Recent applications of synthetic biology tools for yeast metabolic engineering

DEFF Research Database (Denmark)

Jensen, Michael Krogh; Keasling, Jay

2015-01-01

to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together...... with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed...... synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead....

7th Annual Systems Biology Symposium: Systems Biology and Engineering

Energy Technology Data Exchange (ETDEWEB)

Galitski, Timothy P.

2008-04-01

Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering are now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

Science.gov (United States)

Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

Directory of Open Access Journals (Sweden)

Lihong Jiang

2018-06-01

Full Text Available Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors to speed up design-build-test (DBT cycles of metabolic engineering and synthetic biology. Keywords: Cell-free protein synthesis, Metabolic pathway optimization, Genetic circuits, Metabolic engineering, Synthetic biology

Engineering Review Information System

Science.gov (United States)

Grems, III, Edward G. (Inventor); Henze, James E. (Inventor); Bixby, Jonathan A. (Inventor); Roberts, Mark (Inventor); Mann, Thomas (Inventor)

2015-01-01

A disciplinal engineering review computer information system and method by defining a database of disciplinal engineering review process entities for an enterprise engineering program, opening a computer supported engineering item based upon the defined disciplinal engineering review process entities, managing a review of the opened engineering item according to the defined disciplinal engineering review process entities, and closing the opened engineering item according to the opened engineering item review.

Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

Science.gov (United States)

Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

2016-01-01

In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthetic biology and metabolic engineering for marine carotenoids: new opportunities and future prospects.

Science.gov (United States)

Wang, Chonglong; Kim, Jung-Hun; Kim, Seon-Won

2014-09-17

Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops.

Science.gov (United States)

Shih, Patrick M; Liang, Yan; Loqué, Dominique

2016-07-01

The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Multiplexed Engineering in Biology.

Science.gov (United States)

Rogers, Jameson K; Church, George M

2016-03-01

Biotechnology is the manufacturing technology of the future. However, engineering biology is complex, and many possible genetic designs must be evaluated to find cells that produce high levels of a desired drug or chemical. Recent advances have enabled the design and construction of billions of genetic variants per day, but evaluation capacity remains limited to thousands of variants per day. Here we evaluate biological engineering through the lens of the design–build–test cycle framework and highlight the role that multiplexing has had in transforming the design and build steps. We describe a multiplexed solution to the ‘test’ step that is enabled by new research. Achieving a multiplexed test step will permit a fully multiplexed engineering cycle and boost the throughput of biobased product development by up to a millionfold.

Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects

Directory of Open Access Journals (Sweden)

Chonglong Wang

2014-09-01

Full Text Available Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations.

Synthetic Biology and Metabolic Engineering for Marine Carotenoids: New Opportunities and Future Prospects

Science.gov (United States)

Wang, Chonglong; Kim, Jung-Hun; Kim, Seon-Won

2014-01-01

Carotenoids are a class of diverse pigments with important biological roles such as light capture and antioxidative activities. Many novel carotenoids have been isolated from marine organisms to date and have shown various utilizations as nutraceuticals and pharmaceuticals. In this review, we summarize the pathways and enzymes of carotenoid synthesis and discuss various modifications of marine carotenoids. The advances in metabolic engineering and synthetic biology for carotenoid production are also reviewed, in hopes that this review will promote the exploration of marine carotenoid for their utilizations. PMID:25233369

Engineering and Biology: Counsel for a Continued Relationship

Science.gov (United States)

Levy, Arnon; Siegal, Mark L.; Soyer, Orkun S.; Wagner, Andreas

2015-01-01

Biologists frequently draw on ideas and terminology from engineering. Evolutionary systems biology—with its circuits, switches, and signal processing—is no exception. In parallel with the frequent links drawn between biology and engineering, there is ongoing criticism against this cross-fertilization, using the argument that over-simplistic metaphors from engineering are likely to mislead us as engineering is fundamentally different from biology. In this article, we clarify and reconfigure the link between biology and engineering, presenting it in a more favorable light. We do so by, first, arguing that critics operate with a narrow and incorrect notion of how engineering actually works, and of what the reliance on ideas from engineering entails. Second, we diagnose and diffuse one significant source of concern about appeals to engineering, namely that they are inherently and problematically metaphorical. We suggest that there is plenty of fertile ground left for a continued, healthy relationship between engineering and biology. PMID:26085824

Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

Science.gov (United States)

Kogge, Werner; Richter, Michael

2013-06-01

The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reverse engineering development: Crosstalk opportunities between developmental biology and tissue engineering.

Science.gov (United States)

Marcucio, Ralph S; Qin, Ling; Alsberg, Eben; Boerckel, Joel D

2017-11-01

The fields of developmental biology and tissue engineering have been revolutionized in recent years by technological advancements, expanded understanding, and biomaterials design, leading to the emerging paradigm of "developmental" or "biomimetic" tissue engineering. While developmental biology and tissue engineering have long overlapping histories, the fields have largely diverged in recent years at the same time that crosstalk opportunities for mutual benefit are more salient than ever. In this perspective article, we will use musculoskeletal development and tissue engineering as a platform on which to discuss these emerging crosstalk opportunities and will present our opinions on the bright future of these overlapping spheres of influence. The multicellular programs that control musculoskeletal development are rapidly becoming clarified, represented by shifting paradigms in our understanding of cellular function, identity, and lineage specification during development. Simultaneously, advancements in bioartificial matrices that replicate the biochemical, microstructural, and mechanical properties of developing tissues present new tools and approaches for recapitulating development in tissue engineering. Here, we introduce concepts and experimental approaches in musculoskeletal developmental biology and biomaterials design and discuss applications in tissue engineering as well as opportunities for tissue engineering approaches to inform our understanding of fundamental biology. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 35:2356-2368, 2017. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Fabrication of scaffolds in tissue engineering: A review

Science.gov (United States)

Zhao, Peng; Gu, Haibing; Mi, Haoyang; Rao, Chengchen; Fu, Jianzhong; Turng, Lih-sheng

2018-03-01

Tissue engineering (TE) is an integrated discipline that involves engineering and natural science in the development of biological materials to replace, repair, and improve the function of diseased or missing tissues. Traditional medical and surgical treatments have been reported to have side effects on patients caused by organ necrosis and tissue loss. However, engineered tissues and organs provide a new way to cure specific diseases. Scaffold fabrication is an important step in the TE process. This paper summarizes and reviews the widely used scaffold fabrication methods, including conventional methods, electrospinning, three-dimensional printing, and a combination of molding techniques. Furthermore, the differences among the properties of tissues, such as pore size and distribution, porosity, structure, and mechanical properties, are elucidated and critically reviewed. Some studies that combine two or more methods are also reviewed. Finally, this paper provides some guidance and suggestions for the future of scaffold fabrication.

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

An engineering design approach to systems biology.

Science.gov (United States)

Janes, Kevin A; Chandran, Preethi L; Ford, Roseanne M; Lazzara, Matthew J; Papin, Jason A; Peirce, Shayn M; Saucerman, Jeffrey J; Lauffenburger, Douglas A

2017-07-17

Measuring and modeling the integrated behavior of biomolecular-cellular networks is central to systems biology. Over several decades, systems biology has been shaped by quantitative biologists, physicists, mathematicians, and engineers in different ways. However, the basic and applied versions of systems biology are not typically distinguished, which blurs the separate aspirations of the field and its potential for real-world impact. Here, we articulate an engineering approach to systems biology, which applies educational philosophy, engineering design, and predictive models to solve contemporary problems in an age of biomedical Big Data. A concerted effort to train systems bioengineers will provide a versatile workforce capable of tackling the diverse challenges faced by the biotechnological and pharmaceutical sectors in a modern, information-dense economy.

Biology: An Important Agricultural Engineering Mechanism

Science.gov (United States)

Henderson, S. M.

1974-01-01

Describes the field of bioengineering with particular emphasis on agricultural engineering, and presents the results of a survey of schools that combine biology and engineering in their curricula. (JR)

SYSTEMS BIOLOGY AND METABOLIC ENGINEERING OF ARTHROSPIRA CELL FACTORIES

Directory of Open Access Journals (Sweden)

Amornpan Klanchui

2012-10-01

Full Text Available Arthrospira are attractive candidates to serve as cell factories for production of many valuable compounds useful for food, feed, fuel and pharmaceutical industries. In connection with the development of sustainable bioprocessing, it is a challenge to design and develop efficient Arthrospira cell factories which can certify effective conversion from the raw materials (i.e. CO2 and sun light into desired products. With the current availability of the genome sequences and metabolic models of Arthrospira, the development of Arthrospira factories can now be accelerated by means of systems biology and the metabolic engineering approach. Here, we review recent research involving the use of Arthrospira cell factories for industrial applications, as well as the exploitation of systems biology and the metabolic engineering approach for studying Arthrospira. The current status of genomics and proteomics through the development of the genome-scale metabolic model of Arthrospira, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies are discussed. At the end, the perspective and future direction on Arthrospira cell factories for industrial biotechnology are presented.

Synthetic Biology to Engineer Bacteriophage Genomes.

Science.gov (United States)

Rita Costa, Ana; Milho, Catarina; Azeredo, Joana; Pires, Diana Priscila

2018-01-01

Recent advances in the synthetic biology field have enabled the development of new molecular biology techniques used to build specialized bacteriophages with new functionalities. Bacteriophages have been engineered towards a wide range of applications including pathogen control and detection, targeted drug delivery, or even assembly of new materials.In this chapter, two strategies that have been successfully used to genetically engineer bacteriophage genomes are addressed: a yeast-based platform and bacteriophage recombineering of electroporated DNA.

Strategies for the chemical and biological functionalization of scaffolds for cardiac tissue engineering: a review.

Science.gov (United States)

Tallawi, Marwa; Rosellini, Elisabetta; Barbani, Niccoletta; Cascone, Maria Grazia; Rai, Ranjana; Saint-Pierre, Guillaume; Boccaccini, Aldo R

2015-07-06

The development of biomaterials for cardiac tissue engineering (CTE) is challenging, primarily owing to the requirement of achieving a surface with favourable characteristics that enhances cell attachment and maturation. The biomaterial surface plays a crucial role as it forms the interface between the scaffold (or cardiac patch) and the cells. In the field of CTE, synthetic polymers (polyglycerol sebacate, polyethylene glycol, polyglycolic acid, poly-l-lactide, polyvinyl alcohol, polycaprolactone, polyurethanes and poly(N-isopropylacrylamide)) have been proven to exhibit suitable biodegradable and mechanical properties. Despite the fact that they show the required biocompatible behaviour, most synthetic polymers exhibit poor cell attachment capability. These synthetic polymers are mostly hydrophobic and lack cell recognition sites, limiting their application. Therefore, biofunctionalization of these biomaterials to enhance cell attachment and cell material interaction is being widely investigated. There are numerous approaches for functionalizing a material, which can be classified as mechanical, physical, chemical and biological. In this review, recent studies reported in the literature to functionalize scaffolds in the context of CTE, are discussed. Surface, morphological, chemical and biological modifications are introduced and the results of novel promising strategies and techniques are discussed.

Dental pulp stem cells. Biology and use for periodontal tissue engineering.

Science.gov (United States)

Ashri, Nahid Y; Ajlan, Sumaiah A; Aldahmash, Abdullah M

2015-12-01

Inflammatory periodontal disease is a major cause of loss of tooth-supporting structures. Novel approaches for regeneration of periodontal apparatus is an area of intensive research. Periodontal tissue engineering implies the use of appropriate regenerative cells, delivered through a suitable scaffold, and guided through signaling molecules. Dental pulp stem cells have been used in an increasing number of studies in dental tissue engineering. Those cells show mesenchymal (stromal) stem cell-like properties including self-renewal and multilineage differentiation potentials, aside from their relative accessibility and pleasant handling properties. The purpose of this article is to review the biological principles of periodontal tissue engineering, along with the challenges facing the development of a consistent and clinically relevant tissue regeneration platform. This article includes an updated review on dental pulp stem cells and their applications in periodontal regeneration, in combination with different scaffolds and growth factors.

‘Can Simple Biological Systems be Built from Standardized Interchangeable Parts?’:Negotiating Biology and Engineering in a Synthetic Biology Competition

OpenAIRE

Frow, Emma; Calvert, Jane

2013-01-01

Synthetic biology represents a recent attempt to bring engineering principles and practices to working with biology. In practice, the nature of the relationship between engineering and biology in synthetic biology is a subject of ongoing debate. The disciplines of biology and engineering are typically seen to involve differentways of knowing and doing, and to embody different assumptions and objectives. Tensions between these approaches are playing out as the field of synthetic biology is bei...

Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

Directory of Open Access Journals (Sweden)

Laura R. Jarboe

2010-01-01

Full Text Available Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

IntegromeDB: an integrated system and biological search engine.

Science.gov (United States)

Baitaluk, Michael; Kozhenkov, Sergey; Dubinina, Yulia; Ponomarenko, Julia

2012-01-19

With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines are not specialized for the search of biological data. Here, we present an approach at developing a biological web search engine based on the Semantic Web technologies and demonstrate its implementation for retrieving gene- and protein-centered knowledge. The engine is available at http://www.integromedb.org. The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage community feedback.

International Conference on Medical and Biological Engineering 2017

CERN Document Server

2017-01-01

This volume presents the proceedings of the International Conference on Medical and Biological Engineering held from 16 to 18 March 2017 in Sarajevo, Bosnia and Herzegovina. Focusing on the theme of ‘Pursuing innovation. Shaping the future’, it highlights the latest advancements in Biomedical Engineering and also presents the latest findings, innovative solutions and emerging challenges in this field. Topics include: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education - Pharmaceutical Engineering.

Engineering Technical Review Planning Briefing

Science.gov (United States)

Gardner, Terrie

2012-01-01

The general topics covered in the engineering technical planning briefing are 1) overviews of NASA, Marshall Space Flight Center (MSFC), and Engineering, 2) the NASA Systems Engineering(SE) Engine and its implementation , 3) the NASA Project Life Cycle, 4) MSFC Technical Management Branch Services in relation to the SE Engine and the Project Life Cycle , 5) Technical Reviews, 6) NASA Human Factor Design Guidance , and 7) the MSFC Human Factors Team. The engineering technical review portion of the presentation is the primary focus of the overall presentation and will address the definition of a design review, execution guidance, the essential stages of a technical review, and the overall review planning life cycle. Examples of a technical review plan content, review approaches, review schedules, and the review process will be provided and discussed. The human factors portion of the presentation will focus on the NASA guidance for human factors. Human factors definition, categories, design guidance, and human factor specialist roles will be addressed. In addition, the NASA Systems Engineering Engine description, definition, and application will be reviewed as background leading into the NASA Project Life Cycle Overview and technical review planning discussion.

Basic science through engineering? Synthetic modeling and the idea of biology-inspired engineering.

Science.gov (United States)

Knuuttila, Tarja; Loettgers, Andrea

2013-06-01

Synthetic biology is often understood in terms of the pursuit for well-characterized biological parts to create synthetic wholes. Accordingly, it has typically been conceived of as an engineering dominated and application oriented field. We argue that the relationship of synthetic biology to engineering is far more nuanced than that and involves a sophisticated epistemic dimension, as shown by the recent practice of synthetic modeling. Synthetic models are engineered genetic networks that are implanted in a natural cell environment. Their construction is typically combined with experiments on model organisms as well as mathematical modeling and simulation. What is especially interesting about this combinational modeling practice is that, apart from greater integration between these different epistemic activities, it has also led to the questioning of some central assumptions and notions on which synthetic biology is based. As a result synthetic biology is in the process of becoming more "biology inspired." Copyright © 2013 Elsevier Ltd. All rights reserved.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

Science.gov (United States)

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

Science.gov (United States)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

Engineering a Biological Revolution.

Science.gov (United States)

Matheson, Susan

2017-01-26

The new field of synthetic biology promises to change health care, computer technology, the production of biofuels, and more. Students participating in the International Genetically Engineered Machine (iGEM) competition are on the front lines of this revolution. Copyright © 2017 Elsevier Inc. All rights reserved.

Challenges and opportunities in synthetic biology for chemical engineers.

Science.gov (United States)

Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

2013-11-15

Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement.

Challenges and opportunities in synthetic biology for chemical engineers

Science.gov (United States)

Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

2012-01-01

Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. PMID:24222925

Synthetic biology approaches to engineer T cells.

Science.gov (United States)

Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell A

2015-08-01

There is rapidly growing interest in learning how to engineer immune cells, such as T lymphocytes, because of the potential of these engineered cells to be used for therapeutic applications such as the recognition and killing of cancer cells. At the same time, our knowhow and capability to logically engineer cellular behavior is growing rapidly with the development of synthetic biology. Here we describe how synthetic biology approaches are being used to rationally alter the behavior of T cells to optimize them for therapeutic functions. We also describe future developments that will be important in order to construct safe and precise T cell therapeutics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications.

Science.gov (United States)

Bober, Josef R; Beisel, Chase L; Nair, Nikhil U

2018-03-12

An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies. 277 Expected final online publication date for the Annual Review of Biomedical Engineering Volume 20 is June 4, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

Biological variability in biomechanical engineering research: Significance and meta-analysis of current modeling practices.

Science.gov (United States)

Cook, Douglas; Julias, Margaret; Nauman, Eric

2014-04-11

Biological systems are characterized by high levels of variability, which can affect the results of biomechanical analyses. As a review of this topic, we first surveyed levels of variation in materials relevant to biomechanics, and compared these values to standard engineered materials. As expected, we found significantly higher levels of variation in biological materials. A meta-analysis was then performed based on thorough reviews of 60 research studies from the field of biomechanics to assess the methods and manner in which biological variation is currently handled in our field. The results of our meta-analysis revealed interesting trends in modeling practices, and suggest a need for more biomechanical studies that fully incorporate biological variation in biomechanical models and analyses. Finally, we provide some case study example of how biological variability may provide valuable insights or lead to surprising results. The purpose of this study is to promote the advancement of biomechanics research by encouraging broader treatment of biological variability in biomechanical modeling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Simple glycolipids of microbes: Chemistry, biological activity and metabolic engineering

Directory of Open Access Journals (Sweden)

Ahmad Mohammad Abdel-Mawgoud

2018-03-01

Full Text Available Glycosylated lipids (GLs are added-value lipid derivatives of great potential. Besides their interesting surface activities that qualify many of them to act as excellent ecological detergents, they have diverse biological activities with promising biomedical and cosmeceutical applications. Glycolipids, especially those of microbial origin, have interesting antimicrobial, anticancer, antiparasitic as well as immunomodulatory activities. Nonetheless, GLs are hardly accessing the market because of their high cost of production. We believe that experience of metabolic engineering (ME of microbial lipids for biofuel production can now be harnessed towards a successful synthesis of microbial GLs for biomedical and other applications. This review presents chemical groups of bacterial and fungal GLs, their biological activities, their general biosynthetic pathways and an insight on ME strategies for their production.

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials.

Science.gov (United States)

Esensten, Jonathan H; Bluestone, Jeffrey A; Lim, Wendell A

2017-01-24

Engineered T cells are currently in clinical trials to treat patients with cancer, solid organ transplants, and autoimmune diseases. However, the field is still in its infancy. The design, and manufacturing, of T cell therapies is not standardized and is performed mostly in academic settings by competing groups. Reliable methods to define dose and pharmacokinetics of T cell therapies need to be developed. As of mid-2016, there are no US Food and Drug Administration (FDA)-approved T cell therapeutics on the market, and FDA regulations are only slowly adapting to the new technologies. Further development of engineered T cell therapies requires advances in immunology, synthetic biology, manufacturing processes, and government regulation. In this review, we outline some of these challenges and discuss the contributions that pathologists can make to this emerging field.

Review of spectral imaging technology in biomedical engineering: achievements and challenges.

Science.gov (United States)

Li, Qingli; He, Xiaofu; Wang, Yiting; Liu, Hongying; Xu, Dongrong; Guo, Fangmin

2013-10-01

Spectral imaging is a technology that integrates conventional imaging and spectroscopy to get both spatial and spectral information from an object. Although this technology was originally developed for remote sensing, it has been extended to the biomedical engineering field as a powerful analytical tool for biological and biomedical research. This review introduces the basics of spectral imaging, imaging methods, current equipment, and recent advances in biomedical applications. The performance and analytical capabilities of spectral imaging systems for biological and biomedical imaging are discussed. In particular, the current achievements and limitations of this technology in biomedical engineering are presented. The benefits and development trends of biomedical spectral imaging are highlighted to provide the reader with an insight into the current technological advances and its potential for biomedical research.

Building biological foundries for next-generation synthetic biology.

Science.gov (United States)

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Introduction to bioengineering: melding of engineering and biological sciences.

Science.gov (United States)

Shoureshi, Rahmat A

2005-04-01

Engineering has traditionally focused on the external extensions of organisms, such as transportation systems, high-rise buildings, and entertainment systems. In contrast, bioengineering is concerned with inward processes of biologic organisms. Utilization of engineering principles and techniques in the analysis and solution of problems in medicine and biology is the basis for bioengineering. This article discusses subspecialties in bioengineering and presents examples of projects in this discipline.

On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

Science.gov (United States)

Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

2017-12-05

The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

Science.gov (United States)

Ganguli, Suman; Hunt, C Anthony

2004-01-01

Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

Mechanical Engineering Department technical review

Energy Technology Data Exchange (ETDEWEB)

Carr, R.B.; Abrahamson, L.; Denney, R.M.; Dubois, B.E (eds.)

1982-01-01

Technical achievements and publication abstracts related to research in the following Divisions of Lawrence Livermore Laboratory are reported in this biannual review: Nuclear Fuel Engineering; Nuclear Explosives Engineering; Weapons Engineering; Energy Systems Engineering; Engineering Sciences; Magnetic Fusion Engineering; and Material Fabrication. (LCL)

1st Global Conference on Biomedical Engineering & 9th Asian-Pacific Conference on Medical and Biological Engineering

CERN Document Server

Wang, Shyh-Hau; Yeh, Ming-Long

2015-01-01

This volume presents the proceedings of the 9th Asian-Pacific Conference on Medical and Biological Engineering (APCMBE 2014). The proceedings address a broad spectrum of topics from Bioengineering and Biomedicine, like Biomaterials, Artificial Organs, Tissue Engineering, Nanobiotechnology and Nanomedicine, Biomedical Imaging, Bio MEMS, Biosignal Processing, Digital Medicine, BME Education. It helps medical and biological engineering professionals to interact and exchange their ideas and experiences.

Challenges of medical and biological engineering and science

Energy Technology Data Exchange (ETDEWEB)

Magjarevic, R [University of Zagreb, Faculty of Electrical Engineering and Computing, Zagreb (Croatia)

2004-07-01

All aspects of biomedical engineering and science, from research and development, education and training, implementation in health care systems, internationalisation and globalisation, and other, new issues are present in the strategy and in action plans of the International Federation for Medical and Biological Engineering (IFMBE) which, with help of a large number of highly motivated volunteers, will stay in leading position in biomedical engineering and science.

Challenges of medical and biological engineering and science

International Nuclear Information System (INIS)

Magjarevic, R.

2004-01-01

All aspects of biomedical engineering and science, from research and development, education and training, implementation in health care systems, internationalisation and globalisation, and other, new issues are present in the strategy and in action plans of the International Federation for Medical and Biological Engineering (IFMBE) which, with help of a large number of highly motivated volunteers, will stay in leading position in biomedical engineering and science

Experiential Engineering through iGEM--An Undergraduate Summer Competition in Synthetic Biology

Science.gov (United States)

Mitchell, Rudolph; Dori, Yehudit Judy; Kuldell, Natalie H.

2011-01-01

Unlike students in other engineering disciplines, undergraduates in biological engineering typically have limited opportunity to develop design competencies, and even fewer chances to implement their designed projects. The international Genetically Engineered Machines (iGEM) competition is a student Synthetic Biology competition that, in 2009,…

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Energy Technology Data Exchange (ETDEWEB)

Madhavan, Aravind [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Rajiv Gandhi Centre for Biotechnology, Trivandrum (India); Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran, E-mail: sindhurgcb@gmail.com; Sukumaran, Rajeev K. [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Pandey, Ashok [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Center for Innovative and Applied Bioprocessing, Mohali, Punjab (India); Castro, Galliano Eulogio [Dpt. Ingeniería Química, Ambiental y de los Materiales Edificio, Universidad de Jaén, Jaén (Spain)

2017-04-25

The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Directory of Open Access Journals (Sweden)

Raveendran Sindhu

2017-04-01

Full Text Available The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

International Nuclear Information System (INIS)

Madhavan, Aravind; Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran; Sukumaran, Rajeev K.; Pandey, Ashok; Castro, Galliano Eulogio

2017-01-01

The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.

Future of Chemical Engineering: Integrating Biology into the Undergraduate ChE Curriculum

Science.gov (United States)

Mosto, Patricia; Savelski, Mariano; Farrell, Stephanie H.; Hecht, Gregory B.

2007-01-01

Integrating biology in the chemical engineering curriculum seems to be the future for chemical engineering programs nation and worldwide. Rowan University's efforts to address this need include a unique chemical engineering curriculum with an intensive biology component integrated throughout from freshman to senior years. Freshman and Sophomore…

Biofuel production in Escherichia coli. The role of metabolic engineering and synthetic biology

Energy Technology Data Exchange (ETDEWEB)

Clomburg, James M. [Rice Univ., Houston, TX (United States). Dept. of Chemical and Biomolecular Engineering; Gonzalez, Ramon [Rice Univ., Houston, TX (United States). Dept. of Chemical and Biomolecular Engineering; Rice Univ., Houston, TX (United States). Dept. of Bioengineering

2010-03-15

The microbial production of biofuels is a promising avenue for the development of viable processes for the generation of fuels from sustainable resources. In order to become cost and energy effective, these processes must utilize organisms that can be optimized to efficiently produce candidate fuels from a variety of feedstocks. Escherichia coli has become a promising host organism for the microbial production of biofuels in part due to the ease at which this organism can be manipulated. Advancements in metabolic engineering and synthetic biology have led to the ability to efficiently engineer E. coli as a biocatalyst for the production of a wide variety of potential biofuels from several biomass constituents. This review focuses on recent efforts devoted to engineering E. coli for the production of biofuels, with emphasis on the key aspects of both the utilization of a variety of substrates as well as the synthesis of several promising biofuels. Strategies for the efficient utilization of carbohydrates, carbohydrate mixtures, and noncarbohydrate carbon sources will be discussed along with engineering efforts for the exploitation of both fermentative and nonfermentative pathways for the production of candidate biofuels such as alcohols and higher carbon biofuels derived from fatty acid and isoprenoid pathways. Continued advancements in metabolic engineering and synthetic biology will help improve not only the titers, yields, and productivities of biofuels discussed herein, but also increase the potential range of compounds that can be produced. (orig.)

TOPICAL REVIEW: Stem cells engineering for cell-based therapy

Science.gov (United States)

Taupin, Philippe

2007-09-01

Stem cells carry the promise to cure a broad range of diseases and injuries, from diabetes, heart and muscular diseases, to neurological diseases, disorders and injuries. Significant progresses have been made in stem cell research over the past decade; the derivation of embryonic stem cells (ESCs) from human tissues, the development of cloning technology by somatic cell nuclear transfer (SCNT) and the confirmation that neurogenesis occurs in the adult mammalian brain and that neural stem cells (NSCs) reside in the adult central nervous system (CNS), including that of humans. Despite these advances, there may be decades before stem cell research will translate into therapy. Stem cell research is also subject to ethical and political debates, controversies and legislation, which slow its progress. Cell engineering has proven successful in bringing genetic research to therapy. In this review, I will review, in two examples, how investigators are applying cell engineering to stem cell biology to circumvent stem cells' ethical and political constraints and bolster stem cell research and therapy.

Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products

Directory of Open Access Journals (Sweden)

Weihua Guo

Full Text Available With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem. In brief, by reconstituting a biosynthetic pathway in a cell-free environment with the supplement of cofactors and substrates, the performance of each biosynthetic pathway could be evaluated and optimized systematically. Several value-added products, including chemicals, nutraceuticals, and drug precursors, have been biosynthesized as proof-of-concept demonstrations of in vitro metabolic engineering. This mini-review summarizes the recent progresses on the emerging topic of in vitro metabolic engineering and comments on the potential application of cell-free technology to speed up the “design-build-test” cycles of biomanufacturing. Keywords: Cell-free, Biosynthesis, Metabolic pathways, Design-build-test cycle

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

DEFF Research Database (Denmark)

Jullesson, David; David, Florian; Pfleger, Brian

2015-01-01

Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played...... chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes....... an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine...

XIV Mediterranean Conference on Medical and Biological Engineering and Computing

CERN Document Server

Christofides, Stelios; Pattichis, Constantinos

2016-01-01

This volume presents the proceedings of Medicon 2016, held in Paphos, Cyprus. Medicon 2016 is the XIV in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon 2016 is to provide updated information on the state of the art on Medical and Biological Engineering and Computing under the main theme “Systems Medicine for the Delivery of Better Healthcare Services”. Medical and Biological Engineering and Computing cover complementary disciplines that hold great promise for the advancement of research and development in complex medical and biological systems. Research and development in these areas are impacting the science and technology by advancing fundamental concepts in translational medicine, by helping us understand human physiology and function at multiple levels, by improving tools and techniques for the detection, prevention and treatment of disease. Medicon 2016 provides a common platform for the cross fer...

Expanding the chemical palate of cells by combining systems biology and metabolic engineering.

Science.gov (United States)

Curran, Kathleen A; Alper, Hal S

2012-07-01

The field of Metabolic Engineering has recently undergone a transformation that has led to a rapid expansion of the chemical palate of cells. Now, it is conceivable to produce nearly any organic molecule of interest using a cellular host. Significant advances have been made in the production of biofuels, biopolymers and precursors, pharmaceuticals and nutraceuticals, and commodity and specialty chemicals. Much of this rapid expansion in the field has been, in part, due to synergies and advances in the area of systems biology. Specifically, the availability of functional genomics, metabolomics and transcriptomics data has resulted in the potential to produce a wealth of new products, both natural and non-natural, in cellular factories. The sheer amount and diversity of this data however, means that uncovering and unlocking novel chemistries and insights is a non-obvious exercise. To address this issue, a number of computational tools and experimental approaches have been developed to help expedite the design process to create new cellular factories. This review will highlight many of the systems biology enabling technologies that have reduced the design cycle for engineered hosts, highlight major advances in the expanded diversity of products that can be synthesized, and conclude with future prospects in the field of metabolic engineering. Copyright © 2012 Elsevier Inc. All rights reserved.

Concise Review: Organ Engineering: Design, Technology, and Integration.

Science.gov (United States)

Kaushik, Gaurav; Leijten, Jeroen; Khademhosseini, Ali

2017-01-01

Engineering complex tissues and whole organs has the potential to dramatically impact translational medicine in several avenues. Organ engineering is a discipline that integrates biological knowledge of embryological development, anatomy, physiology, and cellular interactions with enabling technologies including biocompatible biomaterials and biofabrication platforms such as three-dimensional bioprinting. When engineering complex tissues and organs, core design principles must be taken into account, such as the structure-function relationship, biochemical signaling, mechanics, gradients, and spatial constraints. Technological advances in biomaterials, biofabrication, and biomedical imaging allow for in vitro control of these factors to recreate in vivo phenomena. Finally, organ engineering emerges as an integration of biological design and technical rigor. An overall workflow for organ engineering and guiding technology to advance biology as well as a perspective on necessary future iterations in the field is discussed. Stem Cells 2017;35:51-60. © 2016 AlphaMed Press.

Software Engineering Reviews and Audits

CERN Document Server

Summers, Boyd L

2011-01-01

Accurate software engineering reviews and audits have become essential to the success of software companies and military and aerospace programs. These reviews and audits define the framework and specific requirements for verifying software development efforts. Authored by an industry professional with three decades of experience, Software Engineering Reviews and Audits offers authoritative guidance for conducting and performing software first article inspections, and functional and physical configuration software audits. It prepares readers to answer common questions for conducting and perform

Science and engineering of nanodiamond particle surfaces for biological applications (Review).

