir.umn.edu/cefinder/     

A taxonomic database and linked iconograph for diatoms

Hydrobiologia - The Royal Botanic Garden Edinburgh and the Natural History Museum are collaborating to establish a database and linked iconograph, wherever possible using TDWG (Taxonomic Databases...     

PCR引物设计及软件使用技巧

介绍了使用软件设计PCR引物的技巧。在PCR引物设计原则的基础上 ,详细介绍了两种常用引物设计软件的基本使用方法 ,并对其各自的优缺点进行了比较。一般性引物自动搜索可采用“PremierPrimer 5”软件 ,而引物的评价分析则可采用“Oli go6”软件。     

Robust design and optimization of retroaldol enzymes

Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.     

Protein design in systems metabolic engineering for industrial strain development

Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering.     

提高木霉逆境适应性与生物防治效果的基因工程研究进展

木霉生存范围广、生长繁殖迅速,对其他真菌有一定的拮抗能力,并能促进植物生长、诱导植物对病原菌产生抗性,是迄今开发最成功的植物病害生防真菌。目前,运用基因工程的方法对木霉进行遗传改良,提高它对环境的适应性与对致病菌的防治能力,已经取得了很大的进展,就近年来采用基因工程的方法对木霉进行改良的研究进行综述。     

Mycobacteriophage genome database

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. AVAILABILITY: The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.     

生物防治杆状病毒基因工程研究进展

杆状病毒作为杀虫剂应用已成为生物防治中不可缺少的环节,但杆状病毒过高的宿主特异性与缓慢的发病致死作用是制约其推广应用的原因之一。我们就如何通过基因工程的方法提高杆状病毒的生物防治效果,从整合外源基因、改造内源基因及生物安全性评价等3个方面,对近年来的相关研究进行了概括,并对基因工程杆状病毒用于生物防治进行了展望。