Engineering biological systems using automated biofoundries

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges.     

Tissue banking for research: connecting the disconnected

Delivering the promise of personalised medicine is the challenge that the current generation of scientists face. The variations in human physiology and disease are considerable, and designing appropriate strategies to deliver what has been promised will require access to tissue from a large number of volunteers. The NHS provides an ideal infrastructure for sample acquisition, but requires two things to make this available—public consent and support for extra manpower and administration. There is a disconnection between the NHS and tissue based research that needs to be addressed on a number of levels to provide a translational platform. This should enable the path to be beaten to provide the ideal tailored treatment for future patients; one that preserves quality of life by curing the disease with minimal side effects.     

An Integrated Pipeline for de Novo Assembly of Microbial Genomes

Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron''s Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the other assembly algorithm. In particular, the assemblies produced by A5 exhibit 50% or more reduction in broken protein coding sequences relative to SOAPdenovo assemblies. The A5 pipeline can also assemble Illumina sequence data from libraries constructed by the Nextera (transposon-catalyzed) protocol, which have markedly different characteristics to mechanically sheared libraries. Finally, A5 has modest compute requirements, and can assemble a typical bacterial genome on current desktop or laptop computer hardware in under two hours, depending on depth of coverage.     

Integrated pest management theory and practice

Integration in pest management may be conceived at three distinct levels: (a) integration of tactics, (b) integration of the effects of multiple pest stresses, and (c) systems integration. The ecological basis of each is found in population, community or ecosystems processes, respectively. Most current IPM programs are attempts to integrate control tactics into management strategies and therefore only require knowledge of species and population ecology. Further advancement of IPM will require higher levels of integration but the experimental basis of and information on community and ecosystems processes are insufficient to permit reaching these levels. Mostly entomological examples in the grain legumes are used to demonstrate achievements of IPM at level a (tactical integration), and the difficulties involved in advancing towards integration of multiple pest stresses and systems integration (levels b and c). General requisites towards the design and implementation of IPM programs are outlined.     

Current millennium biotechniques for biomedical research on parasites and host-parasite interactions

The development of biotechnology in the last three decades has generated the feeling that the newest scientific achievements will deliver high standard quality of life through abundance of food and means for successfully combating diseases. Where the new biotechnologies give access to genetic information, there is a common belief that physiological and pathological processes result from subtle modifications of gene expression. Trustfully, modern genetics has produced genetic maps, physical maps and complete nucleotide sequences from 141 viruses, 51 organelles, two eubacteria, one archeon and one eukaryote (Saccharomices cerevisiae). In addition, during the Centennial Commemoration of the Oswaldo Cruz Institute the nearly complete human genome map was proudly announced, whereas the latest Brazilian key stone contribution to science was the publication of the Shillela fastidiosa genomic sequence highlythed on a Nature cover issue. There exists a belief among the populace that further scientific accomplishments will rapidly lead to new drugs and methodological approaches to cure genetic diseases and other incurable ailments. Yet, much evidence has been accumulated, showing that a large information gap exists between the knowledge of genome sequence and our knowledge of genome function. Now that many genome maps are available, people wish to know what are we going to do with them. Certainly, all these scientific accomplishments will shed light on many more secrets of life. Nevertheless, parsimony in the weekly announcements of promising scientific achievements is necessary. We also need many more creative experimental biologists to discover new, as yet un-envisaged biotechnological approaches, and the basic resource needed for carrying out mile stone research necessary for leading us to that "promised land" often proclaimed by the mass media.     

Bringing Web 2.0 to bioinformatics

Enabling deft data integration from numerous, voluminous andheterogeneous data sources is a major bioinformatic challenge.Several approaches have been proposed to address this challenge,including data warehousing and federated databasing. Yet despitethe rise of these approaches, integration of data from multiplesources remains problematic and toilsome. These two approachesfollow a user-to-computer communication model for data exchange,and do not facilitate a broader concept of data sharing or collaborationamong users. In this report, we discuss the potential of Web2.0 technologies to transcend this model and enhance bioinformaticsresearch. We propose a Web 2.0-based Scientific Social Community(SSC) model for the implementation of these technologies. Byestablishing a social, collective and collaborative platformfor data creation, sharing and integration, we promote a webservices-based pipeline featuring web services for computer-to-computerdata exchange as users add value. This pipeline aims to simplifydata integration and creation, to realize automatic analysis,and to facilitate reuse and sharing of data. SSC can fostercollaboration and harness collective intelligence to createand discover new knowledge. In addition to its research potential,we also describe its potential role as an e-learning platformin education. We discuss lessons from information technology,predict the next generation of Web (Web 3.0), and describe itspotential impact on the future of bioinformatics studies.      