Science.gov (United States)

Shenderova, Olga A; McGuire, Gary E

2015-09-05

Diamond has outstanding bulk properties such as super hardness, chemical inertness, biocompatibility, luminescence, to name just a few. In the nanoworld, in order to exploit these outstanding bulk properties, the surfaces of nanodiamond (ND) particles must be accordingly engineered for specific applications. Modification of functional groups on the ND's surface and the corresponding electrostatic properties determine their colloidal stability in solvents, formation of photonic crystals, controlled adsorption and release of cargo molecules, conjugation with biomolecules and polymers, and cellular uptake. The optical activity of the luminescent color centers in NDs depends on their proximity to the ND's surface and surface termination. In order to engineer the ND surface, a fundamental understanding of the specific structural features and sp(3)-sp(2) phase transformations on the surface of ND particles is required. In the case of ND particles produced by detonation of carbon containing explosives (detonation ND), it should also be taken into account that its structure depends on the synthesis parameters and subsequent processing. Thus, for development of a strategy of surface modification of detonation ND, it is imperative to know details of its production. In this review, the authors discuss ND particles structure, strategies for surface modification, electrokinetic properties of NDs in suspensions, and conclude with a brief overview of the relevant bioapplications.

From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

Science.gov (United States)

Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

Science.gov (United States)

McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals.

Science.gov (United States)

Jullesson, David; David, Florian; Pfleger, Brian; Nielsen, Jens

2015-11-15

Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes. Copyright © 2015 Elsevier Inc. All rights reserved.

Smart Polymeric Hydrogels for Cartilage Tissue Engineering: A Review on the Chemistry and Biological Functions.

Science.gov (United States)

Eslahi, Niloofar; Abdorahim, Marjan; Simchi, Abdolreza

2016-11-14

Stimuli responsive hydrogels (SRHs) are attractive bioscaffolds for tissue engineering. The structural similarity of SRHs to the extracellular matrix (ECM) of many tissues offers great advantages for a minimally invasive tissue repair. Among various potential applications of SRHs, cartilage regeneration has attracted significant attention. The repair of cartilage damage is challenging in orthopedics owing to its low repair capacity. Recent advances include development of injectable hydrogels to minimize invasive surgery with nanostructured features and rapid stimuli-responsive characteristics. Nanostructured SRHs with more structural similarity to natural ECM up-regulate cell-material interactions for faster tissue repair and more controlled stimuli-response to environmental changes. This review highlights most recent advances in the development of nanostructured or smart hydrogels for cartilage tissue engineering. Different types of stimuli-responsive hydrogels are introduced and their fabrication processes through physicochemical procedures are reported. The applications and characteristics of natural and synthetic polymers used in SRHs are also reviewed with an outline on clinical considerations and challenges.

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

NARCIS (Netherlands)

He, F.; Murabito, E.; Westerhoff, H.V.

2016-01-01

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

Proceedings of the European medical and biological engineering conference EMBEC '99 (Part I)

International Nuclear Information System (INIS)

Rehak, P.; Hutten, H.

1999-01-01

The proceedings books of the EMBEC '99 - European Medical and Biological Engineering Conference - are published in two parts as supplement 2 to the volume 37 of 'Medical and Biological Engineering and Computing', the official journal of the International Federation for Medical and Biological Engineering. More then 800 papers have been arranged in the order of the main topics and the topics of the special sessions of the conference. The paper of INIS relevance were worked up for INIS data bank. (author)

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Review of domestic radiation biology research

International Nuclear Information System (INIS)

Zheng Chun; Song Lingli; Ai Zihui

2011-01-01

Radiation biology research in China during the past ten years are reviewed. It should be noticed that radiation-biology should focus on microdosimetry, microbeam application, and radiation biological mechanism. (authors)

Cell-free synthetic biology for in vitro prototype engineering.

Science.gov (United States)

Moore, Simon J; MacDonald, James T; Freemont, Paul S

2017-06-15

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

6th European Conference of the International Federation for Medical and Biological Engineering

CERN Document Server

Vasic, Darko

2015-01-01

This volume presents the Proceedings of the 6th European Conference of the International Federation for Medical and Biological Engineering (MBEC2014), held in Dubrovnik September 7 – 11, 2014. The general theme of MBEC 2014 is "Towards new horizons in biomedical engineering" The scientific discussions in these conference proceedings include the following themes: - Biomedical Signal Processing - Biomedical Imaging and Image Processing - Biosensors and Bioinstrumentation - Bio-Micro/Nano Technologies - Biomaterials - Biomechanics, Robotics and Minimally Invasive Surgery - Cardiovascular, Respiratory and Endocrine Systems Engineering - Neural and Rehabilitation Engineering - Molecular, Cellular and Tissue Engineering - Bioinformatics and Computational Biology - Clinical Engineering and Health Technology Assessment - Health Informatics, E-Health and Telemedicine - Biomedical Engineering Education

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

Science.gov (United States)

Chiel, Hillel J.; McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge…

Plant synthetic biology.

Science.gov (United States)

Liu, Wusheng; Stewart, C Neal

2015-05-01

Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Applications of Engineered DNA-Binding Molecules Such as TAL Proteins and the CRISPR/Cas System in Biology Research

Directory of Open Access Journals (Sweden)

Toshitsugu Fujita

2015-09-01

Full Text Available Engineered DNA-binding molecules such as transcription activator-like effector (TAL or TALE proteins and the clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated proteins (Cas (CRISPR/Cas system have been used extensively for genome editing in cells of various types and species. The sequence-specific DNA-binding activities of these engineered DNA-binding molecules can also be utilized for other purposes, such as transcriptional activation, transcriptional repression, chromatin modification, visualization of genomic regions, and isolation of chromatin in a locus-specific manner. In this review, we describe applications of these engineered DNA-binding molecules for biological purposes other than genome editing.

Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

DEFF Research Database (Denmark)

Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

2016-01-01

Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches...... for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites....... The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production....

Synthetic Biology for Specialty Chemicals.

Science.gov (United States)

Markham, Kelly A; Alper, Hal S

2015-01-01

In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

A review of fibrin and fibrin composites for bone tissue engineering.

Science.gov (United States)

Noori, Alireza; Ashrafi, Seyed Jamal; Vaez-Ghaemi, Roza; Hatamian-Zaremi, Ashraf; Webster, Thomas J

2017-01-01

Tissue engineering has emerged as a new treatment approach for bone repair and regeneration seeking to address limitations associated with current therapies, such as autologous bone grafting. While many bone tissue engineering approaches have traditionally focused on synthetic materials (such as polymers or hydrogels), there has been a lot of excitement surrounding the use of natural materials due to their biologically inspired properties. Fibrin is a natural scaffold formed following tissue injury that initiates hemostasis and provides the initial matrix useful for cell adhesion, migration, proliferation, and differentiation. Fibrin has captured the interest of bone tissue engineers due to its excellent biocompatibility, controllable biodegradability, and ability to deliver cells and biomolecules. Fibrin is particularly appealing because its precursors, fibrinogen, and thrombin, which can be derived from the patient's own blood, enable the fabrication of completely autologous scaffolds. In this article, we highlight the unique properties of fibrin as a scaffolding material to treat bone defects. Moreover, we emphasize its role in bone tissue engineering nanocomposites where approaches further emulate the natural nanostructured features of bone when using fibrin and other nanomaterials. We also review the preparation methods of fibrin glue and then discuss a wide range of fibrin applications in bone tissue engineering. These include the delivery of cells and/or biomolecules to a defect site, distributing cells, and/or growth factors throughout other pre-formed scaffolds and enhancing the physical as well as biological properties of other biomaterials. Thoughts on the future direction of fibrin research for bone tissue engineering are also presented. In the future, the development of fibrin precursors as recombinant proteins will solve problems associated with using multiple or single-donor fibrin glue, and the combination of nanomaterials that allow for the

Thermostability of biological systems: fundamentals, challenges, and quantification.

Science.gov (United States)

He, Xiaoming

2011-01-01

This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

Understanding Biological Regulation Through Synthetic Biology.

Science.gov (United States)

Bashor, Caleb J; Collins, James J

2018-03-16

Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function. Expected final online publication date for the Annual Review of Biophysics Volume 47 is May 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

Science.gov (United States)

Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

2014-03-27

Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

A review of fibrin and fibrin composites for bone tissue engineering

Directory of Open Access Journals (Sweden)

Noori A

2017-07-01

Full Text Available Alireza Noori,1 Seyed Jamal Ashrafi,2 Roza Vaez-Ghaemi,3 Ashraf Hatamian-Zaremi,4 Thomas J Webster5 1Department of Tissue Engineering and Applied Cell Sciences, Faculty of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, 2School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran; 3Department of Chemical and Biological Engineering, Faculty of Biomedical Engineering, The University of British Columbia, Vancouver, BC, Canada; 4Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran; 5Department of Chemical Engineering, Northeastern University, Boston, MA, USA Abstract: Tissue engineering has emerged as a new treatment approach for bone repair and regeneration seeking to address limitations associated with current therapies, such as autologous bone grafting. While many bone tissue engineering approaches have traditionally focused on synthetic materials (such as polymers or hydrogels, there has been a lot of excitement surrounding the use of natural materials due to their biologically inspired properties. Fibrin is a natural scaffold formed following tissue injury that initiates hemostasis and provides the initial matrix useful for cell adhesion, migration, proliferation, and differentiation. Fibrin has captured the interest of bone tissue engineers due to its excellent biocompatibility, controllable biodegradability, and ability to deliver cells and biomolecules. Fibrin is particularly appealing because its precursors, fibrinogen, and thrombin, which can be derived from the patient’s own blood, enable the fabrication of completely autologous scaffolds. In this article, we highlight the unique properties of fibrin as a scaffolding material to treat bone defects. Moreover, we emphasize its role in bone tissue engineering nanocomposites where approaches further emulate the natural nanostructured features of bone when using fibrin and other nanomaterials. We also review the

Concise Review: Organ Engineering: Design, Technology, and Integration

NARCIS (Netherlands)

Kaushik, G.; Leijten, Jeroen Christianus Hermanus; Khademhosseini, A.

Engineering complex tissues and whole organs has the potential to dramatically impact translational medicine in several avenues. Organ engineering is a discipline that integrates biological knowledge of embryological development, anatomy, physiology, and cellular interactions with enabling

Biological mechanisms beyond network analysis via mathematical modeling. Comment on "Network science of biological systems at different scales: A review" by Marko Gosak et al.

Science.gov (United States)

Pedersen, Morten Gram

2018-03-01

Methods from network theory are increasingly used in research spanning from engineering and computer science to psychology and the social sciences. In this issue, Gosak et al. [1] provide a thorough review of network science applications to biological systems ranging from the subcellular world via neuroscience to ecosystems, with special attention to the insulin-secreting beta-cells in pancreatic islets.

Bacterial genome engineering and synthetic biology: combating pathogens.

Science.gov (United States)

Krishnamurthy, Malathy; Moore, Richard T; Rajamani, Sathish; Panchal, Rekha G

2016-11-04

The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.

Biomolecular engineering for nanobio/bionanotechnology

Science.gov (United States)

Nagamune, Teruyuki

2017-04-01

Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

Mechanical Engineering Department Technical Review

International Nuclear Information System (INIS)

Carr, R.B.; Denney, R.M.

1981-01-01

The Mechanical Engineering Department Technical Review is published to inform readers of various technical activities within the Department, promote exchange of ideas, and give credit to personnel who are achieving the results. The report is presented in two parts: technical achievements and publication abstracts. The first is divided into seven sections, each of which reports on an engineering division and its specific activities related to nuclear tests, nuclear explosives, weapons, energy systems, engineering sciences, magnetic fusion, and materials fabrication

A Review of Modeling Bioelectrochemical Systems: Engineering and Statistical Aspects

Directory of Open Access Journals (Sweden)

Shuai Luo

2016-02-01

Full Text Available Bioelectrochemical systems (BES are promising technologies to convert organic compounds in wastewater to electrical energy through a series of complex physical-chemical, biological and electrochemical processes. Representative BES such as microbial fuel cells (MFCs have been studied and advanced for energy recovery. Substantial experimental and modeling efforts have been made for investigating the processes involved in electricity generation toward the improvement of the BES performance for practical applications. However, there are many parameters that will potentially affect these processes, thereby making the optimization of system performance hard to be achieved. Mathematical models, including engineering models and statistical models, are powerful tools to help understand the interactions among the parameters in BES and perform optimization of BES configuration/operation. This review paper aims to introduce and discuss the recent developments of BES modeling from engineering and statistical aspects, including analysis on the model structure, description of application cases and sensitivity analysis of various parameters. It is expected to serves as a compass for integrating the engineering and statistical modeling strategies to improve model accuracy for BES development.

Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

Science.gov (United States)

Wang, Harris H; Church, George M

2011-01-01

Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

Plant synthetic biology for molecular engineering of signalling and development.

Science.gov (United States)

Nemhauser, Jennifer L; Torii, Keiko U

2016-03-02

Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes.

Science.gov (United States)

Matsumoto, Ken'ichiro; Taguchi, Seiichi

2013-12-01

The development of synthetic biology has transformed microbes into useful factories for producing valuable polymers and/or their precursors from renewable biomass. Recent progress at the interface of chemistry and biology has enabled the production of a variety of new biopolymers with properties that substantially differ from their petroleum-derived counterparts. This review touches on recent trials and achievements in the field of biopolymer synthesis, including chemo-enzymatically synthesized aliphatic polyesters, wholly biosynthesized lactate-based polyesters, polyhydroxyalkanoates and other unusual bacterially synthesized polyesters. The expanding diversities in structure and the material properties of biopolymers are key for exploring practical applications. The enzyme and metabolic engineering approaches toward this goal are discussed by shedding light on the successful case studies. Copyright © 2013 Elsevier Ltd. All rights reserved.

Designing synthetic biology.

Science.gov (United States)

Agapakis, Christina M

2014-03-21

Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

Aspergilli: Systems biology and industrial applications

DEFF Research Database (Denmark)

Knuf, Christoph; Nielsen, Jens

2012-01-01

possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

CellNet: Network Biology Applied to Stem Cell Engineering

Science.gov (United States)

Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

2014-01-01

SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

CellNet: network biology applied to stem cell engineering.

Science.gov (United States)

Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

2014-08-14

Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

A Biological Porin Engineered into a Molecular, Nanofluidic Diode

NARCIS (Netherlands)

Miedema, Henk; Vrouenraets, Maarten; Wierenga, Jenny; Meijberg, Wim; Robillard, George; Eisenberg, Bob

2007-01-01

We changed the nonrectifying biological porin OmpF into a nanofluidic diode. To that end, we engineered a pore that possesses two spatially separated selectivity filters of opposite charge where either cations or anions accumulate. The observed current inhibition under applied reverse bias voltage

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

Energy Technology Data Exchange (ETDEWEB)

Unkefer, Clifford J.; Sayre, Richard T.; Magnuson, Jon K.; Anderson, Daniel B.; Baxter, Ivan; Blaby, Ian K.; Brown, Judith K.; Carleton, Michael; Cattolico, Rose Ann; Dale, Taraka; Devarenne, Timothy P.; Downes, C. Meghan; Dutcher, Susan K.; Fox, David T.; Goodenough, Ursula; Jaworski, Jan; Holladay, Jonathan E.; Kramer, David M.; Koppisch, Andrew T.; Lipton, Mary S.; Marrone, Babetta L.; McCormick, Margaret; Molnár, István; Mott, John B.; Ogden, Kimberly L.; Panisko, Ellen A.; Pellegrini, Matteo; Polle, Juergen; Richardson, James W.; Sabarsky, Martin; Starkenburg, Shawn R.; Stormo, Gary D.; Teshima, Munehiro; Twary, Scott N.; Unkefer, Pat J.; Yuan, Joshua S.; Olivares, José A.

2017-03-01

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.

Physical activity and biological maturation: a systematic review

Directory of Open Access Journals (Sweden)

Eliane Denise Araújo Bacil

2015-03-01

Full Text Available OBJECTIVE: To analyze the association between physical activity (PA and biological maturation in children and adolescents. DATA SOURCE: We performed a systematic review in April 2013 in the electronic databases of PubMed/MEDLINE, SportDiscus, Web of Science and LILACS without time restrictions. A total of 628 potentially relevant articles were identified and 10 met the inclusion criteria for this review: cross-sectional or longitudinal studies, published in Portuguese, English or Spanish, with schoolchildren aged 9-15 years old of both genders. DATA SYNTHESIS: Despite the heterogeneity of the studies, there was an inverse association between PA and biological maturation. PA decreases with increased biological and chronological age in both genders. Boys tend to be more physically active than girls; however, when controlling for biological age, the gender differences disappear. The association between PA and timing of maturation varies between the genders. Variation in the timing of biological maturation affects the tracking of PA in early adolescent girls. This review suggests that mediators (BMI, depression, low self-esteem, and concerns about body weight can explain the association between PA and biological maturation. CONCLUSIONS: There is an association between PA and biological maturation. PA decreases with increasing biological age with no differences between genders. As for the timing of biological maturation, this association varies between genders.

A review of imaging techniques for systems biology

Directory of Open Access Journals (Sweden)

Po Ming J

2008-08-01

Full Text Available Abstract This paper presents a review of imaging techniques and of their utility in system biology. During the last decade systems biology has matured into a distinct field and imaging has been increasingly used to enable the interplay of experimental and theoretical biology. In this review, we describe and compare the roles of microscopy, ultrasound, CT (Computed Tomography, MRI (Magnetic Resonance Imaging, PET (Positron Emission Tomography, and molecular probes such as quantum dots and nanoshells in systems biology. As a unified application area among these different imaging techniques, examples in cancer targeting are highlighted.

Genome scale engineering techniques for metabolic engineering.

Science.gov (United States)

Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

2015-11-01

Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Using magnetic nanoparticles to manipulate biological objects

International Nuclear Information System (INIS)

Liu Yi; Gao Yu; Xu Chenjie

2013-01-01

The use of magnetic nanoparticles (MNPs) for the manipulation of biological objects, including proteins, genes, cellular organelles, bacteria, cells, and organs, are reviewed. MNPs are popular candidates for controlling and probing biological objects with a magnetic force. In the past decade, progress in the synthesis and surface engineering of MNPs has further enhanced this popularity. (topical review - magnetism, magnetic materials, and interdisciplinary research)

The Future of Metabolic Engineering and Synthetic Biology: Towards a Systematic Practice

Science.gov (United States)

Yadav, Vikramaditya G.; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

2012-01-01

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as ‘multivariate modular metabolic engineering’ (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. PMID:22629571

The Histochemistry and Cell Biology omnium-gatherum: the year 2015 in review.

Science.gov (United States)

Taatjes, Douglas J; Roth, Jürgen

2016-03-01

We provide here our annual review/synopsis of all of the articles published in Histochemistry and Cell Biology (HCB) for the preceding year. In 2015, HCB published 102 articles, representing a wide variety of topics and methodologies. For ease of access to these differing topics, we have created categories, as determined by the types of articles presented to provide a quick index representing the general areas covered. This year, these categories include: (1) advances in methodologies; (2) molecules in health and disease; (3) organelles, subcellular structures, and compartments; (4) the nucleus; (5) stem cells and tissue engineering; (6) cell cultures: properties and capabilities; (7) connective tissues and extracellular matrix; (8) developmental biology; (9) nervous system; (10) musculoskeletal system; (11) respiratory and cardiovascular system; (12) liver and gastrointestinal tract; and (13) male and female reproductive systems. Of note, the categories proceed from methods development, to molecules, intracellular compartments, stem cells and cell culture, extracellular matrix, developmental biology, and finishing with various organ systems, hopefully presenting a logical journey from methods to organismal molecules, cells, and whole tissue systems.

The future of metabolic engineering and synthetic biology: towards a systematic practice.

Science.gov (United States)

Yadav, Vikramaditya G; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

2012-05-01

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. Copyright © 2011 Elsevier Inc. All rights reserved.

Engineering biological systems toward a sustainable bioeconomy.

Science.gov (United States)

Lopes, Mateus Schreiner Garcez

2015-06-01

The nature of our major global risks calls for sustainable innovations to decouple economic growth from greenhouse gases emission. The development of sustainable technologies has been negatively impacted by several factors including sugar production costs, production scale, economic crises, hydraulic fracking development and the market inability to capture externality costs. However, advances in engineering of biological systems allow bridging the gap between exponential growth of knowledge about biology and the creation of sustainable value chains for a broad range of economic sectors. Additionally, industrial symbiosis of different biobased technologies can increase competitiveness and sustainability, leading to the development of eco-industrial parks. Reliable policies for carbon pricing and revenue reinvestments in disruptive technologies and in the deployment of eco-industrial parks could boost the welfare while addressing our major global risks toward the transition from a fossil to a biobased economy.

Milestones in software engineering and knowledge engineering history: a comparative review.

Science.gov (United States)

del Águila, Isabel M; Palma, José; Túnez, Samuel

2014-01-01

We present a review of the historical evolution of software engineering, intertwining it with the history of knowledge engineering because "those who cannot remember the past are condemned to repeat it." This retrospective represents a further step forward to understanding the current state of both types of engineerings; history has also positive experiences; some of them we would like to remember and to repeat. Two types of engineerings had parallel and divergent evolutions but following a similar pattern. We also define a set of milestones that represent a convergence or divergence of the software development methodologies. These milestones do not appear at the same time in software engineering and knowledge engineering, so lessons learned in one discipline can help in the evolution of the other one.

Synthetic biology: programming cells for biomedical applications.

Science.gov (United States)

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

Invited Review Article: Advanced light microscopy for biological space research

Science.gov (United States)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Invited Review Article: Advanced light microscopy for biological space research

International Nuclear Information System (INIS)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; Loon, Jack J. W. A. van; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-01-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy

Invited Review Article: Advanced light microscopy for biological space research

Energy Technology Data Exchange (ETDEWEB)

De Vos, Winnok H., E-mail: winnok.devos@uantwerpen.be [Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp (Belgium); Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, Ghent (Belgium); Beghuin, Didier [Lambda-X, Nivelles (Belgium); Schwarz, Christian J. [European Space Agency (ESA), ESTEC, TEC-MMG, Noordwijk (Netherlands); Jones, David B. [Institute for Experimental Orthopaedics and Biomechanics, Philipps University, Marburg (Germany); Loon, Jack J. W. A. van [Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, Amsterdam (Netherlands); Bereiter-Hahn, Juergen; Stelzer, Ernst H. K. [Physical Biology, BMLS (FB15, IZN), Goethe University, Frankfurt am Main (Germany)

2014-10-15

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Opportunities for Merging Chemical and Biological Synthesis

Science.gov (United States)

Wallace, Stephen; Balskus, Emily P.

2014-01-01

Organic chemists and metabolic engineers use largely orthogonal technologies to access small molecules like pharmaceuticals and commodity chemicals. As the use of biological catalysts and engineered organisms for chemical production grows, it is becoming increasingly evident that future efforts for chemical manufacture will benefit from the integration and unified expansion of these two fields. This review will discuss approaches that combine chemical and biological synthesis for small molecule production. We highlight recent advances in combining enzymatic and non-enzymatic catalysis in vitro, discuss the application of design principles from organic chemistry for engineering non-biological reactivity into enzymes, and describe the development of biocompatible chemistry that can be interfaced with microbial metabolism. PMID:24747284

Systems Biology of Metabolism: Annual Review of Biochemistry

DEFF Research Database (Denmark)

Nielsen, Jens

2017-01-01

Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are descr...

Milestones in Software Engineering and Knowledge Engineering History: A Comparative Review

Science.gov (United States)

del Águila, Isabel M.; Palma, José; Túnez, Samuel

2014-01-01

We present a review of the historical evolution of software engineering, intertwining it with the history of knowledge engineering because “those who cannot remember the past are condemned to repeat it.” This retrospective represents a further step forward to understanding the current state of both types of engineerings; history has also positive experiences; some of them we would like to remember and to repeat. Two types of engineerings had parallel and divergent evolutions but following a similar pattern. We also define a set of milestones that represent a convergence or divergence of the software development methodologies. These milestones do not appear at the same time in software engineering and knowledge engineering, so lessons learned in one discipline can help in the evolution of the other one. PMID:24624046

A Review of the Secondary Metabolites and Biological Activities of ...

African Journals Online (AJOL)

Review Article. A Review of the Secondary Metabolites and Biological. Activities of Tinospora crispa ... triterpenes have been isolated, some of which have also shown corresponding biological activities. The current review is an update on the .... were found to exhibit higher antioxidative potency than the synthetic antioxidant.

Engineering Liposomes and Nanoparticles for Biological Targeting

DEFF Research Database (Denmark)

Jølck, Rasmus Irming; Feldborg, Lise Nørkjær; Andersen, Simon

2011-01-01

Our ability to engineer nanomaterials for biological and medical applications is continuously increasing, and nanomaterial designs are becoming more and more complex. One very good example of this is the drug delivery field where nanoparticle systems can be used to deliver drugs specifically...... to diseased tissue. In the early days, the design of the nanoparticles was relatively simple, but today we can surface functionalize and manipulate material properties to target diseased tissue and build highly complex drug release mechanisms into our designs. One of the most promising strategies in drug...

The JSC Engineering Directorate Product Peer Review Process

Science.gov (United States)

Jenks, Kenneth C.

2009-01-01

The JSC Engineering Directorate has developed a Product Peer Review process in support of NASA policies for project management and systems engineering. The process complies with the requirements of NPR 7120.5, NPR 7123.1 and NPR 7150.2 and follows the guidance in NASA/SP-2007-6105. This presentation will give an overview of the process followed by a brief demonstration of an actual peer review, with audience participation.

A Study of Technical Engineering Peer Reviews at NASA

Science.gov (United States)

Chao, Lawrence P.; Tumer, Irem Y.; Bell, David G.

2003-01-01

This report describes the state of practices of design reviews at NASA and research into what can be done to improve peer review practices. There are many types of reviews at NASA: required and not, formalized and informal, programmatic and technical. Standing project formal reviews such as the Preliminary Design Review and Critical Design Review are a required part of every project and mission development. However, the technical, engineering peer reviews that support teams' work on such projects are informal, some times ad hoc, and inconsistent across the organization. The goal of this work is to identify best practices and lessons learned from NASA's experience, supported by academic research and methodologies to ultimately improve the process. This research has determined that the organization, composition, scope, and approach of the reviews impact their success. Failure Modes and Effects Analysis (FMEA) can identify key areas of concern before or in the reviews. Product definition tools like the Project Priority Matrix, engineering-focused Customer Value Chain Analysis (CVCA), and project or system-based Quality Function Deployment (QFD) help prioritize resources in reviews. The use of information technology and structured design methodologies can strengthen the engineering peer review process to help NASA work towards error-proofing the design process.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

Science.gov (United States)

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search

Nanodimensional and Nanocrystalline Apatites and Other Calcium Orthophosphates in Biomedical Engineering, Biology and Medicine

Directory of Open Access Journals (Sweden)

Sergey V. Dorozhkin

2009-11-01

Full Text Available Recent developments in biomineralization have already demonstrated that nanosized particles play an important role in the formation of hard tissues of animals. Namely, the basic inorganic building blocks of bones and teeth of mammals are nanodimensional and nanocrystalline calcium orthophosphates (in the form of apatites of a biological origin. In mammals, tens to hundreds nanocrystals of a biological apatite were found to be combined into self-assembled structures under the control of various bioorganic matrixes. In addition, the structures of both dental enamel and bones could be mimicked by an oriented aggregation of nanosized calcium orthophosphates, determined by the biomolecules. The application and prospective use of nanodimensional and nanocrystalline calcium orthophosphates for a clinical repair of damaged bones and teeth are also known. For example, a greater viability and a better proliferation of various types of cells were detected on smaller crystals of calcium orthophosphates. Thus, the nanodimensional and nanocrystalline forms of calcium orthophosphates have a great potential to revolutionize the field of hard tissue engineering starting from bone repair and augmentation to the controlled drug delivery devices. This paper reviews current state of knowledge and recent developments of this subject starting from the synthesis and characterization to biomedical and clinical applications. More to the point, this review provides possible directions of future research and development.

Engineering Robustness of Microbial Cell Factories.

Science.gov (United States)

Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J

2017-10-01

Metabolic engineering and synthetic biology offer great prospects in developing microbial cell factories capable of converting renewable feedstocks into fuels, chemicals, food ingredients, and pharmaceuticals. However, prohibitively low production rate and mass concentration remain the major hurdles in industrial processes even though the biosynthetic pathways are comprehensively optimized. These limitations are caused by a variety of factors unamenable for host cell survival, such as harsh industrial conditions, fermentation inhibitors from biomass hydrolysates, and toxic compounds including metabolic intermediates and valuable target products. Therefore, engineered microbes with robust phenotypes is essential for achieving higher yield and productivity. In this review, the recent advances in engineering robustness and tolerance of cell factories is described to cope with these issues and briefly introduce novel strategies with great potential to enhance the robustness of cell factories, including metabolic pathway balancing, transporter engineering, and adaptive laboratory evolution. This review also highlights the integration of advanced systems and synthetic biology principles toward engineering the harmony of overall cell function, more than the specific pathways or enzymes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proceedings of Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2015

Energy Technology Data Exchange (ETDEWEB)

Silver, Pamela [Harvard Univ., Cambridge, MA (United States); SEED 2015 Conference Chair; Flach, Evan [American Institute of Chemical Engineers; SEED 2015 Conference Organizer

2016-10-27

Synthetic Biology is an emerging discipline that seeks to accelerate the process of engineering biology. As such, the tools are broadly applicable to application areas, including chemicals and biofuels, materials, medicine and agriculture. A characteristic of the field is to look holistically at cellular design, from sensing and genetic circuitry to the manipulation of cellular processes and actuators, to controlling metabolism, to programming multicellular behaviors. Further, the types of cells that are manipulated are broad, from in vitro systems to microbes and fungi to mammalian and plant cells and living animals. Many of the projects in synthetic biology seek to move biochemical functions across organisms. The field is highly interdisciplinary with faculty and students spread across departments that focus on engineering (biological, chemical, electrical, mechanical, civil, computer science) and basic science (biology and systems biology, chemistry, physics). While there have been many one-off workshops and meeting on synthetic biology, the 2014 Synthetic Biology: Engineering, Evolution and Design (SEED) was the first of an annual conference series that serves as a reliable place to pull together the involved disciplines in order to organize and exchange advances in the science and technology in the field. Further, the SEED conferences have a strong focus on industry, with many companies represented and actively participating. A number of these companies have started major efforts in synthetic biology including large companies (e.g., Pfizer, Novartis, Dow, Dupont, BP, Total), smaller companies have recently gone public (e.g., Amyris, Gevo, Intrexon), and many start-ups (e.g., Teslagen, Refactored Materials, Pivot, Genomatica). There are a number of loosely affiliated Synthetic Biology Centers, including ones at MIT, Boston University, UCSD, UCSF, UC-Berkeley, Imperial College, Oxford, and ETH. SEED 2015 will serve as the primary meeting at which international

Chemical Engineering in the "BIO" World.

Science.gov (United States)

Chiarappa, Gianluca; Grassi, Mario; Abrami, Michela; Abbiati, Roberto Andrea; Barba, Anna Angela; Boisen, Anja; Brucato, Valerio; Ghersi, Giulio; Caccavo, Diego; Cascone, Sara; Caserta, Sergio; Elvassore, Nicola; Giomo, Monica; Guido, Stefano; Lamberti, Gaetano; Larobina, Domenico; Manca, Davide; Marizza, Paolo; Tomaiuolo, Giovanna; Grassi, Gabriele

2017-01-01

Modern Chemical Engineering was born around the end of the 19th century in Great Britain, Germany, and the USA, the most industrialized countries at that time. Milton C. Whitaker, in 1914, affirmed that the difference between Chemistry and Chemical Engineering lies in the capability of chemical engineers to transfer laboratory findings to the industrial level. Since then, Chemical Engineering underwent huge transformations determining the detachment from the original Chemistry nest. The beginning of the sixties of the 20th century saw the development of a new branch of Chemical Engineering baptized Biomedical Engineering by Peppas and Langer and that now we can name Biological Engineering. Interestingly, although Biological Engineering focused on completely different topics from Chemical Engineering ones, it resorted to the same theoretical tools such as, for instance, mass, energy and momentum balances. Thus, the birth of Biological Engineering may be considered as a Darwinian evolution of Chemical Engineering similar to that experienced by mammals which, returning to water, used legs and arms to swim. From 1960 on, Biological Engineering underwent a considerable evolution as witnessed by the great variety of topics covered such as hemodialysis, release of synthetic drugs, artificial organs and, more recently, delivery of small interfering RNAs (siRNA). This review, based on the activities developed in the frame of our PRIN 2010-11 (20109PLMH2) project, tries to recount origins and evolution of Chemical Engineering illustrating several examples of recent and successful applications in the biological field. This, in turn, may stimulate the discussion about the Chemical Engineering students curriculum studiorum update. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Biologically inspired robotic inspectors: the engineering reality and future outlook (Keynote address)

Science.gov (United States)

Bar-Cohen, Yoseph

2005-04-01

Human errors have long been recognized as a major factor in the reliability of nondestructive evaluation results. To minimize such errors, there is an increasing reliance on automatic inspection tools that allow faster and consistent tests. Crawlers and various manipulation devices are commonly used to perform variety of inspection procedures that include C-scan with contour following capability to rapidly inspect complex structures. The emergence of robots has been the result of the need to deal with parts that are too complex to handle by a simple automatic system. Economical factors are continuing to hamper the wide use of robotics for inspection applications however technology advances are increasingly changing this paradigm. Autonomous robots, which may look like human, can potentially address the need to inspect structures with configuration that are not predetermined. The operation of such robots that mimic biology may take place at harsh or hazardous environments that are too dangerous for human presence. Biomimetic technologies such as artificial intelligence, artificial muscles, artificial vision and numerous others are increasingly becoming common engineering tools. Inspired by science fiction, making biomimetic robots is increasingly becoming an engineering reality and in this paper the state-of-the-art will be reviewed and the outlook for the future will be discussed.

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology

DEFF Research Database (Denmark)

Dvořák, Pavel; Nikel, Pablo Ivan; Damborskýc, Jiří

2017-01-01

pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack...... of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow....... In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering...

Developments in the Tools and Methodologies of Synthetic Biology

Science.gov (United States)

Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.; Freemont, Paul

2014-01-01

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a “body of knowledge” from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community. PMID:25505788

Developments in the tools and methodologies of synthetic biology

Directory of Open Access Journals (Sweden)

Richard eKelwick

2014-11-01

Full Text Available Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices or systems. However, biological systems are generally complex and unpredictable and are therefore intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a ‘body of knowledge’ from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled and its functionality tested. At each stage of the design cycle an expanding repertoire of tools is being developed. In this review we highlight several of these tools in terms of their applications and benefits to the synthetic biology community.

A review exploring biological activities of hydrazones

Directory of Open Access Journals (Sweden)

Garima Verma

2014-01-01

Full Text Available The development of novel compounds, hydrazones has shown that they possess a wide variety of biological activities viz. antimicrobial, anticonvulsant, antidepressant, anti-inflammatory, analgesic, antiplatelet, antimalarial, anticancer, antifungal, antitubercular, antiviral, cardio protective etc., Hydrazones/azomethines/imines possess-NHN = CH- and constitute an important class of compounds for new drug development. A number of researchers have synthesized and evaluated the biological activities of hydrazones. This review aims at highlighting the diverse biological activities of hydrazones.

Engineering Parameters in Bioreactor's Design: A Critical Aspect in Tissue Engineering

Science.gov (United States)

Amoabediny, Ghassem; Pouran, Behdad; Tabesh, Hadi; Shokrgozar, Mohammad Ali; Haghighipour, Nooshin; Khatibi, Nahid; Mottaghy, Khosrow; Zandieh-Doulabi, Behrouz

2013-01-01

Bioreactors are important inevitable part of any tissue engineering (TE) strategy as they aid the construction of three-dimensional functional tissues. Since the ultimate aim of a bioreactor is to create a biological product, the engineering parameters, for example, internal and external mass transfer, fluid velocity, shear stress, electrical current distribution, and so forth, are worth to be thoroughly investigated. The effects of such engineering parameters on biological cultures have been addressed in only a few preceding studies. Furthermore, it would be highly inefficient to determine the optimal engineering parameters by trial and error method. A solution is provided by emerging modeling and computational tools and by analyzing oxygen, carbon dioxide, and nutrient and metabolism waste material transports, which can simulate and predict the experimental results. Discovering the optimal engineering parameters is crucial not only to reduce the cost and time of experiments, but also to enhance efficacy and functionality of the tissue construct. This review intends to provide an inclusive package of the engineering parameters together with their calculation procedure in addition to the modeling techniques in TE bioreactors. PMID:24000327

Engineering parameters in bioreactor's design: a critical aspect in tissue engineering.

Science.gov (United States)

Salehi-Nik, Nasim; Amoabediny, Ghassem; Pouran, Behdad; Tabesh, Hadi; Shokrgozar, Mohammad Ali; Haghighipour, Nooshin; Khatibi, Nahid; Anisi, Fatemeh; Mottaghy, Khosrow; Zandieh-Doulabi, Behrouz

2013-01-01

Bioreactors are important inevitable part of any tissue engineering (TE) strategy as they aid the construction of three-dimensional functional tissues. Since the ultimate aim of a bioreactor is to create a biological product, the engineering parameters, for example, internal and external mass transfer, fluid velocity, shear stress, electrical current distribution, and so forth, are worth to be thoroughly investigated. The effects of such engineering parameters on biological cultures have been addressed in only a few preceding studies. Furthermore, it would be highly inefficient to determine the optimal engineering parameters by trial and error method. A solution is provided by emerging modeling and computational tools and by analyzing oxygen, carbon dioxide, and nutrient and metabolism waste material transports, which can simulate and predict the experimental results. Discovering the optimal engineering parameters is crucial not only to reduce the cost and time of experiments, but also to enhance efficacy and functionality of the tissue construct. This review intends to provide an inclusive package of the engineering parameters together with their calculation procedure in addition to the modeling techniques in TE bioreactors.

Neurophysiology and neural engineering: a review.

Science.gov (United States)

Prochazka, Arthur

2017-08-01

Neurophysiology is the branch of physiology concerned with understanding the function of neural systems. Neural engineering (also known as neuroengineering) is a discipline within biomedical engineering that uses engineering techniques to understand, repair, replace, enhance, or otherwise exploit the properties and functions of neural systems. In most cases neural engineering involves the development of an interface between electronic devices and living neural tissue. This review describes the origins of neural engineering, the explosive development of methods and devices commencing in the late 1950s, and the present-day devices that have resulted. The barriers to interfacing electronic devices with living neural tissues are many and varied, and consequently there have been numerous stops and starts along the way. Representative examples are discussed. None of this could have happened without a basic understanding of the relevant neurophysiology. I also consider examples of how neural engineering is repaying the debt to basic neurophysiology with new knowledge and insight. Copyright © 2017 the American Physiological Society.

Value-Engineering Review for Numerical Control

Science.gov (United States)

Warner, J. L.

1984-01-01

Selecting parts for conversion from conventional machining to numerical control, value-engineering review performed for every part to identify potential changes to part design that result in increased production efficiency.

Preparing Synthetic Biology for the World

Directory of Open Access Journals (Sweden)

Gerd H.G. Moe-Behrens

2013-01-01

Full Text Available Synthetic Biology promises low-cost, exponentially scalable products and global health solutions in the form of self-replicating organisms, or living devices. As these promises are realized, proof-of-concept systems will gradually migrate from tightly regulated laboratory or industrial environments into private spaces as, for instance, probiotic health products, food, and even do-it-yourself bioengineered systems. What additional steps, if any, should be taken before releasing engineered self-replicating organisms into a broader user space? In this review, we explain how studies of genetically modified organisms lay groundwork for the future landscape of biosafety. Early in the design process, biological engineers are anticipating potential hazards and developing innovative tools to mitigate risk. Here, we survey lessons learned, ongoing efforts to engineer intrinsic biocontainment, and how different stakeholders in synthetic biology can act to accomplish best practices for biosafety.

Advancing the science of forest hydrology A challenge to agricultural and biological engineers

Science.gov (United States)

Devendra Amatya; Wayne Skaggs; Carl Trettin

2009-01-01

For more than a century, agricultural and biological engineers have provided major advances in science, engineering, and technology to increase food and fiber production to meet the demands of a rapidly growing global population. The land base for these technological advances has originated largely from forested lands, which have experienced dramatic declines over the...

Review of Biological Network Data and Its Applications

Directory of Open Access Journals (Sweden)

Donghyeon Yu

2013-12-01

Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

Multiscale computer modeling in biomechanics and biomedical engineering

CERN Document Server

2013-01-01

This book reviews the state-of-the-art in multiscale computer modeling, in terms of both accomplishments and challenges. The information in the book is particularly useful for biomedical engineers, medical physicists and researchers in systems biology, mathematical biology, micro-biomechanics and biomaterials who are interested in how to bridge between traditional biomedical engineering work at the organ and tissue scales, and the newer arenas of cellular and molecular bioengineering.

Surface modification of polyester biomaterials for tissue engineering

International Nuclear Information System (INIS)

Jiao Yanpeng; Cui Fuzhai

2007-01-01

Surfaces play an important role in a biological system for most biological reactions occurring at surfaces and interfaces. The development of biomaterials for tissue engineering is to create perfect surfaces which can provoke specific cellular responses and direct new tissue regeneration. The improvement in biocompatibility of biomaterials for tissue engineering by directed surface modification is an important contribution to biomaterials development. Among many biomaterials used for tissue engineering, polyesters have been well documented for their excellent biodegradability, biocompatibility and nontoxicity. However, poor hydrophilicity and the lack of natural recognition sites on the surface of polyesters have greatly limited their further application in the tissue engineering field. Therefore, how to introduce functional groups or molecules to polyester surfaces, which ideally adjust cell/tissue biological functions, becomes more and more important. In this review, recent advances in polyester surface modification and their applications are reviewed. The development of new technologies or methods used to modify polyester surfaces for developing their biocompatibility is introduced. The results of polyester surface modifications by surface morphological modification, surface chemical group/charge modification, surface biomacromolecule modification and so on are reported in detail. Modified surface properties of polyesters directly related to in vitro/vivo biological performances are presented as well, such as protein adsorption, cell attachment and growth and tissue response. Lastly, the prospect of polyester surface modification is discussed, especially the current conception of biomimetic and molecular recognition. (topical review)

Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

Science.gov (United States)

Oerther, Daniel B.

2002-01-01

Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

Engineering Parameters in Bioreactor’s Design: A Critical Aspect in Tissue Engineering

Directory of Open Access Journals (Sweden)

Nasim Salehi-Nik

2013-01-01

Full Text Available Bioreactors are important inevitable part of any tissue engineering (TE strategy as they aid the construction of three-dimensional functional tissues. Since the ultimate aim of a bioreactor is to create a biological product, the engineering parameters, for example, internal and external mass transfer, fluid velocity, shear stress, electrical current distribution, and so forth, are worth to be thoroughly investigated. The effects of such engineering parameters on biological cultures have been addressed in only a few preceding studies. Furthermore, it would be highly inefficient to determine the optimal engineering parameters by trial and error method. A solution is provided by emerging modeling and computational tools and by analyzing oxygen, carbon dioxide, and nutrient and metabolism waste material transports, which can simulate and predict the experimental results. Discovering the optimal engineering parameters is crucial not only to reduce the cost and time of experiments, but also to enhance efficacy and functionality of the tissue construct. This review intends to provide an inclusive package of the engineering parameters together with their calculation procedure in addition to the modeling techniques in TE bioreactors.

Bioinspired Hydrogels to Engineer Cancer Microenvironments.

Science.gov (United States)

Park, Kyung Min; Lewis, Daniel; Gerecht, Sharon

2017-06-21

Recent research has demonstrated that tumor microenvironments play pivotal roles in tumor development and metastasis through various physical, chemical, and biological factors, including extracellular matrix (ECM) composition, matrix remodeling, oxygen tension, pH, cytokines, and matrix stiffness. An emerging trend in cancer research involves the creation of engineered three-dimensional tumor models using bioinspired hydrogels that accurately recapitulate the native tumor microenvironment. With recent advances in materials engineering, many researchers are developing engineered tumor models, which are promising platforms for the study of cancer biology and for screening of therapeutic agents for better clinical outcomes. In this review, we discuss the development and use of polymeric hydrogel materials to engineer native tumor ECMs for cancer research, focusing on emerging technologies in cancer engineering that aim to accelerate clinical outcomes.

Synthetic biology approaches to engineering the nitrogen symbiosis in cereals.

Science.gov (United States)

Rogers, Christian; Oldroyd, Giles E D

2014-05-01

Nitrogen is abundant in the earth's atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.

Ethical Risk Management Education in Engineering: A Systematic Review.

Science.gov (United States)

Guntzburger, Yoann; Pauchant, Thierry C; Tanguy, Philippe A

2017-04-01

Risk management is certainly one of the most important professional responsibilities of an engineer. As such, this activity needs to be combined with complex ethical reflections, and this requirement should therefore be explicitly integrated in engineering education. In this article, we analyse how this nexus between ethics and risk management is expressed in the engineering education research literature. It was done by reviewing 135 articles published between 1980 and March 1, 2016. These articles have been selected from 21 major journals that specialize in engineering education, engineering ethics and ethics education. Our review suggests that risk management is mostly used as an anecdote or an example when addressing ethics issues in engineering education. Further, it is perceived as an ethical duty or requirement, achieved through rational and technical methods. However, a small number of publications do offer some critical analyses of ethics education in engineering and their implications for ethical risk and safety management. Therefore, we argue in this article that the link between risk management and ethics should be further developed in engineering education in order to promote the progressive change toward more socially and environmentally responsible engineering practices. Several research trends and issues are also identified and discussed in order to support the engineering education community in this project.

Biosynthesis of therapeutic natural products using synthetic biology.

Science.gov (United States)

Awan, Ali R; Shaw, William M; Ellis, Tom

2016-10-01

Natural products are a group of bioactive structurally diverse chemicals produced by microorganisms and plants. These molecules and their derivatives have contributed to over a third of the therapeutic drugs produced in the last century. However, over the last few decades traditional drug discovery pipelines from natural products have become far less productive and far more expensive. One recent development with promise to combat this trend is the application of synthetic biology to therapeutic natural product biosynthesis. Synthetic biology is a young discipline with roots in systems biology, genetic engineering, and metabolic engineering. In this review, we discuss the use of synthetic biology to engineer improved yields of existing therapeutic natural products. We further describe the use of synthetic biology to combine and express natural product biosynthetic genes in unprecedented ways, and how this holds promise for opening up completely new avenues for drug discovery and production. Copyright © 2016 Elsevier B.V. All rights reserved.

A review of free-piston engine history and applications

Energy Technology Data Exchange (ETDEWEB)

Mikalsen, R.; Roskilly, A.P. [School of Marine Science and Technology, University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU (United Kingdom)

2007-10-15

This document reviews the history of free-piston internal combustion engines, from the air compressors and gas generators used in the mid-20th century through to recent free-piston hydraulic engines and linear electric generators. Unique features of the free-piston engine are presented and their effects on engine operation are discussed, along with potential advantages and disadvantages compared to conventional engines. The paper focuses mainly on developed engines where operational data has been reported. Finally, the potential of the free-piston engine is evaluated and the most promising designs identified. (author)

Toward scalable parts families for predictable design of biological circuits.

Science.gov (United States)

Lucks, Julius B; Qi, Lei; Whitaker, Weston R; Arkin, Adam P

2008-12-01

Our current ability to engineer biological circuits is hindered by design cycles that are costly in terms of time and money, with constructs failing to operate as desired, or evolving away from the desired function once deployed. Synthetic biologists seek to understand biological design principles and use them to create technologies that increase the efficiency of the genetic engineering design cycle. Central to the approach is the creation of biological parts--encapsulated functions that can be composited together to create new pathways with predictable behaviors. We define five desirable characteristics of biological parts--independence, reliability, tunability, orthogonality and composability, and review studies of small natural and synthetic biological circuits that provide insights into each of these characteristics. We propose that the creation of appropriate sets of families of parts with these properties is a prerequisite for efficient, predictable engineering of new function in cells and will enable a large increase in the sophistication of genetic engineering applications.

Tissue engineering for human urethral reconstruction: systematic review of recent literature.

Science.gov (United States)

de Kemp, Vincent; de Graaf, Petra; Fledderus, Joost O; Ruud Bosch, J L H; de Kort, Laetitia M O

2015-01-01

Techniques to treat urethral stricture and hypospadias are restricted, as substitution of the unhealthy urethra with tissue from other origins (skin, bladder or buccal mucosa) has some limitations. Therefore, alternative sources of tissue for use in urethral reconstructions are considered, such as ex vivo engineered constructs. To review recent literature on tissue engineering for human urethral reconstruction. A search was made in the PubMed and Embase databases restricted to the last 25 years and the English language. A total of 45 articles were selected describing the use of tissue engineering in urethral reconstruction. The results are discussed in four groups: autologous cell cultures, matrices/scaffolds, cell-seeded scaffolds, and clinical results of urethral reconstructions using these materials. Different progenitor cells were used, isolated from either urine or adipose tissue, but slightly better results were obtained with in vitro expansion of urothelial cells from bladder washings, tissue biopsies from the bladder (urothelium) or the oral cavity (buccal mucosa). Compared with a synthetic scaffold, a biological scaffold has the advantage of bioactive extracellular matrix proteins on its surface. When applied clinically, a non-seeded matrix only seems suited for use as an onlay graft. When a tubularized substitution is the aim, a cell-seeded construct seems more beneficial. Considerable experience is available with tissue engineering of urethral tissue in vitro, produced with cells of different origin. Clinical and in vivo experiments show promising results.

Synthetic Biology: Engineering, Evolution and Design (SEED) Conference 2014

Energy Technology Data Exchange (ETDEWEB)

Voigt, Christopher [Massachusetts Institute of Technology

2014-07-01

SEED2014 focused on advances in the science and technology emerging from the field of synthetic biology. We broadly define this as technologies that accelerate the process of genetic engineering. It highlighted new tool development, as well as the application of these tools to diverse problems in biotechnology, including therapeutics, industrial chemicals and fuels, natural products, and agriculture. Systems spanned from in vitro experiments and viruses, through diverse bacteria, to eukaryotes (yeast, mammalian cells, plants).

Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient.

Science.gov (United States)

An, Gary; Faeder, James; Vodovotz, Yoram

2008-01-01

The pathophysiology of the burn patient manifests the full spectrum of the complexity of the inflammatory response. In the acute phase, inflammation may have negative effects via capillary leak, the propagation of inhalation injury, and development of multiple organ failure. Attempts to mediate these processes remain a central subject of burn care research. Conversely, inflammation is a necessary prologue and component in the later stage processes of wound healing. Despite the volume of information concerning the cellular and molecular processes involved in inflammation, there exists a significant gap between the knowledge of mechanistic pathophysiology and the development of effective clinical therapeutic regimens. Translational systems biology (TSB) is the application of dynamic mathematical modeling and certain engineering principles to biological systems to integrate mechanism with phenomenon and, importantly, to revise clinical practice. This study will review the existing applications of TSB in the areas of inflammation and wound healing, relate them to specific areas of interest to the burn community, and present an integrated framework that links TSB with traditional burn research.

Structural Interfaces and Attachments in Biology

CERN Document Server

Birman, Victor; Genin, Guy

2013-01-01

Attachment of dissimilar materials in engineering and surgical practice is a perennial challenge. Bimaterial attachment sites are common locations for injury, repeated injury, and mechanical failure. Nature presents several highly effective solutions to the challenge of bimaterial attachment that differ from those found in engineering practice. Structural Interfaces and Attachments in Biology describes the attachment of dissimilar materials from multiple perspectives. The text will simultaneously elucidate natural bimaterial attachments and outline engineering principles underlying successful attachments to the communities of tissue engineers and surgeons. Included an in-depth analysis of the biology of attachments in the body and mechanisms by which robust attachments are formed, a review of current concepts of attaching dissimilar materials in surgical practice and a discussion of bioengineering approaches that are currently being developed. This book also: Provides the first comprehensive treatment of phys...

Bibliographical review on the teaching of Biology and research

Directory of Open Access Journals (Sweden)

Mª Luz Rodríguez Palmero

2000-09-01

Full Text Available This review complements another one done by the same author, in 1997, regarding the role of comprehending the concept of cell in the learning of Biology. In addition, some general papers on science education that provide a better understanding of research approaches used in the investigation of this topic have been included. The reviewed papers have been organized into categories according to the object of study, the relevance assigned to the cell concept, and the framework of analysis. The review shows that the concept of cell is very important in the biological conceptualization, however, it also shows the need of additional research on this matter, from theoretical frameworks that pay more attention to the psychological level, in order to provide some guidance to improve the teaching and learning processes of the biological content that presupose the comprehension of living beings.

Spark ignition natural gas engines-A review

International Nuclear Information System (INIS)

Cho, Haeng Muk; He, Bang-Quan

2007-01-01

Natural gas is a promising alternative fuel to meet strict engine emission regulations in many countries. Natural gas engines can operate at lean burn and stoichiometric conditions with different combustion and emission characteristics. In this paper, the operating envelope, fuel economy, emissions, cycle-to-cycle variations in indicated mean effective pressure and strategies to achieve stable combustion of lean burn natural gas engines are highlighted. Stoichiometric natural gas engines are briefly reviewed. To keep the output power and torque of natural gas engines comparable to those of their gasoline or Diesel counterparts, high boost pressure should be used. High activity catalyst for methane oxidation and lean deNOx system or three way catalyst with precise air-fuel ratio control strategies should be developed to meet future stringent emission standards

5th European Conference of the International Federation for Medical and Biological Engineering

CERN Document Server

European IFMBE MBEC : Cooperation for Effective Healthcare

2012-01-01

This volume presents the 5th European Conference of the International Federation for Medical and Biological Engineering (EMBEC),  held in Budapest, 14-18 September, 2011. The scientific discussion on the conference and in this conference proceedings include the following issues: - Signal & Image Processing - ICT - Clinical Engineering and Applications - Biomechanics and Fluid Biomechanics - Biomaterials and Tissue Repair - Innovations and Nanotechnology - Modeling and Simulation - Education and Professional

A model of engineering materials inspired by biological tissues

Directory of Open Access Journals (Sweden)

Holeček M.

2009-12-01

Full Text Available The perfect ability of living tissues to control and adapt their mechanical properties to varying external conditions may be an inspiration for designing engineering materials. An interesting example is the smooth muscle tissue since this "material" is able to change its global mechanical properties considerably by a subtle mechanism within individual muscle cells. Multi-scale continuum models may be useful in designing essentially simpler engineering materials having similar properties. As an illustration we present the model of an incompressible material whose microscopic structure is formed by flexible, soft but incompressible balls connected mutually by linear springs. This simple model, however, shows a nontrivial nonlinear behavior caused by the incompressibility of balls and is very sensitive on some microscopic parameters. It may elucidate the way by which "small" changes in biopolymer networks within individual muscular cells may control the stiffness of the biological tissue, which outlines a way of designing similar engineering materials. The 'balls and springs' material presents also prestress-induced stiffening and allows elucidating a contribution of extracellular fluids into the tissue’s viscous properties.

Review of Pasteuria penetrans: Biology, Ecology, and Biological Control Potential.

Science.gov (United States)

Chen, Z X; Dickson, D W

1998-09-01

Pasteuria penetrans is a mycelial, endospore-forming, bacterial parasite that has shown great potential as a biological control agent of root-knot nematodes. Considerable progress has been made during the last 10 years in understanding its biology and importance as an agent capable of effectively suppressing root-knot nematodes in field soil. The objective of this review is to summarize the current knowledge of the biology, ecology, and biological control potential of P. penetrans and other Pasteuria members. Pasteuria spp. are distributed worldwide and have been reported from 323 nematode species belonging to 116 genera of free-living, predatory, plant-parasitic, and entomopathogenic nematodes. Artificial cultivation of P. penetrans has met with limited success; large-scale production of endospores depends on in vivo cultivation. Temperature affects endospore attachment, germination, pathogenesis, and completion of the life cycle in the nematode pseudocoelom. The biological control potential of Pasteuria spp. have been demonstrated on 20 crops; host nematodes include Belonolaimus longicaudatus, Heterodera spp., Meloidogyne spp., and Xiphinema diversicaudatum. Pasteuria penetrans plays an important role in some suppressive soils. The efficacy of the bacterium as a biological control agent has been examined. Approximately 100,000 endospores/g of soil provided immediate control of the peanut root-knot nematode, whereas 1,000 and 5,000 endospores/g of soil each amplified in the host nematode and became suppressive after 3 years.

Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective.

Science.gov (United States)

Tadmor, Brigitta; Tidor, Bruce

2005-09-01

Progress in the life sciences, including genome sequencing and high-throughput experimentation, offers an opportunity for understanding biology and medicine from a systems perspective. This 'new view', which complements the more traditional component-based approach, involves the integration of biological research with approaches from engineering disciplines and computer science. The result is more than a new set of technologies. Rather, it promises a fundamental reconceptualization of the life sciences based on the development of quantitative and predictive models to describe crucial processes. To achieve this change, learning communities are being formed at the interface of the life sciences, engineering and computer science. Through these communities, research and education will be integrated across disciplines and the challenges associated with multidisciplinary team-based science will be addressed.

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. PMID:20150964

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Directory of Open Access Journals (Sweden)

Eric Young

2010-01-01

Full Text Available The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1 the process units and associated streams of the central dogma, (2 the intrinsic regulatory mechanisms, and (3 the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Synthetic biology: tools to design, build, and optimize cellular processes.

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Agent-based modelling in synthetic biology.

Science.gov (United States)

Gorochowski, Thomas E

2016-11-30

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

The path to next generation biofuels: successes and challenges in the era of synthetic biology

Science.gov (United States)

2010-01-01

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels. PMID:20089184

A systematic literature review on reviews and meta-analyses of biologically based CAM-practices for cancer patients

DEFF Research Database (Denmark)

Paludan-Müller, Christine; Lunde, Anita; Johannessen, Helle

2010-01-01

levels of evidence and were excluded from further evaluation. Among the 32 high-quality reviews the most reviewed practices were soy/plant hormones (7), Chinese herbal medicine (7), antioxidants (5) and mistletoe (4). Fifteen of the 32 reviews included data on the efficacy of biologically-based CAM......-practices against cancer, but none of the reviews concluded a positive effect on the cancer. Reviews including data on quality of life (10) and/or reduction of side effects (12) showed promising, but yet insufficient evidence for Chinese herbal medicine against pain  and side effects of chemotherapy, and mistletoe......Purpose To provide an overview and evaluate the evidence of biologically based CAM-practices for cancer patients. Methods Pubmed, Social Science Citation Index, AMED and the Cochrane library were systematically searched for reviews on effects of biologically based CAM-practices, including herbal...

Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

Science.gov (United States)

Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

2017-03-01

Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Straight vegetable oils usage in a compression ignition engine - A review

Energy Technology Data Exchange (ETDEWEB)

Misra, R.D.; Murthy, M.S. [Mechanical Engineering Department, National Institute of Technology, Silchar 788010, Assam (India)

2010-12-15

The ever increasing fossil fuel usage and cost, environmental concern has forced the world to look for alternatives. Straight vegetable oils in compression ignition engine are a ready solution available, however, with certain limitations and with some advantages as reported by many researchers. A comprehensive and critical review is presented specifically pertaining to straight vegetable oils usage in diesel engine. A detailed record of historical events described. Research carried out specifically under Indian conditions and international research work on the usage of straight vegetable oils in the diesel engine is separately reviewed. Many researchers have reported that straight vegetable oils in small percentage blends with diesel when used lower capacity diesel engines have shown great promise with regards to the thermal performance as well exhaust emissions. This has been explained in detail. Finally based on the review of international as well as Indian research a SWOT analysis is carried out. The review concludes that there is still scope for research in this area. (author)

Biological and mechanical evaluation of a Bio-Hybrid scaffold for autologous valve tissue engineering

Energy Technology Data Exchange (ETDEWEB)

Jahnavi, S [Stem Cell and Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, TN 600036 (India); Tissue Culture Laboratory, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojappura, Trivandrum, Kerala 695012 (India); Saravanan, U [Department of Civil Engineering, Indian Institute of Technology Madras, Chennai, TN 600036 (India); Arthi, N [Stem Cell and Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, TN 600036 (India); Bhuvaneshwar, G S [Department of Engineering Design, Indian Institute of Technology Madras, Chennai, TN 600036 (India); Kumary, T V [Tissue Culture Laboratory, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojappura, Trivandrum, Kerala 695012 (India); Rajan, S [Madras Medical Mission, Institute of Cardio-Vascular Diseases, Mogappair, Chennai, Tamil Nadu 600037 (India); Verma, R S, E-mail: vermars@iitm.ac.in [Stem Cell and Molecular Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, TN 600036 (India)

2017-04-01

Major challenge in heart valve tissue engineering for paediatric patients is the development of an autologous valve with regenerative capacity. Hybrid tissue engineering approach is recently gaining popularity to design scaffolds with desired biological and mechanical properties that can remodel post implantation. In this study, we fabricated aligned nanofibrous Bio-Hybrid scaffold made of decellularized bovine pericardium: polycaprolactone-chitosan with optimized polymer thickness to yield the desired biological and mechanical properties. CD44{sup +}, αSMA{sup +}, Vimentin{sup +} and CD105{sup −} human valve interstitial cells were isolated and seeded on these Bio-Hybrid scaffolds. Subsequent biological evaluation revealed interstitial cell proliferation with dense extra cellular matrix deposition that indicated the viability for growth and proliferation of seeded cells on the scaffolds. Uniaxial mechanical tests along axial direction showed that the Bio-Hybrid scaffolds has at least 20 times the strength of the native valves and its stiffness is nearly 3 times more than that of native valves. Biaxial and uniaxial mechanical studies on valve interstitial cells cultured Bio-Hybrid scaffolds revealed that the response along the axial and circumferential direction was different, similar to native valves. Overall, our findings suggest that Bio-Hybrid scaffold is a promising material for future development of regenerative heart valve constructs in children. - Highlights: • We report detailed biological and mechanical investigations of a Bio-Hybrid scaffold. • Optimized polymer thickness yielded desired biological and mechanical properties. • Bio-Hybrid scaffold revealed hVIC proliferation with dense ECM deposition. • Biaxial testing indicated that Bio-Hybrid scaffolds are mechanically stronger than native valves. • Bio-Hybrid scaffold is a promising material for autologous valve tissue engineering.

PGASO: A synthetic biology tool for engineering a cellulolytic yeast

Directory of Open Access Journals (Sweden)

Chang Jui-Jen

2012-07-01

Full Text Available Abstract Background To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. Results A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO, that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei, a beta-glucosidase (from a cow rumen fungus, a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. Conclusions This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools.

Synthetic biology for microbial production of lipid-based biofuels.

Science.gov (United States)

d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

2015-12-01

The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing. Published by Elsevier Ltd.

Synthetic biology for microbial production of lipid-based biofuels

Energy Technology Data Exchange (ETDEWEB)

d' Espaux, L; Mendez-Perez, D; Li, R; Keasling, JD

2015-10-23

The risks of maintaining current CO₂ emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO₂ produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here in this paper we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. Lastly, we further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing.

Genetically engineered mouse models of craniopharyngioma: an opportunity for therapy development and understanding of tumor biology.

Science.gov (United States)

Apps, John Richard; Martinez-Barbera, Juan Pedro

2017-05-01

Adamantinomatous craniopharyngioma (ACP) is the commonest tumor of the sellar region in childhood. Two genetically engineered mouse models have been developed and are giving valuable insights into ACP biology. These models have identified novel pathways activated in tumors, revealed an important function of paracrine signalling and extended conventional theories about the role of organ-specific stem cells in tumorigenesis. In this review, we summarize these mouse models, what has been learnt, their limitations and open questions for future research. We then discussed how these mouse models may be used to test novel therapeutics against potentially targetable pathways recently identified in human ACP. © 2017 The Authors. Brain Pathology published by John Wiley & Sons Ltd on behalf of International Society of Neuropathology.

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

Review of biological monitoring programs at nuclear facilities

International Nuclear Information System (INIS)

Quintana, L.R.; Oakes, T.W.; Shank, K.E.