Mapping Cod: Fisheries Science,Fish Harvesters’ Ecological Knowledge and Cod Migrations in the Northern Gulf of St. Lawrence

Some recent scholarship has focused on integrating local and/or traditional knowledge with conventional scientific information in fisheries management to improve the factual foundation of and strengthen support for management decisions. This article compares a sequence of historical and contemporary scientific texts and maps about the migrations and stock structure of cod in the Northern Gulf of St. Lawrence with texts and maps generated by the authors through the collection, aggregation and interpretation of commercial fish harvesters’ ecological knowledge. We find that the relationship between fisheries science and harvesters’ ecological knowledge is dynamic and has changed over time, and that both are ‘situated’ socially and ecologically. Overall, each paints an incomplete picture of cod movements and stock structure but the knowledge of harvesters provides a valuable complement to scientific information, particularly at the local scale, and has the potential to contribute to the identification of local cod stocks that are new to science and management. We end by considering how this case study informs the larger discussion about the challenges and potential benefits of the so-called integration project to bring together science and the ecological knowledge of fish harvesters.

Optimization methods to solve adaptive management problems

Determining the best management actions is challenging when critical information is missing. However, urgency and limited resources require that decisions must be made despite this uncertainty. The best practice method for managing uncertain systems is adaptive management, or learning by doing. Adaptive management problems can be solved optimally using decision-theoretic methods; the challenge for these methods is to represent current and future knowledge using easy-to-optimize representations. Significant methodological advances have been made since the seminal adaptive management work was published in the 1980s, but despite recent advances, guidance for implementing these approaches has been piecemeal and study-specific. There is a need to collate and summarize new work. Here, we classify methods and update the literature with the latest optimal or near-optimal approaches for solving adaptive management problems. We review three mathematical concepts required to solve adaptive management problems: Markov decision processes, sufficient statistics, and Bayes’ theorem. We provide a decision tree to determine whether adaptive management is appropriate and then group adaptive management approaches based on whether they learn only from the past (passive) or anticipate future learning (active). We discuss the assumptions made when using existing models and provide solution algorithms for each approach. Finally, we propose new areas of development that could inspire future research. For a long time, limited by the efficiency of the solution methods, recent techniques to efficiently solve partially observable decision problems now allow us to solve more realistic adaptive management problems such as imperfect detection and non-stationarity in systems.     

User-controlled pipelines for feature integration and head and neck radiation therapy outcome predictions

PurposePrecision cancer medicine is dependent on accurate prediction of disease and treatment outcome, requiring integration of clinical, imaging and interventional knowledge. User controlled pipelines are capable of feature integration with varied levels of human interaction. In this work we present two pipelines designed to combine clinical, radiomic (quantified imaging), and RTx-omic (quantified radiation therapy (RT) plan) information for prediction of locoregional failure (LRF) in head and neck cancer (H&N).MethodsPipelines were designed to extract information and model patient outcomes based on clinical features, computed tomography (CT) imaging, and planned RT dose volumes. We predict H&N LRF using: 1) a highly user-driven pipeline that leverages modular design and machine learning for feature extraction and model development; and 2) a pipeline with minimal user input that utilizes deep learning convolutional neural networks to extract and combine CT imaging, RT dose and clinical features for model development.ResultsClinical features with logistic regression in our highly user-driven pipeline had the highest precision recall area under the curve (PR-AUC) of 0.66 (0.33–0.93), where a PR-AUC = 0.11 is considered random. CONCLUSIONS: Our work demonstrates the potential to aggregate features from multiple specialties for conditional-outcome predictions using pipelines with varied levels of human interaction. Most importantly, our results provide insights into the importance of data curation and quality, as well as user, data and methodology bias awareness as it pertains to result interpretation in user controlled pipelines.     

碳纳米管作为siRNA转运载体的研究进展

随着人们对RNA干扰分子机理的研究愈加深入,siRNA作为一种新的基因治疗药物极有可能为人类攻克癌症等难以治愈的疾病带来希望。然而,目前在RNA干扰应用中遇到的最大挑战就是如何有效地将siRNA导入靶细胞且不致引起严重的细胞毒性。碳纳米管在药物传递和基因传递等生物医学领域的潜在应用受到广泛关注;但要实现碳纳米管在基因治疗领域的应用,碳纳米管的功能化是关键,也是近几年来研究的重点。综述近年来碳纳米管作为siRNA转运载体在基因治疗领域的研究进展。     

民族植物学研究现状(2017-2022)

《生物多样性公约》《名古屋议定书》《植物科学深圳宣言》等指导性文件都强调要认识到生物多样性相关传统知识的重要作用。生物多样性相关传统知识在生物文化多样性保护和可持续发展方面的作用也越来越受到人们的关注。民族植物学研究人与植物的相互作用关系, 是研究生物多样性相关传统知识的最主要学科领域, 近些年来取得了一系列的研究进展, 研究成果对于《植物科学深圳宣言》第六个优先领域目标的完成具有重要的推动作用。本文回顾了近年来特别是《植物科学深圳宣言》发布后的民族植物学研究状况, 主要从认知、利用、保护、管理植物等方面进行概述, 以便全面了解近期民族植物学研究的发展状况, 保护传统知识和植物文化, 为生物文化多样性的保护与发展做出重要贡献。近期获得的民族植物学成果, 说明民族植物学研究可以解决当下的一些热点问题。民族植物学的研究发现, 该学科能极大地促进传统知识、植物文化、生物文化多样性的保护, 尤其在农家品种以及濒危语言的保护方面有着巨大优势。     