Biological monitoring programs, as well as relevant radioecological research studies, are reviewed at specific Department of Energy facilities; the program at Oak Ridge National Laboratory is discussed in detail. The biological measurements that are being used for interpreting the impact of a facility on its surrounding environment and nearby population are given. Suggestions which could facilitate interlaboratory comparison studies are presented

[Synthetic biology and rearrangements of microbial genetic material].

Science.gov (United States)

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

Advances and prospects in metabolic engineering of Zymomonas mobilis.

Science.gov (United States)

Wang, Xia; He, Qiaoning; Yang, Yongfu; Wang, Jingwen; Haning, Katie; Hu, Yun; Wu, Bo; He, Mingxiong; Zhang, Yaoping; Bao, Jie; Contreras, Lydia M; Yang, Shihui

2018-04-05

Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Recent advances in systems metabolic engineering tools and strategies.

Science.gov (United States)

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Applications of synthetic biology in materials science].

Science.gov (United States)

Zhao, Tianxin; Zhong, Chao

2017-03-25

Materials are the basis for human being survival and social development. To keep abreast with the increasing needs from all aspects of human society, there are huge needs in the development of advanced materials as well as high-efficiency but low-cost manufacturing strategies that are both sustainable and tunable. Synthetic biology, a new engineering principle taking gene regulation and engineering design as the core, greatly promotes the development of life sciences. This discipline has also contributed to the development of material sciences and will continuously bring new ideas to future new material design. In this paper, we review recent advances in applications of synthetic biology in material sciences, with the focus on how synthetic biology could enable synthesis of new polymeric biomaterials and inorganic materials, phage display and directed evolution of proteins relevant to materials development, living functional materials, engineered bacteria-regulated artificial photosynthesis system as well as applications of gene circuits for material sciences.

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

Science.gov (United States)

Marcheschi, Ryan J.; Gronenberg, Luisa S.; Liao, James C.

2014-01-01

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. This article reviews advances of 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. PMID:23589443

An Alternative Perspective for Malaysian Engineering Education: A Review from Year 2000-2012

Science.gov (United States)

Jayarajah, Kamaleswaran; Saat, Rohaida Mohd; Rauf, Rose Amnah Abdul

2013-01-01

The purpose of this study is to explore the research base of engineering education in the "Journal of Engineering Education" ("JEE") through an analysis review of articles for a 12-year period, from 2000 to 2012. The research base review focuses on identifying five characteristics of engineering education: (a) temporal…

The PLOS ONE Synthetic Biology Collection: Six Years and Counting

Science.gov (United States)

Peccoud, Jean; Isalan, Mark

2012-01-01

Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community. PMID:22916228

A Systematic Literature Review of US Engineering Ethics Interventions.

Science.gov (United States)

Hess, Justin L; Fore, Grant

2018-04-01

Promoting the ethical formation of engineering students through the cultivation of their discipline-specific knowledge, sensitivity, imagination, and reasoning skills has become a goal for many engineering education programs throughout the United States. However, there is neither a consensus throughout the engineering education community regarding which strategies are most effective towards which ends, nor which ends are most important. This study provides an overview of engineering ethics interventions within the U.S. through the systematic analysis of articles that featured ethical interventions in engineering, published in select peer-reviewed journals, and published between 2000 and 2015. As a core criterion, each journal article reviewed must have provided an overview of the course as well as how the authors evaluated course-learning goals. In sum, 26 articles were analyzed with a coding scheme that included 56 binary items. The results indicate that the most common methods for integrating ethics into engineering involved exposing students to codes/standards, utilizing case studies, and discussion activities. Nearly half of the articles had students engage with ethical heuristics or philosophical ethics. Following the presentation of the results, this study describes in detail four articles to highlight less common but intriguing pedagogical methods and evaluation techniques. The findings indicate that there is limited empirical work on ethics education within engineering across the United States. Furthermore, due to the large variation in goals, approaches, and evaluation methods described across interventions, this study does not detail "best" practices for integrating ethics into engineering. The science and engineering education community should continue exploring the relative merits of different approaches to ethics education in engineering.

Neoproteoglycans in tissue engineering

Science.gov (United States)

Weyers, Amanda; Linhardt, Robert J.

2014-01-01

Proteoglycans, comprised of a core protein to which glycosaminoglycan chains are covalently linked, are an important structural and functional family of macromolecules found in the extracellular matrix. Advances in our understanding of biological interactions have lead to a greater appreciation for the need to design tissue engineering scaffolds that incorporate mimetics of key extracellular matrix components. A variety of synthetic and semisynthetic molecules and polymers have been examined by tissue engineers that serve as structural, chemical and biological replacements for proteoglycans. These proteoglycan mimetics have been referred to as neoproteoglycans and serve as functional and therapeutic replacements for natural proteoglycans that are often unavailable for tissue engineering studies. Although neoproteoglycans have important limitations, such as limited signaling ability and biocompatibility, they have shown promise in replacing the natural activity of proteoglycans through cell and protein binding interactions. This review focuses on the recent in vivo and in vitro tissue engineering applications of three basic types of neoproteoglycan structures, protein–glycosaminoglycan conjugates, nano-glycosaminoglycan composites and polymer–glycosaminoglycan complexes. PMID:23399318

Chemical and biological sensors based on defect-engineered graphene mesh field-effect transistors.

Science.gov (United States)

Cho, Seunghee H; Kwon, Sun Sang; Yi, Jaeseok; Park, Won Il

2016-01-01

Graphene has been intensively studied for applications to high-performance sensors, but the sensing characteristics of graphene devices have varied from case to case, and the sensing mechanism has not been satisfactorily determined thus far. In this review, we describe recent progress in engineering of the defects in graphene grown by a silica-assisted chemical vapor deposition technique and elucidate the effect of the defects upon the electrical response of graphene sensors. This review provides guidelines for engineering and/or passivating defects to improve sensor performance and reliability.

Euclea undulata Thunb.: Review of its botany, ethnomedicinal uses, phytochemistry and biological activities.

Science.gov (United States)

Maroyi, Alfred

2017-11-01

Euclea undulata (E. undulata) is traditionally used for the treatment of body pains, chest complaints, cough, diabetes, diarrhoea, headaches, heart diseases and toothaches in southern Africa. This study was aimed at reviewing the botany, ethnopharmacology and biological activities of E. undulata in southern Africa. Results presented in this study are based on review of literature using search engines such as Science Direct, Springerlink, Scopus, PubMed, Web of Science, BioMed Central and Google Scholar. Herbal medicine is prepared from the decoctions of the roots, bark and leaves, and extracts of these plant parts have demonstrated anticholinesterase, anti-inflammatory, antimicrobial, antimycobacterial, antiplasmodial, antioxidant and hypoglycaemic activities. Multiple classes of phytochemical compounds such alkaloids, diterpenes, fatty acids, flavonoids, glycosides, naphthoquinones, phenolics, phytosterols, reducing sugars, saponins and tannins have been isolated from the species. E. undulata has a lot of potential as herbal medicine in tropical Africa, and advanced research is required aimed at correlating its medicinal uses with the phytochemistry and pharmacological properties. Copyright © 2017 Hainan Medical University. Production and hosting by Elsevier B.V. All rights reserved.

Mechanical Engineering Department. Technical review

Energy Technology Data Exchange (ETDEWEB)

Simecka, W.B.; Condouris, R.A.; Talaber, C. (eds.)

1980-01-01

The Mechanical Engineering Department Technical Review is published to (1) inform the readers of various technical activities within the Department, (2) promote exchange of ideas, and (3) give credit to the personnel who are achieving the results. The report is formatted into two parts: technical achievements and publication abstracts. The first is divided into eight sections, one for each Division in the Department providing the reader with the names of the personnel and the Division accomplishing the work.

Mechanical engineering department technical review

International Nuclear Information System (INIS)

Carr, R.B.; Denney, R.M.

1981-01-01

The Mechanical Engineering Department Technical Review is published to: (1) inform the readers of various technical activities within the department, (2) promote exchange of ideas, and (3) give credit to the personnel who are achieving the results. The report is formatted into two parts: technical acievements and publication abstracts. The first is divided into eight sections, one for each division in the department providing the reader with the names of the personnel and the division accomplishing the work

Mechanical Engineering Department. Technical review

International Nuclear Information System (INIS)

Simecka, W.B.; Condouris, R.A.; Talaber, C.

1980-01-01

The Mechanical Engineering Department Technical Review is published to (1) inform the readers of various technical activities within the Department, (2) promote exchange of ideas, and (3) give credit to the personnel who are achieving the results. The report is formatted into two parts: technical achievements and publication abstracts. The first is divided into eight sections, one for each Division in the Department providing the reader with the names of the personnel and the Division accomplishing the work

Institute for Multiscale Modeling of Biological Interactions

Energy Technology Data Exchange (ETDEWEB)

Paulaitis, Michael E; Garcia-Moreno, Bertrand; Lenhoff, Abraham

2009-12-26

The Institute for Multiscale Modeling of Biological Interactions (IMMBI) has two primary goals: Foster interdisciplinary collaborations among faculty and their research laboratories that will lead to novel applications of multiscale simulation and modeling methods in the biological sciences and engineering; and Building on the unique biophysical/biology-based engineering foundations of the participating faculty, train scientists and engineers to apply computational methods that collectively span multiple time and length scales of biological organization. The success of IMMBI will be defined by the following: Size and quality of the applicant pool for pre-doctoral and post-doctoral fellows; Academic performance; Quality of the pre-doctoral and post-doctoral research; Impact of the research broadly and to the DOE (ASCR program) mission; Distinction of the next career step for pre-doctoral and post-doctoral fellows; and Faculty collaborations that result from IMMBI activities. Specific details about accomplishments during the three years of DOE support for IMMBI have been documented in Annual Progress Reports (April 2005, June 2006, and March 2007) and a Report for a National Academy of Sciences Review (October 2005) that were submitted to DOE on the dates indicated. An overview of these accomplishments is provided.

Artificially Engineered Protein Polymers.

Science.gov (United States)

Yang, Yun Jung; Holmberg, Angela L; Olsen, Bradley D

2017-06-07

Modern polymer science increasingly requires precise control over macromolecular structure and properties for engineering advanced materials and biomedical systems. The application of biological processes to design and synthesize artificial protein polymers offers a means for furthering macromolecular tunability, enabling polymers with dispersities of ∼1.0 and monomer-level sequence control. Taking inspiration from materials evolved in nature, scientists have created modular building blocks with simplified monomer sequences that replicate the function of natural systems. The corresponding protein engineering toolbox has enabled the systematic development of complex functional polymeric materials across areas as diverse as adhesives, responsive polymers, and medical materials. This review discusses the natural proteins that have inspired the development of key building blocks for protein polymer engineering and the function of these elements in material design. The prospects and progress for scalable commercialization of protein polymers are reviewed, discussing both technology needs and opportunities.

[Biomedical engineering today : An overview from the viewpoint of the German Biomedical Engineering Society].

Science.gov (United States)

Schlötelburg, C; Becks, T; Stieglitz, T

2010-08-01

Biomedical engineering is characterized by the interdisciplinary co-operation of technology, science, and ways of thinking, probably more than any other technological area. The close interaction of engineering and information sciences with medicine and biology results in innovative products and methods, but also requires high standards for the interdisciplinary transfer of ideas into products for patients' benefits. This article describes the situation of biomedical engineering in Germany. It displays characteristics of the medical device industry and ranks it with respect to the international market. The research landscape is described as well as up-to-date research topics and trends. The national funding situation of research in biomedical engineering is reviewed and existing innovation barriers are discussed.

Modeling planarian regeneration: a primer for reverse-engineering the worm.

Directory of Open Access Journals (Sweden)

Daniel Lobo

Full Text Available A mechanistic understanding of robust self-assembly and repair capabilities of complex systems would have enormous implications for basic evolutionary developmental biology as well as for transformative applications in regenerative biomedicine and the engineering of highly fault-tolerant cybernetic systems. Molecular biologists are working to identify the pathways underlying the remarkable regenerative abilities of model species that perfectly regenerate limbs, brains, and other complex body parts. However, a profound disconnect remains between the deluge of high-resolution genetic and protein data on pathways required for regeneration, and the desired spatial, algorithmic models that show how self-monitoring and growth control arise from the synthesis of cellular activities. This barrier to progress in the understanding of morphogenetic controls may be breached by powerful techniques from the computational sciences-using non-traditional modeling approaches to reverse-engineer systems such as planaria: flatworms with a complex bodyplan and nervous system that are able to regenerate any body part after traumatic injury. Currently, the involvement of experts from outside of molecular genetics is hampered by the specialist literature of molecular developmental biology: impactful collaborations across such different fields require that review literature be available that presents the key functional capabilities of important biological model systems while abstracting away from the often irrelevant and confusing details of specific genes and proteins. To facilitate modeling efforts by computer scientists, physicists, engineers, and mathematicians, we present a different kind of review of planarian regeneration. Focusing on the main patterning properties of this system, we review what is known about the signal exchanges that occur during regenerative repair in planaria and the cellular mechanisms that are thought to underlie them. By establishing an

A Review of Cell Adhesion Studies for Biomedical and Biological Applications

Science.gov (United States)

Ahmad Khalili, Amelia; Ahmad, Mohd Ridzuan

2015-01-01

Cell adhesion is essential in cell communication and regulation, and is of fundamental importance in the development and maintenance of tissues. The mechanical interactions between a cell and its extracellular matrix (ECM) can influence and control cell behavior and function. The essential function of cell adhesion has created tremendous interests in developing methods for measuring and studying cell adhesion properties. The study of cell adhesion could be categorized into cell adhesion attachment and detachment events. The study of cell adhesion has been widely explored via both events for many important purposes in cellular biology, biomedical, and engineering fields. Cell adhesion attachment and detachment events could be further grouped into the cell population and single cell approach. Various techniques to measure cell adhesion have been applied to many fields of study in order to gain understanding of cell signaling pathways, biomaterial studies for implantable sensors, artificial bone and tooth replacement, the development of tissue-on-a-chip and organ-on-a-chip in tissue engineering, the effects of biochemical treatments and environmental stimuli to the cell adhesion, the potential of drug treatments, cancer metastasis study, and the determination of the adhesion properties of normal and cancerous cells. This review discussed the overview of the available methods to study cell adhesion through attachment and detachment events. PMID:26251901

A Review of Cell Adhesion Studies for Biomedical and Biological Applications

Directory of Open Access Journals (Sweden)

Amelia Ahmad Khalili

2015-08-01

Full Text Available Cell adhesion is essential in cell communication and regulation, and is of fundamental importance in the development and maintenance of tissues. The mechanical interactions between a cell and its extracellular matrix (ECM can influence and control cell behavior and function. The essential function of cell adhesion has created tremendous interests in developing methods for measuring and studying cell adhesion properties. The study of cell adhesion could be categorized into cell adhesion attachment and detachment events. The study of cell adhesion has been widely explored via both events for many important purposes in cellular biology, biomedical, and engineering fields. Cell adhesion attachment and detachment events could be further grouped into the cell population and single cell approach. Various techniques to measure cell adhesion have been applied to many fields of study in order to gain understanding of cell signaling pathways, biomaterial studies for implantable sensors, artificial bone and tooth replacement, the development of tissue-on-a-chip and organ-on-a-chip in tissue engineering, the effects of biochemical treatments and environmental stimuli to the cell adhesion, the potential of drug treatments, cancer metastasis study, and the determination of the adhesion properties of normal and cancerous cells. This review discussed the overview of the available methods to study cell adhesion through attachment and detachment events.

Is nanotechnology the key to unravel and engineer biological processes?

Science.gov (United States)

Navarro, Melba; Planell, Josep A

2012-01-01

Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.

Synthetic biology platform technologies for antimicrobial applications.

Science.gov (United States)

Braff, Dana; Shis, David; Collins, James J

2016-10-01

The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels. Copyright © 2016 Elsevier B.V. All rights reserved.

Biological Activities of Royal Jelly - Review

Directory of Open Access Journals (Sweden)

Crenguţa I. Pavel

2011-10-01

Full Text Available Royal jelly is a secretion product of the cephalic glands of nurse bees that has been used for centuries for itsextraordinary properties and health effects. This bibliographic study aims to review many of the scientific findingsand research that prove many of the remarkable various actions, effects and some uses of royal jelly. There are takeninto consideration numerous biological properties and effects of royal jelly: antioxidant, neurotrophic, hipoglicemiant, hipocholesterolemiant and hepatoprotective, hypotensive and blood pressure regulatory, antitumor, antibiotic, anti-inflammatory, immunomodulatory and anti-allergic, general tonic and antiaging. Royal jelly is one ofthe most studied bee products, but there still remains much to reveal about its biochemistry and biological activity infuture research for our health and life benefit.

Production and comparison of fuel properties, engine performance, and emission characteristics of biodiesel from various non-edible vegetable oils: A review

International Nuclear Information System (INIS)

Ashraful, A.M.; Masjuki, H.H.; Kalam, M.A.; Rizwanul Fattah, I.M.; Imtenan, S.; Shahir, S.A.; Mobarak, H.M.

2014-01-01

Highlights: • Overview of current energy situation. • Overview of biology, distribution and chemistry of various non-edible oil resources. • Comparison of fuel properties of various biodiesels produced from various non-edible oils. • Comparison of engine performance and emission characteristics of reviewed biodiesels. - Abstract: Energy demand is increasing dramatically because of the fast industrial development, rising population, expanding urbanization, and economic growth in the world. To fulfill this energy demand, a large amount of fuel is widely used from different fossil resources. Burning of fossil fuels has caused serious detrimental environmental consequences. The application of biodiesel has shown a positive impact in resolving these issues. Edible vegetable oils are one of the potential feedstocks for biodiesel production. However, as the use of edible oils will jeopardize food supplies and biodiversity, non-edible vegetable oils, also known as second-generation feedstocks, are considered potential substitutes of edible food crops for biodiesel production. This paper introduces some species of non-edible vegetables whose oils are potential sources of biodiesel. These species are Pongamia pinnata (karanja), Calophyllum inophyllum (Polanga), Maduca indica (mahua), Hevea brasiliensis (rubber seed), Cotton seed, Simmondsia chinesnsis (Jojoba), Nicotianna tabacum (tobacco), Azadirachta indica (Neem), Linum usitatissimum (Linseed) and Jatropha curcas (Jatropha). Various aspects of non-edible feedstocks, such as biology, distribution, and chemistry, the biodiesel’s physicochemical properties, and its effect on engine performance and emission, are reviewed based on published articles. From the review, fuel properties are found to considerably vary depending on feedstocks. Analysis of the performance results revealed that most of the biodiesel generally give higher brake thermal efficiency and lower brake-specific fuel consumption. Emission results

Cell microenvironment engineering and monitoring for tissue engineering and regenerative medicine: the recent advances.

Science.gov (United States)

Barthes, Julien; Özçelik, Hayriye; Hindié, Mathilde; Ndreu-Halili, Albana; Hasan, Anwarul; Vrana, Nihal Engin

2014-01-01

In tissue engineering and regenerative medicine, the conditions in the immediate vicinity of the cells have a direct effect on cells' behaviour and subsequently on clinical outcomes. Physical, chemical, and biological control of cell microenvironment are of crucial importance for the ability to direct and control cell behaviour in 3-dimensional tissue engineering scaffolds spatially and temporally. In this review, we will focus on the different aspects of cell microenvironment such as surface micro-, nanotopography, extracellular matrix composition and distribution, controlled release of soluble factors, and mechanical stress/strain conditions and how these aspects and their interactions can be used to achieve a higher degree of control over cellular activities. The effect of these parameters on the cellular behaviour within tissue engineering context is discussed and how these parameters are used to develop engineered tissues is elaborated. Also, recent techniques developed for the monitoring of the cell microenvironment in vitro and in vivo are reviewed, together with recent tissue engineering applications where the control of cell microenvironment has been exploited. Cell microenvironment engineering and monitoring are crucial parts of tissue engineering efforts and systems which utilize different components of the cell microenvironment simultaneously can provide more functional engineered tissues in the near future.

Cell Microenvironment Engineering and Monitoring for Tissue Engineering and Regenerative Medicine: The Recent Advances

Directory of Open Access Journals (Sweden)

Julien Barthes

2014-01-01

Full Text Available In tissue engineering and regenerative medicine, the conditions in the immediate vicinity of the cells have a direct effect on cells’ behaviour and subsequently on clinical outcomes. Physical, chemical, and biological control of cell microenvironment are of crucial importance for the ability to direct and control cell behaviour in 3-dimensional tissue engineering scaffolds spatially and temporally. In this review, we will focus on the different aspects of cell microenvironment such as surface micro-, nanotopography, extracellular matrix composition and distribution, controlled release of soluble factors, and mechanical stress/strain conditions and how these aspects and their interactions can be used to achieve a higher degree of control over cellular activities. The effect of these parameters on the cellular behaviour within tissue engineering context is discussed and how these parameters are used to develop engineered tissues is elaborated. Also, recent techniques developed for the monitoring of the cell microenvironment in vitro and in vivo are reviewed, together with recent tissue engineering applications where the control of cell microenvironment has been exploited. Cell microenvironment engineering and monitoring are crucial parts of tissue engineering efforts and systems which utilize different components of the cell microenvironment simultaneously can provide more functional engineered tissues in the near future.

Proceedings of the 8. Mediterranean Conference on Medical and Biological Engineering and Computing (Medicon `98)

Energy Technology Data Exchange (ETDEWEB)

Christofides, Stelios; Pattichis, Constantinos; Schizas, Christos; Keravnou-Papailiou, Elpida; Kaplanis, Prodromos; Spyros, Spyrou; Christodoulides, George; Theodoulou, Yiannis [eds.

1999-12-31

Medicon `98 is the eighth in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon `98 is to provide updated information on the state of the art on medical and biological engineering and computing. Medicon `98 was held in Lemesos, Cyprus, between 14-17 June, 1998. The full papers of the proceedings were published on CD and consisted of 190 invited and submitted papers. A book of abstracts was also published in paper form and was available to all the participants. Twenty seven papers fall within the scope of INIS and are dealing with Nuclear Medicine,Computerized Tomography, Radiology, Radiotherapy, Magnetic Resonance Imaging and Personnel Dosimetry (eds).

Proceedings of the 8. Mediterranean Conference on Medical and Biological Engineering and Computing (Medicon '98)

International Nuclear Information System (INIS)

Christofides, Stelios; Pattichis, Constantinos; Schizas, Christos; Keravnou-Papailiou, Elpida; Kaplanis, Prodromos; Spyros, Spyrou; Christodoulides, George; Theodoulou, Yiannis

1998-01-01

Medicon '98 is the eighth in the series of regional meetings of the International Federation of Medical and Biological Engineering (IFMBE) in the Mediterranean. The goal of Medicon '98 is to provide updated information on the state of the art on medical and biological engineering and computing. Medicon '98 was held in Lemesos, Cyprus, between 14-17 June, 1998. The full papers of the proceedings were published on CD and consisted of 190 invited and submitted papers. A book of abstracts was also published in paper form and was available to all the participants. Twenty seven papers fall within the scope of INIS and are dealing with Nuclear Medicine,Computerized Tomography, Radiology, Radiotherapy, Magnetic Resonance Imaging and Personnel Dosimetry (eds)

Metabolic engineering of volatile isoprenoids in plants and microbes.

Science.gov (United States)

Vickers, Claudia E; Bongers, Mareike; Liu, Qing; Delatte, Thierry; Bouwmeester, Harro

2014-08-01

The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids. © 2014 John Wiley & Sons Ltd.

Diesel Engine Convert to Port Injection CNG Engine Using Gaseous Injector Nozzle Multi Holes Geometries Improvement: A Review

OpenAIRE

Semin; Abdul R. Ismail; Rosli A. Bakar

2009-01-01

The objective of this study was to review the previous research in the development of gaseous fuel injector for port injection CNG engine converted from diesel engine. Problem statement: The regular development of internal combustion engines change direction to answer the two most important problems determining the development trends of engines technology and in particular, their combustion systems. They were environmental protection against emission and noise, shortage of hydrocarbon fuels, ...

Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.

Science.gov (United States)

Lenas, Petros; Moos, Malcolm; Luyten, Frank P

2009-12-01

The field of tissue engineering is moving toward a new concept of "in vitro biomimetics of in vivo tissue development." In Part I of this series, we proposed a theoretical framework integrating the concepts of developmental biology with those of process design to provide the rules for the design of biomimetic processes. We named this methodology "developmental engineering" to emphasize that it is not the tissue but the process of in vitro tissue development that has to be engineered. To formulate the process design rules in a rigorous way that will allow a computational design, we should refer to mathematical methods to model the biological process taking place in vitro. Tissue functions cannot be attributed to individual molecules but rather to complex interactions between the numerous components of a cell and interactions between cells in a tissue that form a network. For tissue engineering to advance to the level of a technologically driven discipline amenable to well-established principles of process engineering, a scientifically rigorous formulation is needed of the general design rules so that the behavior of networks of genes, proteins, or cells that govern the unfolding of developmental processes could be related to the design parameters. Now that sufficient experimental data exist to construct plausible mathematical models of many biological control circuits, explicit hypotheses can be evaluated using computational approaches to facilitate process design. Recent progress in systems biology has shown that the empirical concepts of developmental biology that we used in Part I to extract the rules of biomimetic process design can be expressed in rigorous mathematical terms. This allows the accurate characterization of manufacturing processes in tissue engineering as well as the properties of the artificial tissues themselves. In addition, network science has recently shown that the behavior of biological networks strongly depends on their topology and has

Identifying and Remediating Student Misconceptions in Introductory Biology via Writing-to-Learn Assignments and Peer Review.

Science.gov (United States)

Halim, Audrey S; Finkenstaedt-Quinn, Solaire A; Olsen, Laura J; Gere, Anne Ruggles; Shultz, Ginger V

2018-06-01

Student misconceptions are an obstacle in science, technology, engineering, and mathematics courses and unless remediated may continue causing difficulties in learning as students advance in their studies. Writing-to-learn assignments (WTL) are characterized by their ability to promote in-depth conceptual learning by allowing students to explore their understanding of a topic. This study sought to determine whether and what types of misconceptions are elicited by WTL assignments and how the process of peer review and revision leads to remediation or propagation of misconceptions. We examined four WTL assignments in an introductory biology course in which students first wrote about content by applying it to a realistic scenario, then participated in a peer-review process before revising their work. Misconceptions were identified in all four assignments, with the greatest number pertaining to protein structure and function. Additionally, in certain contexts, students used scientific terminology incorrectly. Analysis of the drafts and peer-review comments generated six profiles by which misconceptions were addressed through the peer-review process. The prevalent mode of remediation arose through directed peer-review comments followed by correction during revision. It was also observed that additional misconceptions were elicited as students revised their writing in response to general peer-review suggestions.

A systematic review of context bias in invasion biology.

Directory of Open Access Journals (Sweden)

Robert J Warren

Full Text Available The language that scientists use to frame biological invasions may reveal inherent bias-including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

A systematic review of context bias in invasion biology.

Science.gov (United States)

Warren, Robert J; King, Joshua R; Tarsa, Charlene; Haas, Brian; Henderson, Jeremy

2017-01-01

The language that scientists use to frame biological invasions may reveal inherent bias-including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

Environmental concentrations of engineered nanomaterials: Review of modeling and analytical studies

International Nuclear Information System (INIS)

Gottschalk, Fadri; Sun, TianYin; Nowack, Bernd

2013-01-01

Scientific consensus predicts that the worldwide use of engineered nanomaterials (ENM) leads to their release into the environment. We reviewed the available literature concerning environmental concentrations of six ENMs (TiO 2 , ZnO, Ag, fullerenes, CNT and CeO 2 ) in surface waters, wastewater treatment plant effluents, biosolids, sediments, soils and air. Presently, a dozen modeling studies provide environmental concentrations for ENM and a handful of analytical works can be used as basis for a preliminary validation. There are still major knowledge gaps (e.g. on ENM production, application and release) that affect the modeled values, but over all an agreement on the order of magnitude of the environmental concentrations can be reached. True validation of the modeled values is difficult because trace analytical methods that are specific for ENM detection and quantification are not available. The modeled and measured results are not always comparable due to the different forms and sizes of particles that these two approaches target. -- Highlights: •Modeled environmental concentrations of engineered nanomaterials are reviewed. •Measured environmental concentrations of engineered nanomaterials are reviewed. •Possible validation of modeled data by measurements is critically evaluated. •Different approaches in modeling and measurement methods complicate validation. -- Modeled and measured environmental concentrations of engineered nanomaterials are reviewed and critically discussed

ERG [Engineering Review Group] review of the SRP [Salt Repository Project] salt irradiation effects program: Technical report

International Nuclear Information System (INIS)

Clark, D.E.

1986-11-01

The Engineering Review Group (ERG) was established by the Office of Nuclear Waste Isolation (ONWI) to help evaluate engineering-related issues in the US Department of Energy's nuclear waste repository program. The August 1985 meeting of the ERG reviewed the Salt Repository Project (SRP) salt irradiation effects program. This report documents the ERG's comments and recommendations on these subjects and the ONWI response to the specific points raised by the ERG

Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Directory of Open Access Journals (Sweden)

Shuobo Shi

2017-11-01

Full Text Available Oleaginous yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.

REQUIREMENT VERIFICATION AND SYSTEMS ENGINEERING TECHNICAL REVIEW (SETR) ON A COMMERCIAL DERIVATIVE AIRCRAFT (CDA) PROGRAM

Science.gov (United States)

2017-09-01

VERIFICATION AND SYSTEMS ENGINEERING TECHNICAL REVIEW (SETR) ON A COMMERCIAL DERIVATIVE AIRCRAFT (CDA) PROGRAM by Theresa L. Thomas September... ENGINEERING TECHNICAL REVIEW (SETR) ON A COMMERCIAL DERIVATIVE AIRCRAFT (CDA) PROGRAM 5. FUNDING NUMBERS 6. AUTHOR(S) Theresa L. Thomas 7...CODE 13. ABSTRACT (maximum 200 words) The Naval Air Systems Command (NAVAIR) systems engineering technical review (SETR) process does not

Network science of biological systems at different scales: A review

Science.gov (United States)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Slak Rupnik, Marjan; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

Network science is today established as a backbone for description of structure and function of various physical, chemical, biological, technological, and social systems. Here we review recent advances in the study of complex biological systems that were inspired and enabled by methods of network science. First, we present

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

Energy Technology Data Exchange (ETDEWEB)

Kuk Lee, Sung; Chou, Howard; Ham, Timothy S.; Soon Lee, Taek; Keasling, Jay D.

2009-12-02

The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20 g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and synthetic biology will provide new tools for metabolic engineers to better understand how to rewire the cell in order to create the desired phenotypes for the production of economically viable biofuels.

Bio-based materials with novel characteristics for tissue engineering applications - A review.

Science.gov (United States)

Bedian, Luis; Villalba-Rodríguez, Angel M; Hernández-Vargas, Gustavo; Parra-Saldivar, Roberto; Iqbal, Hafiz M N

2017-05-01

Recently, a wider spectrum of bio-based materials and materials-based novel constructs and systems has been engineered with high interests. The key objective is to help for an enhanced/better quality of life in a secure way by avoiding/limiting various adverse effects of some in practice traditional therapies. In this context, different methodological approaches including in vitro, in vivo, and ex vivo techniques have been exploited, so far. Among them, bio-based therapeutic constructs are of supreme interests for an enhanced and efficient delivery in the current biomedical sector of the modern world. The development of new types of novel, effective and highly reliable materials-based novel constructs for multipurpose applications is essential and a core demand to tackle many human health related diseases. Bio-based materials possess several complementary functionalities, e.g. unique chemical structure, bioactivity, non-toxicity, biocompatibility, biodegradability, recyclability, etc. that position them well in the modern world's materials sector. In this context, the utilization of biomaterials provides extensive opportunities for experimentation in the field of interdisciplinary and multidisciplinary scientific research. With an aim to address the global dependence on petroleum-based polymers, researchers have been redirecting their interests to the engineering of biological materials for targeted applications in different industries including cosmetics, pharmaceuticals, and other biotechnological or biomedical applications. Herein, we reviewed biotechnological advancements at large and tissue engineering from a biomaterials perspective in particular and envision directions of future developments. Copyright © 2017 Elsevier B.V. All rights reserved.

Biological Aspects of Emerging Benzothiazoles: A Short Review

Directory of Open Access Journals (Sweden)

Ruhi Ali

2013-01-01

Full Text Available In recent years heterocyclic compounds analogues and derivatives have attracted wide attention due to their useful biological and pharmacological properties. Benzothiazole is among the usually occurring heterocyclic nuclei in many marine as well as natural plant products. Benzothiazole is a privileged bicyclic ring system with multiple applications. It is known to exhibit a wide range of biological properties including anticancer, antimicrobial, and antidiabetic, anticonvulsant, anti-inflammatory, antiviral, antitubercular activities. A large number of therapeutic agents are synthesized with the help of benzothiazole nucleus. During recent years there have been some interesting developments in the biological activities of benzothiazole derivatives. These compounds have special significance in the field of medicinal chemistry due to their remarkable pharmacological potentialities. This review is mainly an attempt to present the research work reported in the recent scientific literature on different biological activities of benzothiazole compounds.

Inverse problems in systems biology

International Nuclear Information System (INIS)

Engl, Heinz W; Lu, James; Müller, Stefan; Flamm, Christoph; Schuster, Peter; Kügler, Philipp

2009-01-01

Systems biology is a new discipline built upon the premise that an understanding of how cells and organisms carry out their functions cannot be gained by looking at cellular components in isolation. Instead, consideration of the interplay between the parts of systems is indispensable for analyzing, modeling, and predicting systems' behavior. Studying biological processes under this premise, systems biology combines experimental techniques and computational methods in order to construct predictive models. Both in building and utilizing models of biological systems, inverse problems arise at several occasions, for example, (i) when experimental time series and steady state data are used to construct biochemical reaction networks, (ii) when model parameters are identified that capture underlying mechanisms or (iii) when desired qualitative behavior such as bistability or limit cycle oscillations is engineered by proper choices of parameter combinations. In this paper we review principles of the modeling process in systems biology and illustrate the ill-posedness and regularization of parameter identification problems in that context. Furthermore, we discuss the methodology of qualitative inverse problems and demonstrate how sparsity enforcing regularization allows the determination of key reaction mechanisms underlying the qualitative behavior. (topical review)

Engineered Proteins: Redox Properties and Their Applications

Science.gov (United States)

Prabhulkar, Shradha; Tian, Hui; Wang, Xiaotang; Zhu, Jun-Jie

2012-01-01

Abstract Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices. Antioxid. Redox Signal. 17, 1796–1822. PMID:22435347

Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology.

Science.gov (United States)

Schmidt, Markus; de Lorenzo, Víctor

2012-07-16

The plausible release of deeply engineered or even entirely synthetic/artificial microorganisms raises the issue of their intentional (e.g. bioremediation) or accidental interaction with the Environment. Containment systems designed in the 1980s-1990s for limiting the spread of genetically engineered bacteria and their recombinant traits are still applicable to contemporary Synthetic Biology constructs. Yet, the ease of DNA synthesis and the uncertainty on how non-natural properties and strains could interplay with the existing biological word poses yet again the challenge of designing safe and efficacious firewalls to curtail possible interactions. Such barriers may include xeno-nucleic acids (XNAs) instead of DNA as information-bearing molecules, rewriting the genetic code to make it non-understandable by the existing gene expression machineries, and/or making growth dependent on xenobiotic chemicals. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering.

Science.gov (United States)

Sardi, Maria; Gasch, Audrey P

2017-08-01

Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Modularity in developmental biology and artificial organs: a missing concept in tissue engineering.

Science.gov (United States)

Lenas, Petros; Luyten, Frank P; Doblare, Manuel; Nicodemou-Lena, Eleni; Lanzara, Andreina Elena

2011-06-01

Tissue engineering is reviving itself, adopting the concept of biomimetics of in vivo tissue development. A basic concept of developmental biology is the modularity of the tissue architecture according to which intermediates in tissue development constitute semiautonomous entities. Both engineering and nature have chosen the modular architecture to optimize the product or organism development and evolution. Bioartificial tissues do not have a modular architecture. On the contrary, artificial organs of modular architecture have been already developed in the field of artificial organs. Therefore the conceptual support of tissue engineering by the field of artificial organs becomes critical in its new endeavor of recapitulating in vitro the in vivo tissue development. © 2011, Copyright the Authors. Artificial Organs © 2011, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Review on film cooling of liquid rocket engines

Directory of Open Access Journals (Sweden)

S.R. Shine

2018-03-01

Full Text Available Film cooling in combination with regenerative cooling is presently considered as an efficient method to guarantee safe operation of liquid rocket engines having higher heat flux densities for long duration. This paper aims to bring all the research carried out in the field of liquid rocket engine film cooling since 1950. The analytical and numerical procedure followed, experimental facilities and measurements made and major inferences drawn are reviewed in detail, and compared where ever possible. Review has been made through a discussion of the analyses methodologies and the factors that influence film cooling performance. An effort has also been made to determine the status of the research, pointing out critical gaps, which are still to be explained and addressed by future generations. Keywords: Heat transfer, Liquid rocket thrust chamber, Film cooling, Cooling effectiveness

Approaches to chemical synthetic biology.

Science.gov (United States)

Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

2012-07-16

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Micro-separation toward systems biology.

Science.gov (United States)

Liu, Bi-Feng; Xu, Bo; Zhang, Guisen; Du, Wei; Luo, Qingming

2006-02-17

Current biology is experiencing transformation in logic or philosophy that forces us to reevaluate the concept of cell, tissue or entire organism as a collection of individual components. Systems biology that aims at understanding biological system at the systems level is an emerging research area, which involves interdisciplinary collaborations of life sciences, computational and mathematical sciences, systems engineering, and analytical technology, etc. For analytical chemistry, developing innovative methods to meet the requirement of systems biology represents new challenges as also opportunities and responsibility. In this review, systems biology-oriented micro-separation technologies are introduced for comprehensive profiling of genome, proteome and metabolome, characterization of biomolecules interaction and single cell analysis such as capillary electrophoresis, ultra-thin layer gel electrophoresis, micro-column liquid chromatography, and their multidimensional combinations, parallel integrations, microfabricated formats, and nano technology involvement. Future challenges and directions are also suggested.

Synthetic biology advances for pharmaceutical production

OpenAIRE

Breitling, Rainer; Takano, Eriko

2015-01-01

Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.

PREFACE: Nanobiology: from physics and engineering to biology

Science.gov (United States)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of

Evolutionary engineering of industrial microorganisms-strategies and applications.

Science.gov (United States)

Zhu, Zhengming; Zhang, Juan; Ji, Xiaomei; Fang, Zhen; Wu, Zhimeng; Chen, Jian; Du, Guocheng

2018-06-01

Microbial cells have been widely used in the industry to obtain various biochemical products, and evolutionary engineering is a common method in biological research to improve their traits, such as high environmental tolerance and improvement of product yield. To obtain better integrate functions of microbial cells, evolutionary engineering combined with other biotechnologies have attracted more attention in recent years. Classical laboratory evolution has been proven effective to letting more beneficial mutations occur in different genes but also has some inherent limitations such as a long evolutionary period and uncontrolled mutation frequencies. However, recent studies showed that some new strategies may gradually overcome these limitations. In this review, we summarize the evolutionary strategies commonly used in industrial microorganisms and discuss the combination of evolutionary engineering with other biotechnologies such as systems biology and inverse metabolic engineering. Finally, we prospect the importance and application prospect of evolutionary engineering as a powerful tool especially in optimization of industrial microbial cell factories.

Using Model-Based Systems Engineering To Provide Artifacts for NASA Project Life-Cycle and Technical Reviews

Science.gov (United States)

Parrott, Edith L.; Weiland, Karen J.

2017-01-01

The ability of systems engineers to use model-based systems engineering (MBSE) to generate self-consistent, up-to-date systems engineering products for project life-cycle and technical reviews is an important aspect for the continued and accelerated acceptance of MBSE. Currently, many review products are generated using labor-intensive, error-prone approaches based on documents, spreadsheets, and chart sets; a promised benefit of MBSE is that users will experience reductions in inconsistencies and errors. This work examines features of SysML that can be used to generate systems engineering products. Model elements, relationships, tables, and diagrams are identified for a large number of the typical systems engineering artifacts. A SysML system model can contain and generate most systems engineering products to a significant extent and this paper provides a guide on how to use MBSE to generate products for project life-cycle and technical reviews. The use of MBSE can reduce the schedule impact usually experienced for review preparation, as in many cases the review products can be auto-generated directly from the system model. These approaches are useful to systems engineers, project managers, review board members, and other key project stakeholders.

Synthetic Biology: A Unifying View and Review Using Analog Circuits.

Science.gov (United States)

Teo, Jonathan J Y; Woo, Sung Sik; Sarpeshkar, Rahul

2015-08-01

We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a `cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.

Building robust functionality in synthetic circuits using engineered feedback regulation.

Science.gov (United States)

Chen, Susan; Harrigan, Patrick; Heineike, Benjamin; Stewart-Ornstein, Jacob; El-Samad, Hana

2013-08-01

The ability to engineer novel functionality within cells, to quantitatively control cellular circuits, and to manipulate the behaviors of populations, has many important applications in biotechnology and biomedicine. These applications are only beginning to be explored. In this review, we advocate the use of feedback control as an essential strategy for the engineering of robust homeostatic control of biological circuits and cellular populations. We also describe recent works where feedback control, implemented in silico or with biological components, was successfully employed for this purpose. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing.

Science.gov (United States)

Chakravarti, Deboki; Cho, Jang Hwan; Weinberg, Benjamin H; Wong, Nicole M; Wong, Wilson W

2016-04-18

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

METABOLIC MODELLING IN THE DEVELOPMENT OF CELL FACTORIES BY SYNTHETIC BIOLOGY

Directory of Open Access Journals (Sweden)

Paula Jouhten

2012-10-01

Full Text Available Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.

Precision control of recombinant gene transcription for CHO cell synthetic biology.

Science.gov (United States)

Brown, Adam J; James, David C

2016-01-01

The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. Copyright © 2015. Published by Elsevier Inc.

Double-Blind Review in Software Engineering Venues : The Community’s Perspective

NARCIS (Netherlands)

Bacchelli, A.; Beller, M.M.

2017-01-01

The peer review process is central to the scientific method, the advancement and spread of research, as well as crucial for individual careers. However, the single-blind review mode currently used in most Software Engineering (SE) venues is susceptible to apparent and hidden biases, since reviewers

Human factors engineering program review model

International Nuclear Information System (INIS)

1994-07-01

The staff of the Nuclear Regulatory Commission is performing nuclear power plant design certification reviews based on a design process plan that describes the human factors engineering (HFE) program elements that are necessary and sufficient to develop an acceptable detailed design specification and an acceptable implemented design. There are two principal reasons for this approach. First, the initial design certification applications submitted for staff review did not include detailed design information. Second, since human performance literature and industry experiences have shown that many significant human factors issues arise early in the design process, review of the design process activities and results is important to the evaluation of an overall design. However, current regulations and guidance documents do not address the criteria for design process review. Therefore, the HFE Program Review Model (HFE PRM) was developed as a basis for performing design certification reviews that include design process evaluations as well as review of the final design. A central tenet of the HFE PRM is that the HFE aspects of the plant should be developed, designed, and evaluated on the basis of a structured top-down system analysis using accepted HFE principles. The HFE PRM consists of ten component elements. Each element in divided into four sections: Background, Objective, Applicant Submittals, and Review Criteria. This report describes the development of the HFE PRM and gives a detailed description of each HFE review element

TOPICAL REVIEW: Progress in engineering high strain lead-free piezoelectric ceramics

Science.gov (United States)

Leontsev, Serhiy O.; Eitel, Richard E.

2010-08-01

Environmental concerns are strongly driving the need to replace the lead-based piezoelectric materials currently employed as multilayer actuators. The current review describes both compositional and structural engineering approaches to achieve enhanced piezoelectric properties in lead-free materials. The review of the compositional engineering approach focuses on compositional tuning of the properties and phase behavior in three promising families of lead-free perovskite ferroelectrics: the titanate, alkaline niobate and bismuth perovskites and their solid solutions. The 'structural engineering' approaches focus instead on optimization of microstructural features including grain size, grain orientation or texture, ferroelectric domain size and electrical bias field as potential paths to induce large piezoelectric properties in lead-free piezoceramics. It is suggested that a combination of both compositional and novel structural engineering approaches will be required in order to realize viable lead-free alternatives to current lead-based materials for piezoelectric actuator applications.

Biological control agent for mosquito larvae: Review on the killifish ...

African Journals Online (AJOL)

This review attempts to give an account on the recent advances on the killifish Aphanius dispar dispar as a biological control agent for mosquito larvae. Thirty six (36) articles of literature (scientific papers, technical and workshop reports) on this subject covering the period between 1980 and 2009 were reviewed.

Applications of Microfluidics in Quantitative Biology.

Science.gov (United States)

Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

2018-05-01

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. © 2017 Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

LPG diesel dual fuel engine – A critical review

Directory of Open Access Journals (Sweden)

B. Ashok

2015-06-01

Full Text Available The engine, which uses both conventional diesel fuel and LPG fuel, is referred to as ‘LPG–diesel dual fuel engines’. LPG dual fuel engines are modified diesel engines which use primary fuel as LPG and secondary fuel as diesel. LPG dual fuel engines have a good thermal efficiency at high output but the performance is less during part load conditions due to the poor utilization of charges. This problem can be overcome by varying factors such as pilot fuel quantity, injection timing, composition of the gaseous fuel and intake charge conditions, for improving the performance, combustion and emissions of dual fuel engines. This article reviews about the research work done by the researchers in order to improve the performance, combustion and emission parameters of a LPG–diesel dual fuel engines. From the studies it is shown that the use of LPG in diesel engine is one of the capable methods to reduce the PM and NOx emissions but at same time at part load condition there is a drop in efficiency and power output with respect to diesel operation.

Invited review liquid crystal models of biological materials and silk spinning.

Science.gov (United States)

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

A review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in vivo liquid crystals. The distinguishing characteristics of liquid crystals (self-assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative information from optical textures and rheometers. It is shown that viscoelastic modeling the silk spinning process using liquid crystal theories sheds light on textural transitions in the duct of spiders and silk worms as well as on tactoidal drops and interfacial structures. The range and consistency of the predictions demonstrates that the use of mesoscopic liquid crystal models is another tool to develop the science and biomimetic applications of mesogenic biological soft matter. Copyright © 2011 Wiley Periodicals, Inc.

Human-factors engineering-control-room design review: Shoreham Nuclear Power Station. Draft audit report

International Nuclear Information System (INIS)

Peterson, L.R.; Preston-Smith, J.; Savage, J.W.; Rousseau, W.F.

1981-01-01

A human factors engineering preliminary design review of the Shoreham control room was performed at the site on March 30 through April 3, 1981. This design review was carried out by a team from the Human Factors Engineering Branch, Division of Human Factors Safety. This report was prepared on the basis of the HFEB's review of the applicant's Preliminary Design Assessment and the human factors engineering design review/audit performed at the site. The presented sections are numbered to conform to the guidelines of the draft version of NUREG-0700. They summarize the teams's observations of the control room design and layout, and of the control room operators' interface with the control room environment

Biological and mechanical evaluation of a Bio-Hybrid scaffold for autologous valve tissue engineering.

Science.gov (United States)

Jahnavi, S; Saravanan, U; Arthi, N; Bhuvaneshwar, G S; Kumary, T V; Rajan, S; Verma, R S

2017-04-01

Major challenge in heart valve tissue engineering for paediatric patients is the development of an autologous valve with regenerative capacity. Hybrid tissue engineering approach is recently gaining popularity to design scaffolds with desired biological and mechanical properties that can remodel post implantation. In this study, we fabricated aligned nanofibrous Bio-Hybrid scaffold made of decellularized bovine pericardium: polycaprolactone-chitosan with optimized polymer thickness to yield the desired biological and mechanical properties. CD44 + , αSMA + , Vimentin + and CD105 - human valve interstitial cells were isolated and seeded on these Bio-Hybrid scaffolds. Subsequent biological evaluation revealed interstitial cell proliferation with dense extra cellular matrix deposition that indicated the viability for growth and proliferation of seeded cells on the scaffolds. Uniaxial mechanical tests along axial direction showed that the Bio-Hybrid scaffolds has at least 20 times the strength of the native valves and its stiffness is nearly 3 times more than that of native valves. Biaxial and uniaxial mechanical studies on valve interstitial cells cultured Bio-Hybrid scaffolds revealed that the response along the axial and circumferential direction was different, similar to native valves. Overall, our findings suggest that Bio-Hybrid scaffold is a promising material for future development of regenerative heart valve constructs in children. Copyright © 2016 Elsevier B.V. All rights reserved.

Tissue engineering and regenerative medicine: manufacturing challenges.

Science.gov (United States)

Williams, D J; Sebastine, I M

2005-12-01

Tissue engineering and regenerative medicine are interdisciplinary fields that apply principles of engineering and life sciences to develop biological substitutes, typically composed of biological and synthetic components, that restore, maintain or improve tissue function. Many tissue engineering technologies are still at a laboratory or pre-commercial scale. The short review paper describes the most significant manufacturing and bio-process challenges inherent in the commercialisation and exploitation of the exciting results emerging from the biological and clinical laboratories exploring tissue engineering and regenerative medicine. A three-generation road map of the industry has been used to structure a view of these challenges and to define where the manufacturing community can contribute to the commercial success of the products from these emerging fields. The first-generation industry is characterised by its demonstrated clinical applications and products in the marketplace, the second is characterised by emerging clinical applications, and the third generation is characterised by aspirational clinical applications. The paper focuses on the cost reduction requirement of the first generation of the industry to allow more market penetration and consequent patient impact. It indicates the technological requirements, for instance the creation of three-dimensional tissue structures, and value chain issues in the second generation of the industry. The third-generation industry challenges lie in fundamental biological and clinical science. The paper sets out a road map of these generations to identify areas for research.

Creative design inspired by biological knowledge: Technologies and methods

Science.gov (United States)

Tan, Runhua; Liu, Wei; Cao, Guozhong; Shi, Yuan

2018-05-01

Biological knowledge is becoming an important source of inspiration for developing creative solutions to engineering design problems and even has a huge potential in formulating ideas that can help firms compete successfully in a dynamic market. To identify the technologies and methods that can facilitate the development of biologically inspired creative designs, this research briefly reviews the existing biological-knowledge-based theories and methods and examines the application of biological-knowledge-inspired designs in various fields. Afterward, this research thoroughly examines the four dimensions of key technologies that underlie the biologically inspired design (BID) process. This research then discusses the future development trends of the BID process before presenting the conclusions.

Synthetic biology advances for pharmaceutical production

Science.gov (United States)

Breitling, Rainer; Takano, Eriko

2015-01-01

Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems. PMID:25744872

Women and Minorities in Engineering: A Review of the Literature

Science.gov (United States)

Mamaril, Natasha J. A; Royal, Kenneth D.

2008-01-01

This review of the literature investigates the various factors identified by researchers to explain women's underrepresentation in the engineering field. Because a great deal of research has been published through the years, a compilation summary of existing research was necessary. This literature review utilized searches from thousands of…

Biological monitoring results for cadmium exposed workers.

Science.gov (United States)

McDiarmid, M A; Freeman, C S; Grossman, E A; Martonik, J

1996-11-01

As part of a settlement agreement with the Occupational Safety and Health Administration (OSHA) involving exposure to cadmium (Cd), a battery production facility provided medical surveillance data to OSHA for review. Measurements of cadmium in blood, cadmium in urine, and beta 2-microglobulin in urine were obtained for more than 100 workers over an 18-month period. Some airborne Cd exposure data were also made available. Two subpopulations of this cohort were of primary interest in evaluating compliance with the medical surveillance provisions of the Cadmium Standard. These were a group of 16 workers medically removed from cadmium exposure due to elevations in some biological parameter, and a group of platemakers. Platemaking had presented a particularly high exposure opportunity and had recently undergone engineering interventions to minimize exposure. The effect on three biological monitoring parameters of medical removal protection in the first group and engineering controls in platemakers is reported. Results reveal that both medical removal from cadmium exposures and exposure abatement through the use of engineering and work practice controls generally result in declines in biological monitoring parameters of exposed workers. Implications for the success of interventions are discussed.

Engineered phages for electronics.

Science.gov (United States)

Cui, Yue

2016-11-15

Phages are traditionally widely studied in biology and chemistry. In recent years, engineered phages have attracted significant attentions for functionalization or construction of electronic devices, due to their specific binding, catalytic, nucleating or electronic properties. To apply the engineered phages in electronics, these are a number of interesting questions: how to engineer phages for electronics? How are the engineered phages characterized? How to assemble materials with engineered phages? How are the engineered phages micro or nanopatterned? What are the strategies to construct electronics devices with engineered phages? This review will highlight the early attempts to address these questions and explore the fundamental and practical aspects of engineered phages in electronics, including the approaches for selection or expression of specific peptides on phage coat proteins, characterization of engineered phages in electronics, assembly of electronic materials, patterning of engineered phages, and construction of electronic devices. It provides the methodologies and opens up ex-cit-ing op-por-tu-ni-ties for the development of a variety of new electronic materials and devices based on engineered phages for future applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Selection platforms for directed evolution in synthetic biology.

Science.gov (United States)

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

A review of phosphate mineral nucleation in biology and geobiology.

Science.gov (United States)

Omelon, Sidney; Ariganello, Marianne; Bonucci, Ermanno; Grynpas, Marc; Nanci, Antonio

2013-10-01

Relationships between geological phosphorite deposition and biological apatite nucleation have often been overlooked. However, similarities in biological apatite and phosphorite mineralogy suggest that their chemical formation mechanisms may be similar. This review serves to draw parallels between two newly described phosphorite mineralization processes, and proposes a similar novel mechanism for biologically controlled apatite mineral nucleation. This mechanism integrates polyphosphate biochemistry with crystal nucleation theory. Recently, the roles of polyphosphates in the nucleation of marine phosphorites were discovered. Marine bacteria and diatoms have been shown to store and concentrate inorganic phosphate (Pi) as amorphous, polyphosphate granules. Subsequent release of these P reserves into the local marine environment as Pi results in biologically induced phosphorite nucleation. Pi storage and release through an intracellular polyphosphate intermediate may also occur in mineralizing oral bacteria. Polyphosphates may be associated with biologically controlled apatite nucleation within vertebrates and invertebrates. Historically, biological apatite nucleation has been attributed to either a biochemical increase in local Pi concentration or matrix-mediated apatite nucleation control. This review proposes a mechanism that integrates both theories. Intracellular and extracellular amorphous granules, rich in both calcium and phosphorus, have been observed in apatite-biomineralizing vertebrates, protists, and atremate brachiopods. These granules may represent stores of calcium-polyphosphate. Not unlike phosphorite nucleation by bacteria and diatoms, polyphosphate depolymerization to Pi would be controlled by phosphatase activity. Enzymatic polyphosphate depolymerization would increase apatite saturation to the level required for mineral nucleation, while matrix proteins would simultaneously control the progression of new biological apatite formation.

Special issue: engineering toxins for 21st-century therapies: introduction.

Science.gov (United States)

Acharya, K Ravi

2011-12-01

This special issue on 'Engineering toxins for 21st century therapies' provides a critical review of the current state of multifaceted aspects of toxin research by some of the leading researchers in the field. It also highlights the clinical potential and challenges for development of novel biologics based on engineered toxin derived products. © 2011 The Author Journal compilation © 2011 FEBS.

[Improving industrial microbial stress resistance by metabolic engineering: a review].

Science.gov (United States)

Fu, Ruiyan; Li, Yin

2010-09-01

Metabolic engineering is a technologic platform for industrial strain improvement and aims not only at modifying microbial metabolic fluxes, but also improving the physiological performance of industrial microbes. Microbes will meet multiple stresses in industrial processes. Consequently, elicited gene responses might result in a decrease in overall cell fitness and the efficiency of biotransformation. Thus, it is crucial to develop robust and productive microbial strains that can be integrated into industrial-scale bioprocesses. In this review, we focus on the progress of these novel methods and strategies for engineering stress-tolerance phenotypes referring to rational metabolic engineering and inverse metabolic engineering in recent years. In addition, we also address problems existing in this area and future research needs of microbial physiological functionality engineering.

Magnetic separation techniques in sample preparation for biological analysis: a review.

Science.gov (United States)

He, Jincan; Huang, Meiying; Wang, Dongmei; Zhang, Zhuomin; Li, Gongke

2014-12-01

Sample preparation is a fundamental and essential step in almost all the analytical procedures, especially for the analysis of complex samples like biological and environmental samples. In past decades, with advantages of superparamagnetic property, good biocompatibility and high binding capacity, functionalized magnetic materials have been widely applied in various processes of sample preparation for biological analysis. In this paper, the recent advancements of magnetic separation techniques based on magnetic materials in the field of sample preparation for biological analysis were reviewed. The strategy of magnetic separation techniques was summarized. The synthesis, stabilization and bio-functionalization of magnetic nanoparticles were reviewed in detail. Characterization of magnetic materials was also summarized. Moreover, the applications of magnetic separation techniques for the enrichment of protein, nucleic acid, cell, bioactive compound and immobilization of enzyme were described. Finally, the existed problems and possible trends of magnetic separation techniques for biological analysis in the future were proposed. Copyright © 2014 Elsevier B.V. All rights reserved.

The bioartificial pancreas (BAP): Biological, chemical and engineering challenges.

Science.gov (United States)

Iacovacci, Veronica; Ricotti, Leonardo; Menciassi, Arianna; Dario, Paolo

2016-01-15

The bioartificial pancreas (BAP) represents a viable solution for the treatment of type 1 diabetes (T1D). By encapsulating pancreatic cells in a semipermeable membrane to allow nutrient, insulin and glucose exchange, the side effects produced by islets and whole organ transplantation-related immunosuppressive therapy can be circumvented. Several factors, mainly related to materials properties, capsule morphology and biological environment, play a key role in optimizing BAP systems. The BAP is an extremely complex delivery system for insulin. Despite considerable efforts, in some instances meeting with limited degree of success, a BAP capable of restoring physiological pancreas functions without the need for immunosuppressive drugs and of controlling blood glucose levels especially in large animal models and a few clinical trials, does not exist. The state of the art in terms of materials, fabrication techniques and cell sources, as well as the current status of commercial devices and clinical trials, are described in this overview from an interdisciplinary viewpoint. In addition, challenges to the creation of effective BAP systems are highlighted including future perspectives in terms of component integration from both a biological and an engineering viewpoint. Copyright © 2015 Elsevier Inc. All rights reserved.

Protein design in systems metabolic engineering for industrial strain development.

Science.gov (United States)

Chen, Zhen; Zeng, An-Ping

2013-05-01

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. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The emerging age of cell-free synthetic biology.

Science.gov (United States)

Smith, Mark Thomas; Wilding, Kristen M; Hunt, Jeremy M; Bennett, Anthony M; Bundy, Bradley C

2014-08-25

The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Computational Tools for Stem Cell Biology.

Science.gov (United States)

Bian, Qin; Cahan, Patrick

2016-12-01

For over half a century, the field of developmental biology has leveraged computation to explore mechanisms of developmental processes. More recently, computational approaches have been critical in the translation of high throughput data into knowledge of both developmental and stem cell biology. In the past several years, a new subdiscipline of computational stem cell biology has emerged that synthesizes the modeling of systems-level aspects of stem cells with high-throughput molecular data. In this review, we provide an overview of this new field and pay particular attention to the impact that single cell transcriptomics is expected to have on our understanding of development and our ability to engineer cell fate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Human-factors engineering control-room design review/audit: Waterford 3 SES Generating Station, Louisiana Power and Light Company

International Nuclear Information System (INIS)

Savage, J.W.

1983-01-01

A human factors engineering design review/audit of the Waterford-3 control room was performed at the site on May 10 through May 13, 1982. The report was prepared on the basis of the HFEB's review of the applicant's Preliminary Human Engineering Discrepancy (PHED) report and the human factors engineering design review performed at the site. This design review was carried out by a team from the Human Factors Engineering Branch, Division of Human Factors Safety. The review team was assisted by consultants from Lawrence Livermore National Laboratory (University of California), Livermore, California

Proceedings of the Joint Conference of Australasian College of Physical Scientists and Engineers in Medicine and IEAust College of Biomedical Engineers; Asia/Pacific Region of the IEEE Engineering in Medicine and Biology Society

International Nuclear Information System (INIS)

1996-01-01

This is a celebration of the centenary of Rontgen''s discovery of Xrays. It is also the 50th anniversary of the first hospital physicist appointment in New Zealand. The historical element of the programme will complement the emphasis on current applications of the physical and engineering sciences to medicine and an anticipation of future developments. For the first time the Australasian College of Physical Scientists and Engineers in Medicine, together with the IEAust College of Biomedical Engineers, are joined by the Asia/Pacific Region of the IEEE Engineering in Medicine and Biology Society to make this a truly international conference. The proceedings include many papers on radiology and radiotherapy

Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Borodina, Irina; Li, Mingji

2015-01-01

Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof...... biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae. We describe......-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic...

77 FR 18268 - Proposal Review Panel for Engineering Education and Centers; Notice of Meeting

Science.gov (United States)

2012-03-27

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Engineering Education and Centers; Notice of... Science Foundation announces the following meeting: Name: Proposal Review Panel for Engineering Education...--ERC Research Program 3:30 p.m.--7:30 p.m. Closed--ERC Education Program Thursday, March 29, 2012 8 a.m...

Tissue Engineering: Toward a New Era of Medicine.

Science.gov (United States)

Shafiee, Ashkan; Atala, Anthony

2017-01-14

The goal of tissue engineering is to mitigate the critical shortage of donor organs via in vitro fabrication of functional biological structures. Tissue engineering is one of the most prominent examples of interdisciplinary fields, where scientists with different backgrounds work together to boost the quality of life by addressing critical health issues. Many different fields, such as developmental and molecular biology, as well as technologies, such as micro- and nanotechnologies and additive manufacturing, have been integral for advancing the field of tissue engineering. Over the past 20 years, spectacular advancements have been achieved to harness nature's ability to cure diseased tissues and organs. Patients have received laboratory-grown tissues and organs made out of their own cells, thus eliminating the risk of rejection. However, challenges remain when addressing more complex solid organs such as the heart, liver, and kidney. Herein, we review recent accomplishments as well as challenges that must be addressed in the field of tissue engineering and provide a perspective regarding strategies in further development.

Engineering Complex Tissues

Science.gov (United States)

MIKOS, ANTONIOS G.; HERRING, SUSAN W.; OCHAREON, PANNEE; ELISSEEFF, JENNIFER; LU, HELEN H.; KANDEL, RITA; SCHOEN, FREDERICK J.; TONER, MEHMET; MOONEY, DAVID; ATALA, ANTHONY; VAN DYKE, MARK E.; KAPLAN, DAVID; VUNJAK-NOVAKOVIC, GORDANA

2010-01-01

This article summarizes the views expressed at the third session of the workshop “Tissue Engineering—The Next Generation,” which was devoted to the engineering of complex tissue structures. Antonios Mikos described the engineering of complex oral and craniofacial tissues as a “guided interplay” between biomaterial scaffolds, growth factors, and local cell populations toward the restoration of the original architecture and function of complex tissues. Susan Herring, reviewing osteogenesis and vasculogenesis, explained that the vascular arrangement precedes and dictates the architecture of the new bone, and proposed that engineering of osseous tissues might benefit from preconstruction of an appropriate vasculature. Jennifer Elisseeff explored the formation of complex tissue structures based on the example of stratified cartilage engineered using stem cells and hydrogels. Helen Lu discussed engineering of tissue interfaces, a problem critical for biological fixation of tendons and ligaments, and the development of a new generation of fixation devices. Rita Kandel discussed the challenges related to the re-creation of the cartilage-bone interface, in the context of tissue engineered joint repair. Frederick Schoen emphasized, in the context of heart valve engineering, the need for including the requirements derived from “adult biology” of tissue remodeling and establishing reliable early predictors of success or failure of tissue engineered implants. Mehmet Toner presented a review of biopreservation techniques and stressed that a new breakthrough in this field may be necessary to meet all the needs of tissue engineering. David Mooney described systems providing temporal and spatial regulation of growth factor availability, which may find utility in virtually all tissue engineering and regeneration applications, including directed in vitro and in vivo vascularization of tissues. Anthony Atala offered a clinician’s perspective for functional tissue

A review on the engine performance and exhaust emission characteristics of diesel engines fueled with biodiesel blends.