医药类高等院校生物物理课程建设的思考

医用生物物理学是研究生命物质的物理性质,生命过程的物理和物理化学规律以及物理因素对生物系统作用机制的科学,是物理学和生物学相结合而产生的一门边缘学科。在促进物理学和生命科学进步方面都显现出强大的生命力和推动力。基于医用生物物理学发展和我校学科建设发展的现实需要,本文讨论了我校建设医用生物物理学必修课或者选修课的必要性,并从本课程和学校学生特点两个方面考虑,对该课程建设的内容进行了初步的整合。旨在对教学内容进行整合、优化,增加一些新概念、新知识及前沿动态,把新旧知识联系到了一起,教会学生如何应用基础知识解决问题的方法以及缓解目前学时少、内容多这一矛盾。     

Customary management as precautionary and adaptive principles for protecting coral reefs in Oceania

Marine conservation programs in Oceania are increasingly turning to precautionary and adaptive management, particularly approaches which emphasize local participation and customary management. Although the application of community-based natural resource management is widespread in the region, the full integration of local knowledge and practices into the design, implementation, and monitoring of community-based conservation programs has been limited. There is also little empirical data to show whether or not community-based conservation projects are meeting their stated objectives. This paper summarizes an integrated method for selecting Marine Protected Area (MPA) sites and presents empirical evidence that illustrates how an MPA that was largely conceived using indigenous ecological knowledge and existing sea tenure governance (i.e., customary management practices), as part of a regional precautionary and adaptive community-based management plan, is showing signs of biological and social success. More generally, the paper shows how hybrid natural and social research approaches in tandem with customary management for designing MPAs can protect coral reefs in Oceania.     

Orymold: ontology based gene expression data integration and analysis tool applied to rice

Background  

Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A widely accepted approach to solve these issues has been the creation and use of controlled vocabularies (ontologies). Ontologies allow for the formalization of domain knowledge, which in turn enables generalization in the creation of querying interfaces as well as in the integration of heterogeneous data, providing both human and machine readable interfaces.     

Functional foods from biotech--an unappetizing prospect?

In the early 1990s, functional foods promised to solve global malnutrition and put palatable options for treating ailments on grocery shelves. Since then, a meager number of products have ripened while the rest have turned sour.     

Adolescents’ Functional Numeracy Is Predicted by Their School Entry Number System Knowledge

One in five adults in the United States is functionally innumerate; they do not possess the mathematical competencies needed for many modern jobs. We administered functional numeracy measures used in studies of young adults’ employability and wages to 180 thirteen-year-olds. The adolescents began the study in kindergarten and participated in multiple assessments of intelligence, working memory, mathematical cognition, achievement, and in-class attentive behavior. Their number system knowledge at the beginning of first grade was defined by measures that assessed knowledge of the systematic relations among Arabic numerals and skill at using this knowledge to solve arithmetic problems. Early number system knowledge predicted functional numeracy more than six years later (ß = 0.195, p = .0014) controlling for intelligence, working memory, in-class attentive behavior, mathematical achievement, demographic and other factors, but skill at using counting procedures to solve arithmetic problems did not. In all, we identified specific beginning of schooling numerical knowledge that contributes to individual differences in adolescents’ functional numeracy and demonstrated that performance on mathematical achievement tests underestimates the importance of this early knowledge.     

Failed promises: economic integration, bureaucratic encounters, and the EU-Turkey Customs Union

European integration is based upon the promise to bring prosperity by creating economic and social equilibrium among member states and its regions via integrationist policies jointly managed by states and the institutions of the EU. As one common market initiative for greater economic integration in the wider region, goods circulate without tariff and customs duty barriers in the EU’s common customs area. Turkey, not an EU member, has been in this common market since 1996. The EU-Turkey Customs Union, which promised to bring deeper economic and political integration through eventual Turkish membership, represents Turkey’s aspirations to move from the periphery of Europe into its core. As an anthropological contribution to investigations of advanced European capitalism, this paper examines fundamental conflicts of interest between the EU and Turkey and locates them in their unequal power relations and in the disjuncture of each side’s overall objectives from economic integration. Most importantly, it shows that these interest conflicts have ramifications at the individual bureaucratic level and in daily bureaucratic practice. Dramatic expressions of Turkish state power, which are initially geared toward balancing out power inequities, exacerbate Turkish and EU officials’ failures to maintain at least a facade of mutually sustainable interests. Interpreted by EU officials as Turkish bureaucratic inertia, such disintegration of interests has implications for ongoing economic integration and membership negotiations between the two parties, with Turkish officials experiencing loss of control. The paper calls for a critical political economy that pays due attention to the cultural settings in which the former is embedded.