Science.gov (United States)

Damanik, Natalina; Ong, Hwai Chyuan; Tong, Chong Wen; Mahlia, Teuku Meurah Indra; Silitonga, Arridina Susan

2018-06-01

Biodiesels have gained much popularity because they are cleaner alternative fuels and they can be used directly in diesel engines without modifications. In this paper, a brief review of the key studies pertaining to the engine performance and exhaust emission characteristics of diesel engines fueled with biodiesel blends, exhaust aftertreatment systems, and low-temperature combustion technology is presented. In general, most biodiesel blends result in a significant decrease in carbon monoxide and total unburned hydrocarbon emissions. There is also a decrease in carbon monoxide, nitrogen oxide, and total unburned hydrocarbon emissions while the engine performance increases for diesel engines fueled with biodiesels blended with nano-additives. The development of automotive technologies, such as exhaust gas recirculation systems and low-temperature combustion technology, also improves the thermal efficiency of diesel engines and reduces nitrogen oxide and particulate matter emissions.

Engineering the mechanical and biological properties of nanofibrous vascular grafts for in situ vascular tissue engineering.

Science.gov (United States)

Henry, Jeffrey J D; Yu, Jian; Wang, Aijun; Lee, Randall; Fang, Jun; Li, Song

2017-08-17

Synthetic small diameter vascular grafts have a high failure rate, and endothelialization is critical for preventing thrombosis and graft occlusion. A promising approach is in situ tissue engineering, whereby an acellular scaffold is implanted and provides stimulatory cues to guide the in situ remodeling into a functional blood vessel. An ideal scaffold should have sufficient binding sites for biomolecule immobilization and a mechanical property similar to native tissue. Here we developed a novel method to blend low molecular weight (LMW) elastic polymer during electrospinning process to increase conjugation sites and to improve the mechanical property of vascular grafts. LMW elastic polymer improved the elasticity of the scaffolds, and significantly increased the amount of heparin conjugated to the micro/nanofibrous scaffolds, which in turn increased the loading capacity of vascular endothelial growth factor (VEGF) and prolonged the release of VEGF. Vascular grafts were implanted into the carotid artery of rats to evaluate the in vivo performance. VEGF treatment significantly enhanced endothelium formation and the overall patency of vascular grafts. Heparin coating also increased cell infiltration into the electrospun grafts, thus increasing the production of collagen and elastin within the graft wall. This work demonstrates that LMW elastic polymer blending is an approach to engineer the mechanical and biological property of micro/nanofibrous vascular grafts for in situ vascular tissue engineering.

A proposal to enhance Engineering education in biology and Medicine by following the legacy of René Favaloro.

Science.gov (United States)

Armentano, Ricardo L; Cardelino, Juan; Wray, Sandra; Cymberknop, Leandro J; Kun, Luis

2015-01-01

The synergy amongst Engineering, Medicine and Biology evolves as fast as these disciplines. We propose to articulate these specialties based on the premise that new professionals must face different situations or crisis due to the so-called islands of excellence. René Favaloro focused his work and struggles against poverty, since malnutrition and environmental degradation may increase the propensity to cardiovascular diseases. Doctor Favaloro has dedicated, throughout his career, a considerable amount of time to prepare and qualify a research group, aware of the importance that an adequate working environment has over the final results. He created a team of young students, engineers, medical doctors, physicists, mathematicians and other specialists. He centered his attention on human resources, in order to disseminate his latest advances in Biology, Medicine and Engineering. We are revising the programs of biomedical engineering education and the application of new pedagogic paradigms, where critical thinking is the key: a holistic challenge that consists of a new way of learning, innovating, communicating and shearing, with a creative attitude that represents quality of perception.

Human-factors engineering control-room design review/audit report: Byron Generating Station, Commonwealth Edison Company

International Nuclear Information System (INIS)

Savage, J.W.

1983-01-01

A human factors engineering design review/audit of the Byron Unit 1 control room was performed at the site on November 17 through November 19, 1981. This review was accomplished using the Unit 2 control room appropriately mocked-up to reflect design changes already committed to be incorporated in Unit 1. The report was prepared on the basis of the HFEB's audit of the applicant's Preliminary Design Assessment report and the human factors engineering design review performed at the site. This design review was carried out by a team from the Human Factors Engineering Branch, Division of Human Factors Safety. The review team was assisted by consultants from BioTechnology, Inc. (Falls Church, Virginia), and from Lawrence Livermore National Laboratory (University of California), Livermore, California

Programming Morphogenesis through Systems and Synthetic Biology.

Science.gov (United States)

Velazquez, Jeremy J; Su, Emily; Cahan, Patrick; Ebrahimkhani, Mo R

2018-04-01

Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synthetic and systems biology for microbial production of commodity chemicals.

Science.gov (United States)

Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J; Keasling, Jay D; Martín, Héctor García

2016-01-01

The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.

Design Approaches to Myocardial and Vascular Tissue Engineering.

Science.gov (United States)

Akintewe, Olukemi O; Roberts, Erin G; Rim, Nae-Gyune; Ferguson, Michael A H; Wong, Joyce Y

2017-06-21

Engineered tissues represent an increasingly promising therapeutic approach for correcting structural defects and promoting tissue regeneration in cardiovascular diseases. One of the challenges associated with this approach has been the necessity for the replacement tissue to promote sufficient vascularization to maintain functionality after implantation. This review highlights a number of promising prevascularization design approaches for introducing vasculature into engineered tissues. Although we focus on encouraging blood vessel formation within myocardial implants, we also discuss techniques developed for other tissues that could eventually become relevant to engineered cardiac tissues. Because the ultimate solution to engineered tissue vascularization will require collaboration between wide-ranging disciplines such as developmental biology, tissue engineering, and computational modeling, we explore contributions from each field.

Circulating immune complexes – reviewing the biological roles in ...

African Journals Online (AJOL)

Circulating immune complexes – reviewing the biological roles in human immune function and exercise. ... studies that have investigated CIC's following exercise and proposes that a comprehensive understanding and interpretation of immune system responses to exercise should take these complexes into consideration.

Systematic Applications of Metabolomics in Metabolic Engineering

Directory of Open Access Journals (Sweden)

Robert A. Dromms

2012-12-01

Full Text Available The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.

An Interdisciplinary Approach for Biology, Technology, Engineering and Mathematics (BTEM to Enhance 21st Century Skills in Malaysia.

Directory of Open Access Journals (Sweden)

Lee Chuo Hiong

2015-07-01

Full Text Available An interdisciplinary approach for Biology, Technology, Engineering and Mathematics (BTEM is suggested to develop 21st century skills in the Malaysian context. BTEM allows students to master biological knowledge and at the same time to be adroit in other sub discipline skills. Students master factual knowledge of biology and skills of the 21st century simultaneously. The two main teaching and learning strategies applied in BTEM are problem-based learning and inquiry-based learning. Students are exposed to real world problems that require them to undergo inquiry processes to discover the inventive solutions. The content knowledge of biology adheres to the Malaysian Integrated Curriculum for Secondary Schools. The essence of engineering is inventive problem solving. Incorporation of information communication technologies in teaching and learning will be able to fulfil the needs of the current Net Generation. Mathematics plays an important role as computational tools, especially in analysing data. The highlighted 21st century skills in BTEM include digital literacy, inventive thinking, effective communication, high productivity, and spiritual and noble values.

Safety review for human factors engineering and control rooms of nuclear power plants

International Nuclear Information System (INIS)

Yang Mengzhuo

1998-01-01

Safety review for human factors engineering and control rooms of nuclear power plants (NPP) is in a forward position of science and technology, which began at American TMI severe accident and had been implemented in China. The importance and the significance of the safety review are expounded, the requirements of its scope and profundity are explained in detail. In addition, the situation of the technical document system for nuclear safety regulation on human factors engineering and control rooms of NPP in China is introduced briefly, on which the safety review is based

Biological role of lectins: A review

Directory of Open Access Journals (Sweden)

K Kiran Kumar

2012-01-01

Full Text Available Lectins comprise a stracturally vary diverse class of proteins charecterized by their ability to selectively bind carbohydrate moieties of the glycoproteins of the cell surface. Lectins may be derived from plants, microbial or animal sources and may be soluble or membrane bound. Lectins is a tetramer made up of four nearly identical subunits. In human, lectins have been reported to cause food poisoning, hemolytic anemia, jaundice, digestive distress, protein and carbohydrate malabsorption and type I allergies. The present review focuses on the classification, structures, biological significance and application of lectins.

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

Science.gov (United States)

Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

2017-04-01

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

Biologically Hazardous Agents at Work and Efforts to Protect Workers' Health: A Review of Recent Reports

Directory of Open Access Journals (Sweden)

Kyung-Taek Rim

2014-06-01

Full Text Available Because information on biological agents in the workplace is lacking, biological hazard analyses at the workplace to securely recognize the harmful factors with biological basis are desperately needed. This review concentrates on literatures published after 2010 that attempted to detect biological hazards to humans, especially workers, and the efforts to protect them against these factors. It is important to improve the current understanding of the health hazards caused by biological factors at the workplace. In addition, this review briefly describes these factors and provides some examples of their adverse health effects. It also reviews risk assessments, protection with personal protective equipment, prevention with training of workers, regulations, as well as vaccinations.

Risks and health effects from exposure to engineered nanostructures: A critical review

International Nuclear Information System (INIS)

Nikodinovska, Violeta Vasilevska; Mladenovska, Kristina; Grozdanov, Anita

2015-01-01

Nanotechnology and engineered nanostructures (ENSs) are becoming part of everyday life, starting from industrial application, even in food products, to gene therapy. Thus, tons and tons of nanoparticles (NPs) enter the environment and indirectly or directly - into the biological systems, including the human body. There are many controversial papers that describe interactions of the ENSs with biological systems and raise concern that intentional or unintentional human exposure to certain types of ENSs, may lead to significant health, i.e. toxicological effects. Because of our insufficient and contradictory knowledge about the health effects associated with the ENSs exposure, the aim of this paper is to summarize and systematize the already confirmed data and the latest found facts about ENSs and their health effects and to discuss the future opportunities and tasks in the field of nanotoxicology. Keywords: engineered nano sized structures, nanotoxicology.

Review: bioprinting: a beginning.

Science.gov (United States)

Mironov, Vladimir; Reis, Nuno; Derby, Brian

2006-04-01

An increasing demand for directed assembly of biologically relevant materials, with prescribed three-dimensional hierarchical organizations, is stimulating technology developments with the ultimate goal of re-creating multicellular tissues and organs de novo. Existing techniques, mostly adapted from other applications or fields of research, are capable of independently meeting partial requirements for engineering biological or biomimetic structures, but their integration toward organ engineering is proving difficult. Inspired by recent developments in material transfer processes operating at all relevant length scales--from nano to macro--which are amenable to biological elements, a new research field of bioprinting and biopatterning has emerged. Here we present a short review regarding the framework, state of the art, and perspectives of this new field, based on the findings presented at a recent international workshop.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology.

Science.gov (United States)

Koutinas, Michalis; Kiparissides, Alexandros; Pistikopoulos, Efstratios N; Mantalaris, Athanasios

2012-01-01

The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology

Directory of Open Access Journals (Sweden)

Michalis Koutinas

2012-10-01

Full Text Available The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control & optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

BIOPROCESS SYSTEMS ENGINEERING: TRANSFERRING TRADITIONAL PROCESS ENGINEERING PRINCIPLES TO INDUSTRIAL BIOTECHNOLOGY

Directory of Open Access Journals (Sweden)

Michalis Koutinas

2012-10-01

Full Text Available The complexity of the regulatory network and the interactions that occur in the intracellular environment of microorganisms highlight the importance in developing tractable mechanistic models of cellular functions and systematic approaches for modelling biological systems. To this end, the existing process systems engineering approaches can serve as a vehicle for understanding, integrating and designing biological systems and processes. Here, we review the application of a holistic approach for the development of mathematical models of biological systems, from the initial conception of the model to its final application in model-based control and optimisation. We also discuss the use of mechanistic models that account for gene regulation, in an attempt to advance the empirical expressions traditionally used to describe micro-organism growth kinetics, and we highlight current and future challenges in mathematical biology. The modelling research framework discussed herein could prove beneficial for the design of optimal bioprocesses, employing rational and feasible approaches towards the efficient production of chemicals and pharmaceuticals.

Recombinant protein scaffolds for tissue engineering

International Nuclear Information System (INIS)

Werkmeister, Jerome A; Ramshaw, John A M

2012-01-01

New biological materials for tissue engineering are now being developed using common genetic engineering capabilities to clone and express a variety of genetic elements that allow cost-effective purification and scaffold fabrication from these recombinant proteins, peptides or from chimeric combinations of these. The field is limitless as long as the gene sequences are known. The utility is dependent on the ease, product yield and adaptability of these protein products to the biomedical field. The development of recombinant proteins as scaffolds, while still an emerging technology with respect to commercial products, is scientifically superior to current use of natural materials or synthetic polymer scaffolds, in terms of designing specific structures with desired degrees of biological complexities and motifs. In the field of tissue engineering, next generation scaffolds will be the key to directing appropriate tissue regeneration. The initial period of biodegradable synthetic scaffolds that provided shape and mechanical integrity, but no biological information, is phasing out. The era of protein scaffolds offers distinct advantages, particularly with the combination of powerful tools of molecular biology. These include, for example, the production of human proteins of uniform quality that are free of infectious agents and the ability to make suitable quantities of proteins that are found in low quantity or are hard to isolate from tissue. For the particular needs of tissue engineering scaffolds, fibrous proteins like collagens, elastin, silks and combinations of these offer further advantages of natural well-defined structural scaffolds as well as endless possibilities of controlling functionality by genetic manipulation. (topical review)

Tissue engineering of urethra: Systematic review of recent literature.

Science.gov (United States)

Žiaran, Stanislav; Galambošová, Martina; Danišovič, L'uboš

2017-12-01

The purpose of this article was to perform a systematic review of the recent literature on urethral tissue engineering. A total of 31 articles describing the use of tissue engineering for urethra reconstruction were included. The obtained results were discussed in three groups: cells, scaffolds, and clinical results of urethral reconstructions using these components. Stem cells of different origin were used in many experimental studies, but only autologous urothelial cells, fibroblasts, and keratinocytes were applied in clinical trials. Natural and synthetic scaffolds were studied in the context of urethral tissue engineering. The main advantage of synthetic ones is the fact that they can be obtained in unlimited amount and modified by different techniques, but scaffolds of natural origin normally contain chemical groups and bioactive proteins which increase the cell attachment and may promote the cell proliferation and differentiation. The most promising are smart scaffolds delivering different bioactive molecules or those that can be tubularized. In two clinical trials, only onlay-fashioned transplants were used for urethral reconstruction. However, the very promising results were obtained from animal studies where tubularized scaffolds, both non-seeded and cell-seeded, were applied. Impact statement The main goal of this article was to perform a systematic review of the recent literature on urethral tissue engineering. It summarizes the most recent information about cells, seeded or non-seeded scaffolds and clinical application with respect to regeneration of urethra.

Prospects of pyrolysis oil from plastic waste as fuel for diesel engines: A review

Science.gov (United States)

Mangesh, V. L.; Padmanabhan, S.; Ganesan, S.; PrabhudevRahul, D.; Reddy, T. Dinesh Kumar

2017-05-01

The purpose ofthis study is to review the existing literature about chemical recycling of plastic waste and its potential as fuel for diesel engines. This is a review covering on the field of converting waste plastics into liquid hydrocarbon fuels for diesel engines. Disposal and recycling of waste plastics have become an incremental problem and environmental threat with increasing demand for plastics. One of the effective measures is by converting waste plastic into combustible hydrocarbon liquid as an alternative fuel for running diesel engines. Continued research efforts have been taken by researchers to convert waste plastic in to combustible pyrolysis oil as alternate fuel for diesel engines. An existing literature focuses on the study of chemical structure of the waste plastic pyrolysis compared with diesel oil. Converting waste plastics into fuel oil by different catalysts in catalytic pyrolysis process also reviewed in this paper. The methodology with subsequent hydro treating and hydrocracking of waste plastic pyrolysis oil can reduce unsaturated hydrocarbon bonds which would improve the combustion performance in diesel engines as an alternate fuel.

Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes.

Science.gov (United States)

Kang, Zhen; Zhang, Junli; Jin, Peng; Yang, Sen

2015-01-01

Owing to our limited understanding of the relationship between sequence and function and the interaction between intracellular pathways and regulatory systems, the rational design of enzyme-coding genes and de novo assembly of a brand-new artificial genome for a desired functionality or phenotype are difficult to achieve. As an alternative approach, directed evolution has been widely used to engineer genomes and enzyme-coding genes. In particular, significant developments toward DNA synthesis, DNA assembly (in vitro or in vivo), recombination-mediated genetic engineering, and high-throughput screening techniques in the field of synthetic biology have been matured and widely adopted, enabling rapid semi-rational genome engineering to generate variants with desired properties. In this commentary, these novel tools and their corresponding applications in the directed evolution of genomes and enzymes are discussed. Moreover, the strategies for genome engineering and rapid in vitro enzyme evolution are also proposed.

Biological physics in México: Review and new challenges.

Science.gov (United States)

Hernández-Lemus, Enrique

2011-03-01

Biological and physical sciences possess a long-standing tradition of cooperativity as separate but related subfields of science. For some time, this cooperativity has been limited by their obvious differences in methods and views. Biological physics has recently experienced a kind of revival (or better a rebirth) due to the growth of molecular research on animate matter. New avenues for research have been opened for both theoretical and experimental physicists. Nevertheless, in order to better travel for such paths, the contemporary biological physicist should be armed with a set of specialized tools and methods but also with a new attitude toward multidisciplinarity. In this review article, we intend to somehow summarize what has been done in the past (in particular, as an example we will take a closer look at the Mexican case), to show some examples of fruitful investigations in the biological physics area and also to set a proposal of new curricula for physics students and professionals interested in applying their science to get a better understanding of the physical basis of biological function.

Review of organic Rankine cycles for internal combustion engine exhaust waste heat recovery

International Nuclear Information System (INIS)

Sprouse, Charles; Depcik, Christopher

2013-01-01

Escalating fuel prices and future carbon dioxide emission limits are creating a renewed interest in methods to increase the thermal efficiency of engines beyond the limit of in-cylinder techniques. One promising mechanism that accomplishes both objectives is the conversion of engine waste heat to a more useful form of energy, either mechanical or electrical. This paper reviews the history of internal combustion engine exhaust waste heat recovery focusing on Organic Rankine Cycles since this thermodynamic cycle works well with the medium-grade energy of the exhaust. Selection of the cycle expander and working fluid are the primary focus of the review, since they are regarded as having the largest impact on system performance. Results demonstrate a potential fuel economy improvement around 10% with modern refrigerants and advancements in expander technology. -- Highlights: ► This review article focuses on engine exhaust waste heat recovery works. ► The organic Rankine cycle is superior for low to medium exergy heat sources. ► Working fluid and expander selection strongly influence efficiency. ► Several authors demonstrate viable systems for vehicle installation

Computational protein design-the next generation tool to expand synthetic biology applications.

Science.gov (United States)

Gainza-Cirauqui, Pablo; Correia, Bruno Emanuel

2018-05-02

One powerful approach to engineer synthetic biology pathways is the assembly of proteins sourced from one or more natural organisms. However, synthetic pathways often require custom functions or biophysical properties not displayed by natural proteins, limitations that could be overcome through modern protein engineering techniques. Structure-based computational protein design is a powerful tool to engineer new functional capabilities in proteins, and it is beginning to have a profound impact in synthetic biology. Here, we review efforts to increase the capabilities of synthetic biology using computational protein design. We focus primarily on computationally designed proteins not only validated in vitro, but also shown to modulate different activities in living cells. Efforts made to validate computational designs in cells can illustrate both the challenges and opportunities in the intersection of protein design and synthetic biology. We also highlight protein design approaches, which although not validated as conveyors of new cellular function in situ, may have rapid and innovative applications in synthetic biology. We foresee that in the near-future, computational protein design will vastly expand the functional capabilities of synthetic cells. Copyright © 2018. Published by Elsevier Ltd.

Models for synthetic biology.

Science.gov (United States)

Kaznessis, Yiannis N

2007-11-06

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

Molecular Cloning Designer Simulator (MCDS: All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

Full Text Available Molecular Cloning Designer Simulator (MCDS is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1 it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2 it can perform a user-defined workflow of cloning steps in a single execution of the software; (3 it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4 it includes experimental information to conveniently guide wet lab work; and (5 it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. Keywords: BioCAD, Genetic engineering software, Molecular cloning software, Synthetic biology, Workflow simulation and management

Piezoelectric materials for tissue regeneration: A review.

Science.gov (United States)

Rajabi, Amir Hossein; Jaffe, Michael; Arinzeh, Treena Livingston

2015-09-01

The discovery of piezoelectricity, endogenous electric fields and transmembrane potentials in biological tissues raised the question whether or not electric fields play an important role in cell function. It has kindled research and the development of technologies in emulating biological electricity for tissue regeneration. Promising effects of electrical stimulation on cell growth and differentiation and tissue growth has led to interest in using piezoelectric scaffolds for tissue repair. Piezoelectric materials can generate electrical activity when deformed. Hence, an external source to apply electrical stimulation or implantation of electrodes is not needed. Various piezoelectric materials have been employed for different tissue repair applications, particularly in bone repair, where charges induced by mechanical stress can enhance bone formation; and in neural tissue engineering, in which electric pulses can stimulate neurite directional outgrowth to fill gaps in nervous tissue injuries. In this review, a summary of piezoelectricity in different biological tissues, mechanisms through which electrical stimulation may affect cellular response, and recent advances in the fabrication and application of piezoelectric scaffolds will be discussed. The discovery of piezoelectricity, endogenous electric fields and transmembrane potentials in biological tissues has kindled research and the development of technologies using electrical stimulation for tissue regeneration. Piezoelectric materials generate electrical activity in response to deformations and allow for the delivery of an electrical stimulus without the need for an external power source. As a scaffold for tissue engineering, growing interest exists due to its potential of providing electrical stimulation to cells to promote tissue formation. In this review, we cover the discovery of piezoelectricity in biological tissues, its connection to streaming potentials, biological response to electrical stimulation and

Procedure for developing biological input for the design, location, or modification of water-intake structures

Energy Technology Data Exchange (ETDEWEB)

Neitzel, D.A.; McKenzie, D.H.

1981-12-01

To minimize adverse impact on aquatic ecosystems resulting from the operation of water intake structures, design engineers must have relevant information on the behavior, physiology and ecology of local fish and shellfish. Identification of stimulus/response relationships and the environmental factors that influence them is the first step in incorporating biological information in the design, location or modification of water intake structures. A procedure is presented in this document for providing biological input to engineers who are designing, locating or modifying a water intake structure. The authors discuss sources of stimuli at water intakes, historical approaches in assessing potential/actual impact and review biological information needed for intake design.

Genetic Engineering of Alfalfa (Medicago sativa L.).

Science.gov (United States)

Wang, Dan; Khurshid, Muhammad; Sun, Zhan Min; Tang, Yi Xiong; Zhou, Mei Liang; Wu, Yan Min

2016-01-01

Alfalfa is excellent perennial legume forage for its extensive ecological adaptability, high nutrition value, palatability and biological nitrogen fixation. It plays a very important role in the agriculture, animal husbandry and ecological construction. It is cultivated in all continents. With the development of modern plant breeding and genetic engineering techniques, a large amount of work has been carried out on alfalfa. Here we summarize the recent research advances in genetic engineering of alfalfa breeding, including transformation, quality improvement, stress resistance and as a bioreactor. The review article can enables us to understand the research method, direction and achievements of genetic engineering technology of Alfalfa.

76 FR 55389 - Federal Acquisition Regulation; Submission for OMB Review; Architect-Engineer Qualifications (SF...

Science.gov (United States)

2011-09-07

...; Submission for OMB Review; Architect-Engineer Qualifications (SF 330) AGENCIES: Department of Defense (DOD... extension of a previously approved information collection requirement for the Architect-Engineer... 330, Part I is used by all Executive agencies to obtain information from architect-engineer firms...

Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Science.gov (United States)

Baghalian, Kambiz; Hajirezaei, Mohammad-Reza; Schreiber, Falk

2014-10-01

Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology. © 2014 American Society of Plant Biologists. All rights reserved.

77 FR 1704 - Center for Scientific Review; Notice of Closed Meetings

Science.gov (United States)

2012-01-11

...: Center for Scientific Review Special Emphasis Panel; R15: Musculoskeletal Tissue Engineering, Oral, Bone and Skeletal Muscle Biology. Date: February 7-8, 2012. Time: 8 a.m. to 6 p.m. Agenda: To review and...

DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development.

Science.gov (United States)

Ye, Dekai; Zuo, Xiaolei; Fan, Chunhai

2018-06-12

Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.

Mammalian designer cells: Engineering principles and biomedical applications.

Science.gov (United States)

Xie, Mingqi; Fussenegger, Martin

2015-07-01

Biotechnology is a widely interdisciplinary field focusing on the use of living cells or organisms to solve established problems in medicine, food production and agriculture. Synthetic biology, the science of engineering complex biological systems that do not exist in nature, continues to provide the biotechnology industry with tools, technologies and intellectual property leading to improved cellular performance. One key aspect of synthetic biology is the engineering of deliberately reprogrammed designer cells whose behavior can be controlled over time and space. This review discusses the most commonly used techniques to engineer mammalian designer cells; while control elements acting on the transcriptional and translational levels of target gene expression determine the kinetic and dynamic profiles, coupling them to a variety of extracellular stimuli permits their remote control with user-defined trigger signals. Designer mammalian cells with novel or improved biological functions not only directly improve the production efficiency during biopharmaceutical manufacturing but also open the door for cell-based treatment strategies in molecular and translational medicine. In the future, the rational combination of multiple sets of designer cells could permit the construction and regulation of higher-order systems with increased complexity, thereby enabling the molecular reprogramming of tissues, organisms or even populations with highest precision. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Applying Peer Reviews in Software Engineering Education: An Experiment and Lessons Learned

Science.gov (United States)

Garousi, V.

2010-01-01

Based on the demonstrated value of peer reviews in the engineering industry, numerous industry experts have listed it at the top of the list of desirable development practices. Experience has shown that problems (defects) are eliminated earlier if a development process incorporates peer reviews and that these reviews are as effective as or even…

Research on the NPP human factors engineering operating experience review

International Nuclear Information System (INIS)

Ren Xiangchen; Miao Hongxing; Ning Zhonghe

2006-01-01

This paper addresses the importance of the human factors engineering (HFE) for the design of nuclear power plant (NPP), especially for the design of human-machine interface in the NPP. It also summarizes the scope and content of the NPP HFE. The function, scope, content and process of the NPP human factors engineering operating experience review (OER) are mainly focused on, and significantly discussed. Finally, it briefly introduces the situation of the studies on the OER in China. (authors)

MORE: mixed optimization for reverse engineering--an application to modeling biological networks response via sparse systems of nonlinear differential equations.

Science.gov (United States)

Sambo, Francesco; de Oca, Marco A Montes; Di Camillo, Barbara; Toffolo, Gianna; Stützle, Thomas

2012-01-01

Reverse engineering is the problem of inferring the structure of a network of interactions between biological variables from a set of observations. In this paper, we propose an optimization algorithm, called MORE, for the reverse engineering of biological networks from time series data. The model inferred by MORE is a sparse system of nonlinear differential equations, complex enough to realistically describe the dynamics of a biological system. MORE tackles separately the discrete component of the problem, the determination of the biological network topology, and the continuous component of the problem, the strength of the interactions. This approach allows us both to enforce system sparsity, by globally constraining the number of edges, and to integrate a priori information about the structure of the underlying interaction network. Experimental results on simulated and real-world networks show that the mixed discrete/continuous optimization approach of MORE significantly outperforms standard continuous optimization and that MORE is competitive with the state of the art in terms of accuracy of the inferred networks.

Remediation of water and wastewater by using engineered nanomaterials: A review.

Science.gov (United States)

Bishoge, Obadia K; Zhang, Lingling; Suntu, Shaldon L; Jin, Hui; Zewde, Abraham A; Qi, Zhongwei

2018-05-12

Nanotechnology is currently a fast-rising socioeconomic and political knowledge-based technology owing to the unique characteristics of its engineered nanomaterials. This branch of technology is useful for water and wastewater remediation. Many scientists and researchers have been conducting different studies and experiments on the applications of engineered nanomaterials at the local to international level. This review mainly aims to provide a current overview of existing knowledge on engineered nanomaterials and their applications in water and wastewater remediation. Furthermore, the present risks and challenges of nanotechnology are examined.

[Research progress of mammalian synthetic biology in biomedical field].

Science.gov (United States)

Yang, Linfeng; Yin, Jianli; Wang, Meiyan; Ye, Haifeng

2017-03-25

Although still in its infant stage, synthetic biology has achieved remarkable development and progress during the past decade. Synthetic biology applies engineering principles to design and construct gene circuits uploaded into living cells or organisms to perform novel or improved functions, and it has been widely used in many fields. In this review, we describe the recent advances of mammalian synthetic biology for the treatment of diseases. We introduce common tools and design principles of synthetic gene circuits, and then we demonstrate open-loop gene circuits induced by different trigger molecules used in disease diagnosis and close-loop gene circuits used for biomedical applications. Finally, we discuss the perspectives and potential challenges of synthetic biology for clinical applications.

Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

Science.gov (United States)

Dvořák, Pavel; Nikel, Pablo I; Damborský, Jiří; de Lorenzo, Víctor

2017-11-15

Elimination or mitigation of the toxic effects of chemical waste released to the environment by industrial and urban activities relies largely on the catalytic activities of microorganisms-specifically bacteria. Given their capacity to evolve rapidly, they have the biochemical power to tackle a large number of molecules mobilized from their geological repositories through human action (e.g., hydrocarbons, heavy metals) or generated through chemical synthesis (e.g., xenobiotic compounds). Whereas naturally occurring microbes already have considerable ability to remove many environmental pollutants with no external intervention, the onset of genetic engineering in the 1980s allowed the possibility of rational design of bacteria to catabolize specific compounds, which could eventually be released into the environment as bioremediation agents. The complexity of this endeavour and the lack of fundamental knowledge nonetheless led to the virtual abandonment of such a recombinant DNA-based bioremediation only a decade later. In a twist of events, the last few years have witnessed the emergence of new systemic fields (including systems and synthetic biology, and metabolic engineering) that allow revisiting the same environmental pollution challenges through fresh and far more powerful approaches. The focus on contaminated sites and chemicals has been broadened by the phenomenal problems of anthropogenic emissions of greenhouse gases and the accumulation of plastic waste on a global scale. In this article, we analyze how contemporary systemic biology is helping to take the design of bioremediation agents back to the core of environmental biotechnology. We inspect a number of recent strategies for catabolic pathway construction and optimization and we bring them together by proposing an engineering workflow. Copyright © 2017 Elsevier Inc. All rights reserved.

Surgical Engineering in Cranio-Maxillofacial Surgery: A Literature Review

Directory of Open Access Journals (Sweden)

Raphael Olszewski

2012-01-01

Full Text Available A systematic review of the literature concerning surgical engineering in cranio-maxillofacial surgery was performed. APubMed search yielded 1721 papers published between 1999 and 2011. Based on the inclusion/exclusion criteria, 1428 articles were excluded after review of titles and abstracts. Atotal of 292 articles were finally selected covering the following topics: finite element analysis (n = 18, computer-assisted surgery (n = 111, rapid prototyping models (n = 41, preoperative training simulators (n = 4, surgical guides (n = 23, image-guided navigation (n = 58, augmented reality (n = 2, video tracking (n = 1, distraction osteogenesis (n = 19, robotics (n = 8, and minimal invasive surgery (n = 7. The results show that surgical engineering plays a pivotal role in the development and improvement of cranio-maxillofacial surgery. Some technologies, such as computer-assisted surgery, image-guided navigation, and three-dimensional rapid prototyping models, have reached maturity and allow for multiple clinical applications, while augmented reality, robotics, and endoscopy still need to be improved.

X-ray diffraction and infrared spectroscopy analyses on the crystallinity of engineered biological hydroxyapatite for medical application

Science.gov (United States)

Poralan, G. M., Jr.; Gambe, J. E.; Alcantara, E. M.; Vequizo, R. M.

2015-06-01

Biological hydroxyapatite (BHAp) derived from thermally-treated fish bones was successfully produced. However, the obtained biological HAp was amorphous and thus making it unfavorable for medical application. Consequently, this research exploits and engineers the crystallinity of BHAp powders by addition of CaCO3 and investigates its degree of crystallinity using XRD and IR spectroscopy. On XRD, the HAp powders with [Ca]/[P] ratios 1.42, 1.46, 1.61 and 1.93 have degree of crystallinity equal to 58.08, 72.13, 85.79, 75.85% and crystal size equal to 0.67, 0.74, 0.75, 0.72 nm, respectively. The degree of crystallinity and crystal size of the obtained calcium deficient biological HAp powders increase as their [Ca]/[P] ratio approaches the stoichiometric ratio by addition of CaCO3 as source of Ca2+ ions. These results show the possibility of engineering the crystallinity and crystal size of biological HAp by addition of CaCO3. Moreover, the splitting factor of PO4 vibration matches the result with % crystallinity on XRD. Also, the area of phosphate-substitution site of PO4 vibration shows linear relationship (R2 = 0.994) with crystal size calculated from XRD. It is worth noting that the crystallinity of the biological HAp with [Ca]/[P] ratios 1.42 and 1.48 fall near the range 60-70% for highly resorbable HAp used in the medical application.

Paradigms for biologically inspired design

DEFF Research Database (Denmark)

Lenau, T. A.; Metzea, A.-L.; Hesselberg, T.

2018-01-01

engineering, medical engineering, nanotechnology, photonics,environmental protection and agriculture. However, a major obstacle for the wider use of biologically inspired design isthe knowledge barrier that exist between the application engineers that have insight into how to design suitable productsand......Biologically inspired design is attracting increasing interest since it offers access to a huge biological repository of wellproven design principles that can be used for developing new and innovative products. Biological phenomena can inspireproduct innovation in as diverse areas as mechanical...... the biologists with detailed knowledge and experience in understanding how biological organisms function in theirenvironment. The biologically inspired design process can therefore be approached using different design paradigmsdepending on the dominant opportunities, challenges and knowledge characteristics...

Rotary engine developments at Curtiss-Wright over the past 20 years and review of general aviation engine potential. [with direct chamber injection

Science.gov (United States)

Jones, C.

1978-01-01

The development of the rotary engine as a viable power plant capable of wide application is reviewed. Research results on the stratified charge engine with direct chamber injection are included. Emission control, reduced fuel consumption, and low noise level are among the factors discussed in terms of using the rotary engine in general aviation aircraft.

Systems biology: the reincarnation of systems theory applied in biology?

Science.gov (United States)

Wolkenhauer, O

2001-09-01

With the availability of quantitative data on the transcriptome and proteome level, there is an increasing interest in formal mathematical models of gene expression and regulation. International conferences, research institutes and research groups concerned with systems biology have appeared in recent years and systems theory, the study of organisation and behaviour per se, is indeed a natural conceptual framework for such a task. This is, however, not the first time that systems theory has been applied in modelling cellular processes. Notably in the 1960s systems theory and biology enjoyed considerable interest among eminent scientists, mathematicians and engineers. Why did these early attempts vanish from research agendas? Here we shall review the domain of systems theory, its application to biology and the lessons that can be learned from the work of Robert Rosen. Rosen emerged from the early developments in the 1960s as a main critic but also developed a new alternative perspective to living systems, a concept that deserves a fresh look in the post-genome era of bioinformatics.

Reverse engineering biological networks :applications in immune responses to bio-toxins.

Energy Technology Data Exchange (ETDEWEB)

Martino, Anthony A.; Sinclair, Michael B.; Davidson, George S.; Haaland, David Michael; Timlin, Jerilyn Ann; Thomas, Edward Victor; Slepoy, Alexander; Zhang, Zhaoduo; May, Elebeoba Eni; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

2005-12-01

Our aim is to determine the network of events, or the regulatory network, that defines an immune response to a bio-toxin. As a model system, we are studying T cell regulatory network triggered through tyrosine kinase receptor activation using a combination of pathway stimulation and time-series microarray experiments. Our approach is composed of five steps (1) microarray experiments and data error analysis, (2) data clustering, (3) data smoothing and discretization, (4) network reverse engineering, and (5) network dynamics analysis and fingerprint identification. The technological outcome of this study is a suite of experimental protocols and computational tools that reverse engineer regulatory networks provided gene expression data. The practical biological outcome of this work is an immune response fingerprint in terms of gene expression levels. Inferring regulatory networks from microarray data is a new field of investigation that is no more than five years old. To the best of our knowledge, this work is the first attempt that integrates experiments, error analyses, data clustering, inference, and network analysis to solve a practical problem. Our systematic approach of counting, enumeration, and sampling networks matching experimental data is new to the field of network reverse engineering. The resulting mathematical analyses and computational tools lead to new results on their own and should be useful to others who analyze and infer networks.

Biologi og/eller engineering?

DEFF Research Database (Denmark)

Daugbjerg, Peer

2018-01-01

Engineering i skolen er en anvendelsesorienteret og problemløsende undervisning, hvor eleverne lærer at udvikle konkrete løsninger på praktiske problemer. I elevernes arbejde indgår faglig viden og teknologi...

Rabi model as a quantum coherent heat engine: From quantum biology to superconducting circuits

Science.gov (United States)

Altintas, Ferdi; Hardal, Ali Ü. C.; Müstecaplıoǧlu, Özgür E.

2015-02-01

We propose a multilevel quantum heat engine with a working medium described by a generalized Rabi model which consists of a two-level system coupled to a single-mode bosonic field. The model is constructed to be a continuum limit of a quantum biological description of light-harvesting complexes so that it can amplify quantum coherence by a mechanism which is a quantum analog of classical Huygens clocks. The engine operates in a quantum Otto cycle where the working medium is coupled to classical heat baths in the isochoric processes of the four-stroke cycle, while either the coupling strength or the resonance frequency is changed in the adiabatic stages. We found that such an engine can produce work with an efficiency close to the Carnot bound when it operates at low temperatures and in the ultrastrong-coupling regime. The interplay of the effects of quantum coherence and quantum correlations on the engine performance is discussed in terms of second-order coherence, quantum mutual information, and the logarithmic negativity of entanglement. We point out that the proposed quantum Otto engine can be implemented experimentally with modern circuit quantum electrodynamic systems where flux qubits can be coupled ultrastrongly to superconducting transmission-line resonators.

Prostephanus truncatus in Africa: A review of biological trends and ...

African Journals Online (AJOL)

Prostephanus truncatus in Africa: A review of biological trends and perspectives on ... is higher in African countries than in Latin America, its region of origin. ... factors, maize and dry cassava trade routes, and availability of forest host plants.

Experimental and Computational Characterization of Biological Liquid Crystals: A Review of Single-Molecule Bioassays

Directory of Open Access Journals (Sweden)

Sungsoo Na

2009-09-01

Full Text Available Quantitative understanding of the mechanical behavior of biological liquid crystals such as proteins is essential for gaining insight into their biological functions, since some proteins perform notable mechanical functions. Recently, single-molecule experiments have allowed not only the quantitative characterization of the mechanical behavior of proteins such as protein unfolding mechanics, but also the exploration of the free energy landscape for protein folding. In this work, we have reviewed the current state-of-art in single-molecule bioassays that enable quantitative studies on protein unfolding mechanics and/or various molecular interactions. Specifically, single-molecule pulling experiments based on atomic force microscopy (AFM have been overviewed. In addition, the computational simulations on single-molecule pulling experiments have been reviewed. We have also reviewed the AFM cantilever-based bioassay that provides insight into various molecular interactions. Our review highlights the AFM-based single-molecule bioassay for quantitative characterization of biological liquid crystals such as proteins.

Can electronic search engines optimize screening of search results in systematic reviews: an empirical study.

Science.gov (United States)

Sampson, Margaret; Barrowman, Nicholas J; Moher, David; Clifford, Tammy J; Platt, Robert W; Morrison, Andra; Klassen, Terry P; Zhang, Li

2006-02-24

Most electronic search efforts directed at identifying primary studies for inclusion in systematic reviews rely on the optimal Boolean search features of search interfaces such as DIALOG and Ovid. Our objective is to test the ability of an Ultraseek search engine to rank MEDLINE records of the included studies of Cochrane reviews within the top half of all the records retrieved by the Boolean MEDLINE search used by the reviewers. Collections were created using the MEDLINE bibliographic records of included and excluded studies listed in the review and all records retrieved by the MEDLINE search. Records were converted to individual HTML files. Collections of records were indexed and searched through a statistical search engine, Ultraseek, using review-specific search terms. Our data sources, systematic reviews published in the Cochrane library, were included if they reported using at least one phase of the Cochrane Highly Sensitive Search Strategy (HSSS), provided citations for both included and excluded studies and conducted a meta-analysis using a binary outcome measure. Reviews were selected if they yielded between 1000-6000 records when the MEDLINE search strategy was replicated. Nine Cochrane reviews were included. Included studies within the Cochrane reviews were found within the first 500 retrieved studies more often than would be expected by chance. Across all reviews, recall of included studies into the top 500 was 0.70. There was no statistically significant difference in ranking when comparing included studies with just the subset of excluded studies listed as excluded in the published review. The relevance ranking provided by the search engine was better than expected by chance and shows promise for the preliminary evaluation of large results from Boolean searches. A statistical search engine does not appear to be able to make fine discriminations concerning the relevance of bibliographic records that have been pre-screened by systematic reviewers.

[Liver engineering as a new source of donor organs : A systematic review].

Science.gov (United States)

Mußbach, F; Dahmen, U; Dirsch, O; Settmacher, U

2016-06-01

Organ engineering is a new strategy to cope with the shortage of donor organs. A functional scaffold from explanted organs is prepared by removing all cellular components (decellularization) and the reseeding (repopulation) of the organ scaffold to generate a functional organ in vitro for transplantation. This technique was also applied to the liver (liver engineering). Outline of the current state of the art and resulting approaches for future research strategies. Systematic review according to the PRISMA guidelines: a PubMed-based literature search (search terms liver, decellularization), selection of relevant articles based on predetermined criteria for relevance (e.g. decellularization, repopulation and transplantation), extraction and critical appraisal of data and results concerning the conditions for decellularization, repopulation and transplantation. Decellularization was successfully performed in small and large animal models. Hepatocytes as well as stem cells and hepatic cell lines were applied for repopulation and 7 publications could show the successful transplantation of acellular and repopulated organ scaffolds. The current scientific need for further studies concerning the source of donor organs, optimization of the decellularization process, the cell type for the reseeding process and the establishment of the optimal conditions for the repopulation of the scaffold is still tremendous. For successful recellularization of the liver three goals need to be achieved: (1) reseeding of the organ scaffold with a sufficient amount of parenchymal cells, (2) endothelialization of the vascular tree to ensure the supply of oxygen and nutrients to parenchymal cells and (3) an appropriate epithelialization of the biliary tree. In order to progress to clinical trials a suitable transplantation model to verify the function of the organ constructs must be established. Liver engineering using biological cell-free organ scaffolds represents a scientific and ethical

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

Mathur, Melina; Xiang, Joy S; Smolke, Christina D

2017-01-02

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

Draft audit report, human factors engineering control room design review: Saint Lucie Nuclear Power Plant, Unit No. 2

International Nuclear Information System (INIS)

Peterson, L.R.; Lappa, D.A.; Moore, J.W.

1981-01-01

A human factors engineering preliminary design review of the Saint Lucie Unit 2 control room was performed at the site on August 3 through August 7, 1981. This design review was carried out by a team from the Human Factors Engineering Branch, Division of Human Factors Safety. This report was prepared on the basis of the HFEB's review of the applicant's Preliminary Design Assessment and the human factors engineering design review/audit performed at the site. The review team included human factors consultants from BioTechnology, Inc., Falls Church, Virginia, and from Lawrence Livermore National Laboratory (University of California), Livermore, California

Stem cells in bone tissue engineering

Energy Technology Data Exchange (ETDEWEB)

Seong, Jeong Min [Department of Preventive and Social Dentistry and Institute of Oral Biology, College of Dentistry, Kyung Hee University, Seoul 130-701 (Korea, Republic of); Kim, Byung-Chul; Park, Jae-Hong; Kwon, Il Keun; Hwang, Yu-Shik [Department of Maxillofacial Biomedical Engineering and Institute of Oral Biology, College of Dentistry, Kyung Hee University, Seoul 130-701 (Korea, Republic of); Mantalaris, Anathathios, E-mail: yshwang@khu.ac.k [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom)

2010-12-15

Bone tissue engineering has been one of the most promising areas of research, providing a potential clinical application to cure bone defects. Recently, various stem cells including embryonic stem cells (ESCs), bone marrow-derived mesenchymal stem cells (BM-MSCs), umbilical cord blood-derived mesenchymal stem cells (UCB-MSCs), adipose tissue-derived stem cells (ADSCs), muscle-derived stem cells (MDSCs) and dental pulp stem cells (DPSCs) have received extensive attention in the field of bone tissue engineering due to their distinct biological capability to differentiate into osteogenic lineages. The application of these stem cells to bone tissue engineering requires inducing in vitro differentiation of these cells into bone forming cells, osteoblasts. For this purpose, efficient in vitro differentiation towards osteogenic lineage requires the development of well-defined and proficient protocols. This would reduce the likelihood of spontaneous differentiation into divergent lineages and increase the available cell source for application to bone tissue engineering therapies. This review provides a critical examination of the various experimental strategies that could be used to direct the differentiation of ESC, BM-MSC, UCB-MSC, ADSC, MDSC and DPSC towards osteogenic lineages and their potential applications in tissue engineering, particularly in the regeneration of bone. (topical review)

Stem cells in bone tissue engineering

International Nuclear Information System (INIS)

Seong, Jeong Min; Kim, Byung-Chul; Park, Jae-Hong; Kwon, Il Keun; Hwang, Yu-Shik; Mantalaris, Anathathios

2010-01-01

Bone tissue engineering has been one of the most promising areas of research, providing a potential clinical application to cure bone defects. Recently, various stem cells including embryonic stem cells (ESCs), bone marrow-derived mesenchymal stem cells (BM-MSCs), umbilical cord blood-derived mesenchymal stem cells (UCB-MSCs), adipose tissue-derived stem cells (ADSCs), muscle-derived stem cells (MDSCs) and dental pulp stem cells (DPSCs) have received extensive attention in the field of bone tissue engineering due to their distinct biological capability to differentiate into osteogenic lineages. The application of these stem cells to bone tissue engineering requires inducing in vitro differentiation of these cells into bone forming cells, osteoblasts. For this purpose, efficient in vitro differentiation towards osteogenic lineage requires the development of well-defined and proficient protocols. This would reduce the likelihood of spontaneous differentiation into divergent lineages and increase the available cell source for application to bone tissue engineering therapies. This review provides a critical examination of the various experimental strategies that could be used to direct the differentiation of ESC, BM-MSC, UCB-MSC, ADSC, MDSC and DPSC towards osteogenic lineages and their potential applications in tissue engineering, particularly in the regeneration of bone. (topical review)

Aloe Vera for Tissue Engineering Applications

Directory of Open Access Journals (Sweden)

Shekh Rahman

2017-02-01

Full Text Available Aloe vera, also referred as Aloe barbadensis Miller, is a succulent plant widely used for biomedical, pharmaceutical and cosmetic applications. Aloe vera has been used for thousands of years. However, recent significant advances have been made in the development of aloe vera for tissue engineering applications. Aloe vera has received considerable attention in tissue engineering due to its biodegradability, biocompatibility, and low toxicity properties. Aloe vera has been reported to have many biologically active components. The bioactive components of aloe vera have effective antibacterial, anti-inflammatory, antioxidant, and immune-modulatory effects that promote both tissue regeneration and growth. The aloe vera plant, its bioactive components, extraction and processing, and tissue engineering prospects are reviewed in this article. The use of aloe vera as tissue engineering scaffolds, gels, and films is discussed, with a special focus on electrospun nanofibers.

Aloe Vera for Tissue Engineering Applications.

Science.gov (United States)

Rahman, Shekh; Carter, Princeton; Bhattarai, Narayan

2017-02-14

Aloe vera, also referred as Aloe barbadensis Miller, is a succulent plant widely used for biomedical, pharmaceutical and cosmetic applications. Aloe vera has been used for thousands of years. However, recent significant advances have been made in the development of aloe vera for tissue engineering applications. Aloe vera has received considerable attention in tissue engineering due to its biodegradability, biocompatibility, and low toxicity properties. Aloe vera has been reported to have many biologically active components. The bioactive components of aloe vera have effective antibacterial, anti-inflammatory, antioxidant, and immune-modulatory effects that promote both tissue regeneration and growth. The aloe vera plant, its bioactive components, extraction and processing, and tissue engineering prospects are reviewed in this article. The use of aloe vera as tissue engineering scaffolds, gels, and films is discussed, with a special focus on electrospun nanofibers.

Human factors engineering design review acceptance criteria for the safety parameter display

International Nuclear Information System (INIS)

McGevna, V.; Peterson, L.R.

1981-01-01

This report contains human factors engineering design review acceptance criteria developed by the Human Factors Engineering Branch (HFEB) of the Nuclear Regulatory Commission (NRC) to use in evaluating designs of the Safety Parameter Display System (SPDS). These criteria were developed in response to the functional design criteria for the SPDS defined in NUREG-0696, Functional Criteria for Emergency Response Facilities. The purpose of this report is to identify design review acceptance criteria for the SPDS installed in the control room of a nuclear power plant. Use of computer driven cathode ray tube (CRT) displays is anticipated. General acceptance criteria for displays of plant safety status information by the SPDS are developed. In addition, specific SPDS review criteria corresponding to the SPDS functional criteria specified in NUREG-0696 are established

Systems metabolic engineering in an industrial setting.

Science.gov (United States)

Sagt, Cees M J

2013-03-01

Systems metabolic engineering is based on systems biology, synthetic biology, and evolutionary engineering and is now also applied in industry. Industrial use of systems metabolic engineering focuses on strain and process optimization. Since ambitious yields, titers, productivities, and low costs are key in an industrial setting, the use of effective and robust methods in systems metabolic engineering is becoming very important. Major improvements in the field of proteomics and metabolomics have been crucial in the development of genome-wide approaches in strain and process development. This is accompanied by a rapid increase in DNA sequencing and synthesis capacity. These developments enable the use of systems metabolic engineering in an industrial setting. Industrial systems metabolic engineering can be defined as the combined use of genome-wide genomics, transcriptomics, proteomics, and metabolomics to modify strains or processes. This approach has become very common since the technology for generating large data sets of all levels of the cellular processes has developed quite fast into robust, reliable, and affordable methods. The main challenge and scope of this mini review is how to translate these large data sets in relevant biological leads which can be tested for strain or process improvements. Experimental setup, heterogeneity of the culture, and sample pretreatment are important issues which are easily underrated. In addition, the process of structuring, filtering, and visualization of data is important, but also, the availability of a genetic toolbox and equipment for medium/high-throughput fermentation is a key success factor. For an efficient bioprocess, all the different components in this process have to work together. Therefore, mutual tuning of these components is an important strategy.

Human Factors Engineering Review Model for advanced nuclear power reactors

International Nuclear Information System (INIS)

O'Hara, J.; Higgins, J.; Goodman, C.; Galletti, G.: Eckenrode, R.

1993-01-01

One of the major issues to emerge from the initial design reviews under the certification process was that detailed human-systems interface (HSI) design information was not available for staff review. To address the lack of design detail issue. The Nuclear Regulatory Commission (NRC) is performing the design certification reviews based on a design process plan which describes the human factors engineering (HFE) program elements that are necessary and sufficient to develop an acceptable detailed design specification. Since the review of a design process is unprecedented in the nuclear industry. The criteria for review are not addressed by current regulations or guidance documents and. therefore, had to be developed. Thus, an HFE Program Review Model was developed. This paper will describe the model's rationale, scope, objectives, development, general characteristics. and application

Engineering application of anaerobic ammonium oxidation process in wastewater treatment.

Science.gov (United States)

Mao, Nianjia; Ren, Hongqiang; Geng, Jinju; Ding, Lili; Xu, Ke

2017-08-01

Anaerobic ammonium oxidation (Anammox), a promising biological nitrogen removal process, has been verified as an efficient, sustainable and cost-effective alternative to conventional nitrification and denitrification processes. To date, more than 110 full-scale anammox plants have been installed and are in operation, treating industrial NH 4 + -rich wastewater worldwide, and anammox-based technologies are flourishing. This review the current state of the art for engineering applications of the anammox process, including various anammox-based technologies, reactor selection and attempts to apply it at different wastewater plants. Process control and implementation for stable performance are discussed as well as some remaining issues concerning engineering application are exposed, including the start-up period, process disturbances, greenhouse gas emissions and especially mainstream anammox applications. Finally, further development of the anammox engineering application is proposed in this review.

Surface Texture-Based Surface Treatments on Ti6Al4V Titanium Alloys for Tribological and Biological Applications: A Mini Review

Directory of Open Access Journals (Sweden)

Naiming Lin

2018-03-01

Full Text Available Surface texture (ST has been confirmed as an effective and economical surface treatment technique that can be applied to a great range of materials and presents growing interests in various engineering fields. Ti6Al4V which is the most frequently and successfully used titanium alloy has long been restricted in tribological-related operations due to the shortcomings of low surface hardness, high friction coefficient, and poor abrasive wear resistance. Ti6Al4V has benefited from surface texture-based surface treatments over the last decade. This review begins with a brief introduction, analysis approaches, and processing methods of surface texture. The specific applications of the surface texture-based surface treatments for improving surface performance of Ti6Al4V are thoroughly reviewed from the point of view of tribology and biology.

Recoding aminoacyl-tRNA synthetases for synthetic biology by rational protein-RNA engineering.

Science.gov (United States)

Hadd, Andrew; Perona, John J

2014-12-19

We have taken a rational approach to redesigning the amino acid binding and aminoacyl-tRNA pairing specificities of bacterial glutaminyl-tRNA synthetase. The four-stage engineering incorporates generalizable design principles and improves the pairing efficiency of noncognate glutamate with tRNA(Gln) by over 10(5)-fold compared to the wild-type enzyme. Better optimized designs of the protein-RNA complex include substantial reengineering of the globular core region of the tRNA, demonstrating a role for specific tRNA nucleotides in specifying the identity of the genetically encoded amino acid. Principles emerging from this engineering effort open new prospects for combining rational and genetic selection approaches to design novel aminoacyl-tRNA synthetases that ligate noncanonical amino acids onto tRNAs. This will facilitate reconstruction of the cellular translation apparatus for applications in synthetic biology.

Testing the universality of biology: a review

International Nuclear Information System (INIS)

Chela-Flores, J.

2007-08-01

We discuss whether it is possible to test the universality of biology, a quest that is of paramount relevance for one of its most recent branches, namely astrobiology. We review this topic in terms of the relative roles played on the Earth biota by contingency and evolutionary convergence. Following the seminal contribution of Darwin, it is reasonable to assume that all forms of life known to us so far are not only terrestrial, but are descendants of a common ancestor that evolved on this planet at the end of a process of chemical evolution. We also raise the related question of whether the molecular events that were precursors to the origin of life on Earth are bound to occur elsewhere in the universe, wherever the environmental conditions are similar to the terrestrial ones. We refer to 'cosmic convergence' as the possible occurrence elsewhere in the universe of Earth-like environmental conditions. We argue that cosmic convergence is already suggested by observational data. The set of hypotheses for addressing the question of the universality of biology can be tested by future experiments that are feasible with current technology. We focus on landing on Europa and the broader implications of selecting the specific example of the right landing location. We had discussed earlier the corresponding miniaturized equipment that is already in existence. The significance of these crucial points needs to be put into a wider scientific perspective, which is one of the main objectives of this review. (author)

Testing the universality of biology: a review

International Nuclear Information System (INIS)

Chela-Flores, J.

2007-05-01

We discuss whether it is possible to test the universality of biology, a quest that is of paramount relevance for one of its most recent branches, namely astrobiology. We review this topic in terms of the relative roles played on the Earth biota by contingency and evolutionary convergence. Following the seminal contribution of Darwin, it is reasonable to assume that all forms of life known to us so far are not only terrestrial, but are descendants of a common ancestor that evolved on this planet at the end of a process of chemical evolution. We also raise the related question of whether the molecular events that were precursors to the origin of life on Earth are bound to occur elsewhere in the universe, wherever the environmental conditions are similar to the terrestrial ones. We refer to 'cosmic convergence' as the possible occurrence elsewhere in the universe of Earth-like environmental conditions. We argue that cosmic convergence is already suggested by observational data. The set of hypotheses for addressing the question of the universality of biology can be tested by future experiments that are feasible with current technology. We focus on landing on Europe and the broader implications of selecting the specific example of the right landing location. We had discussed earlier the corresponding miniaturized equipment that is already in existence. The significance of these crucial points needs to be put into a wider scientific perspective, which is one of the main objectives of this review. (author)

Engineering microbial electrocatalysis for chemical and fuel production.

Science.gov (United States)

Rosenbaum, Miriam A; Henrich, Alexander W

2014-10-01

In many biotechnological areas, metabolic engineering and synthetic biology have become core technologies for biocatalyst development. Microbial electrocatalysis for biochemical and fuel production is still in its infancy and reactions rates and the product spectrum are currently very low. Therefore, molecular engineering strategies will be crucial for the advancement and realization of many new bioproduction routes using electroactive microorganisms. The complex and unresolved biochemistry and physiology of extracellular electron transfer and the lack of molecular tools for these new non-model hosts for genetic engineering constitute the major challenges for this effort. This review is providing an insight into the current status, challenges and promising approaches of pathway engineering for microbial electrocatalysis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Different methods of dentin processing for application in bone tissue engineering: A systematic review.

Science.gov (United States)

Tabatabaei, Fahimeh Sadat; Tatari, Saeed; Samadi, Ramin; Moharamzadeh, Keyvan

2016-10-01

Dentin has become an interesting potential biomaterial for tissue engineering of oral hard tissues. It can be used as a scaffold or as a source of growth factors in bone tissue engineering. Different forms of dentin have been studied for their potential use as bone substitutes. Here, we systematically review different methods of dentin preparation and the efficacy of processed dentin in bone tissue engineering. An electronic search was carried out in PubMed and Scopus databases for articles published from 2000 to 2016. Studies on dentin preparation for application in bone tissue engineering were selected. The initial search yielded a total of 1045 articles, of which 37 were finally selected. Review of studies showed that demineralization was the most commonly used dentin preparation process for use in tissue engineering. Dentin extract, dentin particles (tooth ash), freeze-dried dentin, and denatured dentin are others method of dentin preparation. Based on our literature review, we can conclude that preparation procedure and the size and shape of dentin particles play an important role in its osteoinductive and osteoconductive properties. Standardization of these methods is important to draw a conclusion in this regard. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2616-2627, 2016. © 2016 Wiley Periodicals, Inc.

Review on biological degradation of mycotoxins

Directory of Open Access Journals (Sweden)

Cheng Ji

2016-09-01

Full Text Available The worldwide contamination of feeds and foods with mycotoxins is a significant problem. Mycotoxins pose huge health threat to animals and humans. As well, mycotoxins bring enormous economic losses in food industry and animal husbandry annually. Thus, strategies to eliminate or inactivate mycotoxins in food and feed are urgently needed. Traditional physical and chemical methods have some limitations such as limited efficacy, safety issues, losses in the nutritional value and the palatability of feeds, as well as the expensive equipment required to implement these techniques. Biological degradation of mycotoxins has shown promise because it works under mild, environmentally friendly conditions. Aflatoxin (AF, zearalenone (ZEA and deoxynivalenol (DON are considered the most economically important mycotoxins in terms of their high prevalence and significant negative effects on animal performance. Therefore, this review will comprehensively describe the biological degradation of AF, ZEA and DON by microorganisms (including fungi and bacteria and specific enzymes isolated from microbial systems that can convert mycotoxins with varied efficiency to non- or less toxic products. Finally, some strategies and advices on existing difficulties of biodegradation research are also briefly proposed in this paper.

PERFORMANCE IMPROVEMENT OF DIESEL ENGINE THROUGH VARIOUS ADVANCEMENTS IN TURBOCHARGING TECHNOLOGY: A REVIEW

OpenAIRE

A.F. Sherwani

2016-01-01

In this paper, the effect of various advancements in turbocharging technology on diesel engine power, fuel consumption, thermal efficiency, volumetric efficiency and emissions are reviewed and analyzed.Turbochargers are used throughout the automotive industry to enhance the output of an internal combustion engine without increasing the cylinder capacity. The emphasis today is to provide a feasible engineering solution to manufacturing economics and greener road vehicles. It is because of thes...

A Review on Atomization and Sprays of Biofuels for IC Engine Applications

Directory of Open Access Journals (Sweden)

Prasad Boggavarapu

2013-06-01

Full Text Available Ever increasing energy requirements, environmental concerns and energy security needs are strongly influencing engine researchers to consider renewable biofuels as alternatives to fossil fuels. Spray process being important in IC engine combustion, existing literature on various biofuel sprays is reviewed and summarized. Both experimental and computational research findings are reviewed in a detailed manner for compression ignition (CI engine sprays and briefly for spark ignition (SI engine sprays. The physics of basic atomization process of sprays from various injectors is included to highlight the most recent research findings followed by discussion highlighting the effect of physico-chemical properties on spray atomization for both biofuels and fossil fuels. Biodiesel sprays are found to penetrate faster and have narrow spray plume angle and larger droplet sizes compared to diesel. Results of analytical and computational models are shown to be useful in shedding light on the actual process of atomization. However, further studies on understanding primary atomization and the effect of fuel properties on primary atomization are required. As far as secondary atomization is concerned, changes in regimes are observed to occur at higher air-jet velocities for biodiesel compared to those of diesel. Evaporating sprays revealed that the liquid length is longer for biodiesel. Pure plant oil sprays with potential use in CI engines may require alternative injector technology due to slower breakup as compared to diesel. Application of ethanol to gasoline engines may be feasible without any modifications to port fuel injection (PFI engines. More studies are required on the application of alternative fuels to high pressure sprays used in Gasoline Direct Injection (GDI engines.

Strategies for Biologic Image-Guided Dose Escalation: A Review

International Nuclear Information System (INIS)

Sovik, Aste; Malinen, Eirik; Olsen, Dag Rune

2009-01-01

There is increasing interest in how to incorporate functional and molecular information obtained by noninvasive, three-dimensional tumor imaging into radiotherapy. The key issues are to identify radioresistant regions that can be targeted for dose escalation, and to develop radiation dose prescription and delivery strategies providing optimal treatment for the individual patient. In the present work, we review the proposed strategies for biologic image-guided dose escalation with intensity-modulated radiation therapy. Biologic imaging modalities and the derived images are discussed, as are methods for target volume delineation. Different dose escalation strategies and techniques for treatment delivery and treatment plan evaluation are also addressed. Furthermore, we consider the need for response monitoring during treatment. We conclude with a summary of the current status of biologic image-based dose escalation and of areas where further work is needed for this strategy to become incorporated into clinical practice

Awareness of Societal Issues among High School Biology Teachers Teaching Genetics

Science.gov (United States)

Lazarowitz, Reuven; Bloch, Ilit

2005-01-01

The purpose of this study was to investigate how aware high school biology teachers are of societal issues (values, moral, ethic, and legal issues) while teaching genetics, genetics engineering, molecular genetics, human heredity, and evolution. The study includes a short historical review of World War II atrocities during the Holocaust when…

Improving the reviewing process in Ecology and Evolutionary Biology

Directory of Open Access Journals (Sweden)

Grossman, G. D.

2014-06-01

Full Text Available I discuss current issues in reviewing and editorial practices in ecology and evolutionary biology and suggest possible solutions for current problems. The reviewing crisis is unlikely to change unless steps are taken by journals to provide greater inclusiveness and incentives to reviewers. In addition, both journals and institutions should reduce their emphasis on publication numbers (least publishable units and impact factors and focus instead on article synthesis and quality which will require longer publications. Academic and research institutions should consider reviewing manuscripts and editorial positions an important part of a researcher’s professional activities and reward them accordingly. Rewarding reviewers either monetarily or via other incentives such as free journal subscriptions may encourage participation in the reviewing process for both profit and non–profit journals. Reviewer performance will likely be improved by measures that increase inclusiveness, such as sending reviews and decision letters to reviewers. Journals may be able to evaluate the efficacy of their reviewing process by comparing citations of rejected but subsequently published papers with those published within the journal at similar times. Finally, constructive reviews: 1 identify important shortcomings and suggest solutions when possible, 2 distinguish trivial from non–trivial problems, and 3 include editor’s evaluations of the reviews including identification of trivial versus substantive comments (i.e., those that must be addressed.

Review of the Space Mapping Approach to Engineering Optimization and Modeling

DEFF Research Database (Denmark)

Bakr, M. H.; Bandler, J. W.; Madsen, Kaj

2000-01-01

We review the Space Mapping (SM) concept and its applications in engineering optimization and modeling. The aim of SM is to avoid computationally expensive calculations encountered in simulating an engineering system. The existence of less accurate but fast physically-based models is exploited. S......-based Modeling (SMM). These include Space Derivative Mapping (SDM), Generalized Space Mapping (GSM) and Space Mapping-based Neuromodeling (SMN). Finally, we address open points for research and future development....

Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology.

Science.gov (United States)

Liljeruhm, Josefine; Funk, Saskia K; Tietscher, Sandra; Edlund, Anders D; Jamal, Sabri; Wistrand-Yuen, Pikkei; Dyrhage, Karl; Gynnå, Arvid; Ivermark, Katarina; Lövgren, Jessica; Törnblom, Viktor; Virtanen, Anders; Lundin, Erik R; Wistrand-Yuen, Erik; Forster, Anthony C

2018-01-01

Coral reefs are colored by eukaryotic chromoproteins (CPs) that are homologous to green fluorescent protein. CPs differ from fluorescent proteins (FPs) by intensely absorbing visible light to give strong colors in ambient light. This endows CPs with certain advantages over FPs, such as instrument-free detection uncomplicated by ultra-violet light damage or background fluorescence, efficient Förster resonance energy transfer (FRET) quenching, and photoacoustic imaging. Thus, CPs have found utility as genetic markers and in teaching, and are attractive for potential cell biosensor applications in the field. Most near-term applications of CPs require expression in a different domain of life: bacteria. However, it is unclear which of the eukaryotic CP genes might be suitable and how best to assay them. Here, taking advantage of codon optimization programs in 12 cases, we engineered 14 CP sequences (meffRed, eforRed, asPink, spisPink, scOrange, fwYellow, amilGFP, amajLime, cjBlue, meffBlue, aeBlue, amilCP, tsPurple and gfasPurple) into a palette of Escherichia coli BioBrick plasmids. BioBricks comply with synthetic biology's most widely used, simplified, cloning standard. Differences in color intensities, maturation times and fitness costs of expression were compared under the same conditions, and visible readout of gene expression was quantitated. A surprisingly large variation in cellular fitness costs was found, resulting in loss of color in some overnight liquid cultures of certain high-copy-plasmid-borne CPs, and cautioning the use of multiple CPs as markers in competition assays. We solved these two problems by integrating pairs of these genes into the chromosome and by engineering versions of the same CP with very different colors. Availability of 14 engineered CP genes compared in E. coli , together with chromosomal mutants suitable for competition assays, should simplify and expand CP study and applications. There was no single plasmid-borne CP that combined

Bioterrorism and Biological Warfare, from Past to the Present: A classic review

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Majid Zare Bidaki

2015-10-01

Full Text Available Bioterrorism is defined as any terrorist action of intentional release or dissemination of highly pathogenic biological agents, including a variety of microorganisms or biological toxins. With the growing threat of terrorism, is necessary that the potential danger of various microorganisms – as a powerful tool of aggression and threat- to be taken seriously. This review tries to explain the concept of biological weapons and their historical development process with an emphasis on efforts to control the proliferation of these types of weapons over the last century. Potential impact of infectious diseases on people and armed forces was known from since 600 BC. Using the victims of the plague as a weapon in medieval warfare and spread of smallpox as a weapon during the war against the Indians when initially America was discovered, the development of biological weapons during the World War I, World War II and the Cold War, and even since the beginning of the third millennium, all show the strategic importance of pathogenic microorganisms as a deterrent power for the superiority of some governments and cults. Historical attempts to use infectious diseases as biological weapons reveal that the distinction between a natural outbreak of an infectious disease and that of a deliberate biological attack is very difficult. Abusing this characteristic of infectious diseases has made it possible for the purposes of superiority. International agreements to control the development of biological weapons, such as “the 1925 Geneva Protocol” and “the Convention on the Prohibition of the Development, Production and Stockpiling of Biological and Toxic Weapons” have not been able to control the development and using of biological warfare.  The current paper is a classic review (Overview article aiming at increasing the knowledge and awareness of people especially of health authorities and government officials.

A Review on Chemical Constituents and Biological Activities of the ...

African Journals Online (AJOL)

The current review is aimed to deliver some updates on the ethnobotany, phytochemistry and biological activities of Beilschmiedia species in order to throw more light on their therapeutic potentials and future research priorities. Phytochemical studies on Beilschmiedia genus yielded essential oils, endiandric acid ...

Engineering and evaluating drug delivery particles in microfluidic devices.

Science.gov (United States)

Björnmalm, Mattias; Yan, Yan; Caruso, Frank

2014-09-28

The development of new and improved particle-based drug delivery is underpinned by an enhanced ability to engineer particles with high fidelity and integrity, as well as increased knowledge of their biological performance. Microfluidics can facilitate these processes through the engineering of spatiotemporally highly controlled environments using designed microstructures in combination with physical phenomena present at the microscale. In this review, we discuss microfluidics in the context of addressing key challenges in particle-based drug delivery. We provide an overview of how microfluidic devices can: (i) be employed to engineer particles, by providing highly controlled interfaces, and (ii) be used to establish dynamic in vitro models that mimic in vivo environments for studying the biological behavior of engineered particles. Finally, we discuss how the flexible and modular nature of microfluidic devices provides opportunities to create increasingly realistic models of the in vivo milieu (including multi-cell, multi-tissue and even multi-organ devices), and how ongoing developments toward commercialization of microfluidic tools are opening up new opportunities for the engineering and evaluation of drug delivery particles. Copyright © 2014 Elsevier B.V. All rights reserved.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions and novel technologies

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Frank eSchreiber

2012-10-01

Full Text Available Nitrous oxide (N2O is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH or the reduction of nitrite (NO2- to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO2- to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria. In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO2-, NH2OH and nitroxyl (HNO. Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser based absorption spectroscopy. In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build-up.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Science.gov (United States)

Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

2012-01-01

Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

Redox cofactor engineering in industrial microorganisms: strategies, recent applications and future directions.

Science.gov (United States)

Liu, Jiaheng; Li, Huiling; Zhao, Guangrong; Caiyin, Qinggele; Qiao, Jianjun

2018-05-01

NAD and NADP, a pivotal class of cofactors, which function as essential electron donors or acceptors in all biological organisms, drive considerable catabolic and anabolic reactions. Furthermore, they play critical roles in maintaining intracellular redox homeostasis. However, many metabolic engineering efforts in industrial microorganisms towards modification or introduction of metabolic pathways, especially those involving consumption, generation or transformation of NAD/NADP, often induce fluctuations in redox state, which dramatically impede cellular metabolism, resulting in decreased growth performance and biosynthetic capacity. Here, we comprehensively review the cofactor engineering strategies for solving the problematic redox imbalance in metabolism modification, as well as their features, suitabilities and recent applications. Some representative examples of in vitro biocatalysis are also described. In addition, we briefly discuss how tools and methods from the field of synthetic biology can be applied for cofactor engineering. Finally, future directions and challenges for development of cofactor redox engineering are presented.

77 FR 3844 - Agency Information Collection (Architect-Engineer Fee Proposal) Activity Under OMB Review

Science.gov (United States)

2012-01-25

... DEPARTMENT OF VETERANS AFFAIRS [OMB Control No. 2900-0208] Agency Information Collection (Architect--Engineer Fee Proposal) Activity Under OMB Review AGENCY: Veterans Health Administration... . Please refer to ``OMB Control No. 2900-0208.'' SUPPLEMENTARY INFORMATION: Titles: a. Architect--Engineer...

Promoting microbiology education through the iGEM synthetic biology competition.

Science.gov (United States)

Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

2015-08-01

Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae.

Science.gov (United States)

Li, Mingji; Borodina, Irina

2015-02-01

Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae We describe computational tools for the prediction of biochemical pathways, molecular biology methods for assembly of DNA parts into pathways, and for introducing the pathways into the host, and finally approaches for optimizing performance of the introduced pathways. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Quality of Design, Analysis and Reporting of Software Engineering Experiments:A Systematic Review

OpenAIRE

By Kampenes, Vigdis

2007-01-01

Background: Like any research discipline, software engineering research must be of a certain quality to be valuable. High quality research in software engineering ensures that knowledge is accumulated and helpful advice is given to the industry. One way of assessing research quality is to conduct systematic reviews of the published research literature. Objective: The purpose of this work was to assess the quality of published experiments in software engineering with respect to the validit...

A review of Curtiss-Wright rotary engine developments with respect to general aviation potential

Science.gov (United States)

Jones, C.

1979-01-01

Aviation related rotary (Wankel-type) engine tests, possible growth directions and relevant developments at Curtiss-Wright have been reviewed. Automotive rotary engines including stratified charge are described and flight test results of rotary aircraft engines are presented. The current 300 HP engine prototype shows basic durability and competitive performance potential. Recent parallel developments have separately confirmed the geometric advantages of the rotary engine for direct injected unthrottled stratified charge. Specific fuel consumption equal to or better than pre- or swirl-chamber diesels, low emission and multi-fuel capability have been shown by rig tests of similar rotary engine.

A review of selected pumping systems in nature and engineering--potential biomimetic concepts for improving displacement pumps and pulsation damping.

Science.gov (United States)

Bach, D; Schmich, F; Masselter, T; Speck, T

2015-09-03

The active transport of fluids by pumps plays an essential role in engineering and biology. Due to increasing energy costs and environmental issues, topics like noise reduction, increase of efficiency and enhanced robustness are of high importance in the development of pumps in engineering. The study compares pumps in biology and engineering and assesses biomimetic potentials for improving man-made pumping systems. To this aim, examples of common challenges, applications and current biomimetic research for state-of-the art pumps are presented. The biomimetic research is helped by the similar configuration of many positive displacement pumping systems in biology and engineering. In contrast, the configuration and underlying pumping principles for fluid dynamic pumps (FDPs) differ to a greater extent in biology and engineering. However, progress has been made for positive displacement as well as for FDPs by developing biomimetic devices with artificial muscles and cilia that improve energetic efficiency and fail-safe operation or reduce noise. The circulatory system of vertebrates holds a high biomimetic potential for the damping of pressure pulsations, a common challenge in engineering. Damping of blood pressure pulsation results from a nonlinear viscoelastic behavior of the artery walls which represent a complex composite material. The transfer of the underlying functional principle could lead to an improvement of existing technical solutions and be used to develop novel biomimetic damping solutions. To enhance efficiency or thrust of man-made fluid transportation systems, research on jet propulsion in biology has shown that a pulsed jet can be tuned to either maximize thrust or efficiency. The underlying principle has already been transferred into biomimetic applications in open channel water systems. Overall there is a high potential to learn from nature in order to improve pumping systems for challenges like the reduction of pressure pulsations, increase of jet

Human factors engineering plan for reviewing nuclear plant modernization programs

International Nuclear Information System (INIS)

O'Hara, John; Higgins, James

2004-12-01

The Swedish Nuclear Power Inspectorate reviews the human factors engineering (HFE) aspects of nuclear power plants (NPPs) involved in the modernization of the plant systems and control rooms. The purpose of a HFE review is to help ensure personnel and public safety by verifying that accepted HFE practices and guidelines are incorporated into the program and nuclear power plant design. Such a review helps to ensure the HFE aspects of an NPP are developed, designed, and evaluated on the basis of a structured top-down system analysis using accepted HFE principles. The review addresses eleven HFE elements: HFE Program Management, Operating Experience Review, Functional Requirements Analysis and Allocation, Task Analysis, Staffing, Human Reliability Analysis, Human-System Interface Design, Procedure Development, Training Program Development, Human Factors Verification and Validation, and Design Implementation

Human factors engineering plan for reviewing nuclear plant modernization programs

Energy Technology Data Exchange (ETDEWEB)

O' Hara, John; Higgins, James [Brookhaven National Laboratory, Upton, NY (United States)

2004-12-01

The Swedish Nuclear Power Inspectorate reviews the human factors engineering (HFE) aspects of nuclear power plants (NPPs) involved in the modernization of the plant systems and control rooms. The purpose of a HFE review is to help ensure personnel and public safety by verifying that accepted HFE practices and guidelines are incorporated into the program and nuclear power plant design. Such a review helps to ensure the HFE aspects of an NPP are developed, designed, and evaluated on the basis of a structured top-down system analysis using accepted HFE principles. The review addresses eleven HFE elements: HFE Program Management, Operating Experience Review, Functional Requirements Analysis and Allocation, Task Analysis, Staffing, Human Reliability Analysis, Human-System Interface Design, Procedure Development, Training Program Development, Human Factors Verification and Validation, and Design Implementation.

Bioreactor design for tendon/ligament engineering.

Science.gov (United States)

Wang, Tao; Gardiner, Bruce S; Lin, Zhen; Rubenson, Jonas; Kirk, Thomas B; Wang, Allan; Xu, Jiake; Smith, David W; Lloyd, David G; Zheng, Ming H

2013-04-01

Tendon and ligament injury is a worldwide health problem, but the treatment options remain limited. Tendon and ligament engineering might provide an alternative tissue source for the surgical replacement of injured tendon. A bioreactor provides a controllable environment enabling the systematic study of specific biological, biochemical, and biomechanical requirements to design and manufacture engineered tendon/ligament tissue. Furthermore, the tendon/ligament bioreactor system can provide a suitable culture environment, which mimics the dynamics of the in vivo environment for tendon/ligament maturation. For clinical settings, bioreactors also have the advantages of less-contamination risk, high reproducibility of cell propagation by minimizing manual operation, and a consistent end product. In this review, we identify the key components, design preferences, and criteria that are required for the development of an ideal bioreactor for engineering tendons and ligaments.

Tissue engineering and regenerative medicine in applied research: a year in review of 2014.

Science.gov (United States)

Lin, Xunxun; Huang, Jia; Shi, Yuan; Liu, Wei

2015-04-01

Tissue engineering and regenerative medicine (TERM) remains to be one of the fastest growing fields, which covers a wide scope of topics of both basic and applied biological researches. This overview article summarized the advancements in applied researches of TERM area, including stem cell-mediated tissue regeneration, material science, and TERM clinical trial. These achievements demonstrated the great potential of clinical regenerative therapy of tissue/organ disease or defect through stem cells and tissue engineering approaches.

Engineering aspects of ferrate in water and wastewater treatment - a review.

Science.gov (United States)

Yates, Brian J; Zboril, Radek; Sharma, Virender K

2014-01-01

There is renewed interest in the tetra-oxy compound of +6 oxidation states of iron, ferrate(VI) (Fe(VI)O4(2-)), commonly called ferrate. Ferrate has the potential in cleaner ("greener") technologies for water treatment and remediation processes, as it produces potentially less toxic byproducts than other treatment chemicals (e.g., chlorine). Ferrate has strong potential to oxidize a number of contaminants, including sulfur- and nitrogen-containing compounds, estrogens, and antibiotics. This oxidation capability of ferrate combines with its efficient disinfection and coagulation properties as a multi-purpose treatment chemical in a single dose. This review focuses on the engineering aspects of ferrate use at the pilot scale to remove contaminants in and enhance physical treatment of water and wastewater. In most of the pilot-scale studies, in-line and on-line electrochemical ferrate syntheses have been applied. In this ferrate synthesis, ferrate was directly prepared in solution from an iron anode, followed by direct addition to the contaminant stream. Some older studies applied ferrate as a solid. This review presents examples of removing a range of contaminants by adding ferrate solution to the stream. Results showed that ferrate alone and in combination with additional coagulants can reduce total suspended solids (TSS), chemical oxygen demand (COD), biological oxygen demand (BOD), and organic matter. Ferrate also oxidizes cyanide, sulfide, arsenic, phenols, anilines, and dyes and disinfects a variety of viruses and bacteria. Limitations and drawbacks of the application of ferrate in treating contaminated water on the pilot scale are also presented.

Recent Advances in Crystal Engineering from Nanoscience Views: A Brief Review

Directory of Open Access Journals (Sweden)

Marzieh Arab Fashapoyeh

2017-01-01

Full Text Available Crystal engineering has recently emerged as a method of choice for the design and construction of organic as well as metal-organic functional materials. Crystal engineering attempts to establish packing trends in whole families of compounds and seeks to establish connections between structure and function. The utility of crystal engineering has also been expanded to the nanoscience and the development of nanomaterials. The crystal engineering of materials on the nanoscale has attracted attention from various fields of research. Using bottom-up assembly strategies, a wide range of functional systems can be accessed. Materials of nanometer-scale dimensions having unique physicochemical properties are of great interest in various fields such as synthetic chemistry, materials science, catalysis and medicine. This review concerns to the recent advances in crystal engineering from nanoscience views. This study was conducted in four categories; nanococrystals, nano metal-organic frameworks, composites of polyoxometalates and also some of the nanocarbons.

High Cholesterol/Low Cholesterol: Effects in Biological Membranes: A Review.

Science.gov (United States)

Subczynski, Witold K; Pasenkiewicz-Gierula, Marta; Widomska, Justyna; Mainali, Laxman; Raguz, Marija

2017-12-01

Lipid composition determines membrane properties, and cholesterol plays a major role in this determination as it regulates membrane fluidity and permeability, as well as induces the formation of coexisting phases and domains in the membrane. Biological membranes display a very diverse lipid composition, the lateral organization of which plays a crucial role in regulating a variety of membrane functions. We hypothesize that, during biological evolution, membranes with a particular cholesterol content were selected to perform certain functions in the cells of eukaryotic organisms. In this review, we discuss the major membrane properties induced by cholesterol, and their relationship to certain membrane functions.

A Review of Three-Dimensional Printing in Tissue Engineering.

Science.gov (United States)

Sears, Nick A; Seshadri, Dhruv R; Dhavalikar, Prachi S; Cosgriff-Hernandez, Elizabeth

2016-08-01

Recent advances in three-dimensional (3D) printing technologies have led to a rapid expansion of applications from the creation of anatomical training models for complex surgical procedures to the printing of tissue engineering constructs. In addition to achieving the macroscale geometry of organs and tissues, a print layer thickness as small as 20 μm allows for reproduction of the microarchitectures of bone and other tissues. Techniques with even higher precision are currently being investigated to enable reproduction of smaller tissue features such as hepatic lobules. Current research in tissue engineering focuses on the development of compatible methods (printers) and materials (bioinks) that are capable of producing biomimetic scaffolds. In this review, an overview of current 3D printing techniques used in tissue engineering is provided with an emphasis on the printing mechanism and the resultant scaffold characteristics. Current practical challenges and technical limitations are emphasized and future trends of bioprinting are discussed.

Synthetic Biology of Cyanobacteria: Unique Challenges and Opportunities

Directory of Open Access Journals (Sweden)

Bertram M Berla

2013-08-01

Full Text Available Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria’s potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as ‘chassis’ strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a ‘green E. coli’. In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

Tsallis Entropy Theory for Modeling in Water Engineering: A Review

Directory of Open Access Journals (Sweden)

Vijay P. Singh

2017-11-01

Full Text Available Water engineering is an amalgam of engineering (e.g., hydraulics, hydrology, irrigation, ecosystems, environment, water resources and non-engineering (e.g., social, economic, political aspects that are needed for planning, designing and managing water systems. These aspects and the associated issues have been dealt with in the literature using different techniques that are based on different concepts and assumptions. A fundamental question that still remains is: Can we develop a unifying theory for addressing these? The second law of thermodynamics permits us to develop a theory that helps address these in a unified manner. This theory can be referred to as the entropy theory. The thermodynamic entropy theory is analogous to the Shannon entropy or the information theory. Perhaps, the most popular generalization of the Shannon entropy is the Tsallis entropy. The Tsallis entropy has been applied to a wide spectrum of problems in water engineering. This paper provides an overview of Tsallis entropy theory in water engineering. After some basic description of entropy and Tsallis entropy, a review of its applications in water engineering is presented, based on three types of problems: (1 problems requiring entropy maximization; (2 problems requiring coupling Tsallis entropy theory with another theory; and (3 problems involving physical relations.

A comprehensive review of cryogels and their roles in tissue engineering applications.

Science.gov (United States)

Hixon, Katherine R; Lu, Tracy; Sell, Scott A

2017-10-15

The extracellular matrix is fundamental in providing an appropriate environment for cell interaction and signaling to occur. Replicating such a matrix is advantageous in the support of tissue ingrowth and regeneration through the field of tissue engineering. While scaffolds can be fabricated in many ways, cryogels have recently become a popular approach due to their macroporous structure and durability. Produced through the crosslinking of gel precursors followed by a subsequent controlled freeze/thaw cycle, the resulting cryogel provides a unique, sponge-like structure. Therefore, cryogels have proven advantageous for many tissue engineering applications including roles in bioreactor systems, cell separation, and scaffolding. Specifically, the matrix has been demonstrated to encourage the production of various molecules, such as antibodies, and has also been used for cryopreservation. Cryogels can pose as a bioreactor for the expansion of cell lines, as well as a vehicle for cell separation. Lastly, this matrix has shown excellent potential as a tissue engineered scaffold, encouraging regrowth at numerous damaged tissue sites in vivo. This review will briefly discuss the fabrication of cryogels, with an emphasis placed on their application in various facets of tissue engineering to provide an overview of this unique scaffold's past and future roles. Cryogels are unique scaffolds produced through the controlled freezing and thawing of a polymer solution. There is an ever-growing body of literature that demonstrates their applicability in the realm of tissue engineering as extracellular matrix analogue scaffolds; with extensive information having been provided regarding the fabrication, porosity, and mechanical integrity of the scaffolds. Additionally, cryogels have been reviewed with respect to their role in bioseparation and as cellular incubators. This all-inclusive view of the roles that cryogels can play is critical to advancing the technology and expanding its

Informing biological design by integration of systems and synthetic biology.

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Smolke, Christina D; Silver, Pamela A

2011-03-18

Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. Copyright © 2011 Elsevier Inc. All rights reserved.

Striking balance between expedited review and expecting efficacious anticancer drug and biologics: An ongoing challenge

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Krishnan Vengadaragava Chary

2017-01-01

Full Text Available Objective: The objective of this study is to assess the postmarketing status: Efficacy and safety drugs and biologics related with cancer approved under expedited review. Methods: This observational, analytical study was carried between January and April 2016 by the Department of Pharmacology and Medical Oncology, Saveetha Medical College. Drugs approved under expedited review, fast-track status and its association with anti-cancer effects, postmarketing efficacy and safety, propensity to induce the second tumor was noted. Drug approval status and average time of review process were obtained from the United States-Food and Drug Administration (FDA, Center for Drugs and Biologics Center (Center for Drug Evaluation and Research and Center for Biologics Evaluation and Research. Postmarketing adverse events and safety issues were collected FDA adverse effects reporting system. Further, evidence efficacy and safety of drugs were taken from various meta-analysis, reports on BioMed journals, and Cochrane systematic reviews. Results: In the last 5 years, 166 products were approved by expedited review. Out of 166, 48 (28.9% drugs/biologics are anticancer drugs and drugs used in precancerous conditions. The average time of review varies from19 months to 8.2 months. Out of these 48 molecules, 37 (77% molecules received serious adverse event alert. Positive correlation is seen between average time of review and number of adverse events reported. Seven (14.5% drugs were proven to induce second tumor among receivers. Conclusion: Although expedited review facilitates faster approval of drugs; selection and assessment criteria should be stringent to prevent clinical failure, serious adverse effects of such drugs exposed to many individuals. Focus should be given developing chemosensitizing molecule and evaluation of metronomic regimen which is being more optimistic in current cancer therapeutics.

Review of methods for the integration of reliability and design engineering

International Nuclear Information System (INIS)

Reilly, J.T.

1978-03-01

A review of methods for the integration of reliability and design engineering was carried out to establish a reliability program philosophy, an initial set of methods, and procedures to be used by both the designer and reliability analyst. The report outlines a set of procedures which implements a philosophy that requires increased involvement by the designer in reliability analysis. Discussions of each method reviewed include examples of its application

Mechanisms Underlying Cytotoxicity Induced by Engineered Nanomaterials: A Review of In Vitro Studies

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Nogueira, Daniele R.; Mitjans, Montserrat; Rolim, Clarice M. B.; Vinardell, M. Pilar

2014-01-01

Engineered nanomaterials are emerging functional materials with technologically interesting properties and a wide range of promising applications, such as drug delivery devices, medical imaging and diagnostics, and various other industrial products. However, concerns have been expressed about the risks of such materials and whether they can cause adverse effects. Studies of the potential hazards of nanomaterials have been widely performed using cell models and a range of in vitro approaches. In the present review, we provide a comprehensive and critical literature overview on current in vitro toxicity test methods that have been applied to determine the mechanisms underlying the cytotoxic effects induced by the nanostructures. The small size, surface charge, hydrophobicity and high adsorption capacity of nanomaterial allow for specific interactions within cell membrane and subcellular organelles, which in turn could lead to cytotoxicity through a range of different mechanisms. Finally, aggregating the given information on the relationships of nanomaterial cytotoxic responses with an understanding of its structure and physicochemical properties may promote the design of biologically safe nanostructures. PMID:28344232

Chitin Scaffolds in Tissue Engineering

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Jayakumar, Rangasamy; Chennazhi, Krishna Prasad; Srinivasan, Sowmya; Nair, Shantikumar V.; Furuike, Tetsuya; Tamura, Hiroshi

2011-01-01

Tissue engineering/regeneration is based on the hypothesis that healthy stem/progenitor cells either recruited or delivered to an injured site, can eventually regenerate lost or damaged tissue. Most of the researchers working in tissue engineering and regenerative technology attempt to create tissue replacements by culturing cells onto synthetic porous three-dimensional polymeric scaffolds, which is currently regarded as an ideal approach to enhance functional tissue regeneration by creating and maintaining channels that facilitate progenitor cell migration, proliferation and differentiation. The requirements that must be satisfied by such scaffolds include providing a space with the proper size, shape and porosity for tissue development and permitting cells from the surrounding tissue to migrate into the matrix. Recently, chitin scaffolds have been widely used in tissue engineering due to their non-toxic, biodegradable and biocompatible nature. The advantage of chitin as a tissue engineering biomaterial lies in that it can be easily processed into gel and scaffold forms for a variety of biomedical applications. Moreover, chitin has been shown to enhance some biological activities such as immunological, antibacterial, drug delivery and have been shown to promote better healing at a faster rate and exhibit greater compatibility with humans. This review provides an overview of the current status of tissue engineering/regenerative medicine research using chitin scaffolds for bone, cartilage and wound healing applications. We also outline the key challenges in this field and the most likely directions for future development and we hope that this review will be helpful to the researchers working in the field of tissue engineering and regenerative medicine. PMID:21673928

A design concept of parallel elasticity extracted from biological muscles for engineered actuators.

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Chen, Jie; Jin, Hongzhe; Iida, Fumiya; Zhao, Jie

2016-08-23

Series elastic actuation that takes inspiration from biological muscle-tendon units has been extensively studied and used to address the challenges (e.g. energy efficiency, robustness) existing in purely stiff robots. However, there also exists another form of passive property in biological actuation, parallel elasticity within muscles themselves, and our knowledge of it is limited: for example, there is still no general design strategy for the elasticity profile. When we look at nature, on the other hand, there seems a universal agreement in biological systems: experimental evidence has suggested that a concave-upward elasticity behaviour is exhibited within the muscles of animals. Seeking to draw possible design clues for elasticity in parallel with actuators, we use a simplified joint model to investigate the mechanisms behind this biologically universal preference of muscles. Actuation of the model is identified from general biological joints and further reduced with a specific focus on muscle elasticity aspects, for the sake of easy implementation. By examining various elasticity scenarios, one without elasticity and three with elasticity of different profiles, we find that parallel elasticity generally exerts contradictory influences on energy efficiency and disturbance rejection, due to the mechanical impedance shift thus caused. The trade-off analysis between them also reveals that concave parallel elasticity is able to achieve a more advantageous balance than linear and convex ones. It is expected that the results could contribute to our further understanding of muscle elasticity and provide a theoretical guideline on how to properly design parallel elasticity behaviours for engineering systems such as artificial actuators and robotic joints.

Recent developments in systems biology and metabolic engineering of plant microbe interactions

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Vishal Kumar

2016-09-01

Full Text Available Microorganisms play a crucial role in the sustainability of the various ecosystems. The characterization of various interactions between microorganisms and other biotic factors is a necessary footstep to understand the association and functions of microbial communities. Among the different microbial interactions in an ecosystem, plant-microbe interaction plays an important role to balance the ecosystem. The present review explores plant microbe interactions using gene editing and system biology tools towards the comprehension in improvement of plant traits. Further, system biology tools like FBA, OptKnock and constrain based modeling helps in understanding such interactions as a whole. In addition, various gene editing tools have been summarized and a strategy has been hypothesized for the development of disease free plants. Furthermore, we have tried to summarize the predictions through data retrieved from various types of sources such as high throughput sequencing data (e.g. single nucleotide polymorphism (SNP detection, RNA-seq, proteomics and metabolic models have been reconstructed from such sequences for species communities. It is well known fact that systems biology approaches and modeling of biological networks will enable us to learn the insight of such network and will also help further in understanding these interactions.

Nitrate removal from drinking water with a focus on biological methods: a review.

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Rezvani, Fariba; Sarrafzadeh, Mohammad-Hossein; Ebrahimi, Sirous; Oh, Hee-Mock

2017-05-31

This article summarizes several developed and industrial technologies for nitrate removal from drinking water, including physicochemical and biological techniques, with a focus on autotrophic nitrate removal. Approaches are primarily classified into separation-based and elimination-based methods according to the fate of the nitrate in water treatment. Biological denitrification as a cost-effective and promising method of biological nitrate elimination is reviewed in terms of its removal process, applicability, efficiency, and associated disadvantages. The various pathways during biological nitrate removal, including assimilatory and dissimilatory nitrate reduction, are also explained. A comparative study was carried out to provide a better understanding of the advantages and disadvantages of autotrophic and heterotrophic denitrification. Sulfur-based and hydrogen-based denitrifications, which are the most common autotrophic processes of nitrate removal, are reviewed with the aim of presenting the salient features of hydrogenotrophic denitrification along with some drawbacks of the technology and research areas in which it could be used but currently is not. The application of algae-based water treatment is also introduced as a nature-inspired approach that may broaden future horizons of nitrate removal technology.

Synthetic biology in cell-based cancer immunotherapy.

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Chakravarti, Deboki; Wong, Wilson W

2015-08-01

The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. We first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing. Copyright © 2015 Elsevier Ltd. All rights reserved.

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

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Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

Improvements in algal lipid production: a systems biology and gene editing approach.

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Banerjee, Avik; Banerjee, Chiranjib; Negi, Sangeeta; Chang, Jo-Shu; Shukla, Pratyoosh

2018-05-01

In the wake of rising energy demands, microalgae have emerged as potential sources of sustainable and renewable carbon-neutral fuels, such as bio-hydrogen and bio-oil. For rational metabolic engineering, the elucidation of metabolic pathways in fine detail and their manipulation according to requirements is the key to exploiting the use of microalgae. Emergence of site-specific nucleases have revolutionized applied research leading to biotechnological gains. Genome engineering as well as modulation of the endogenous genome with high precision using CRISPR systems is being gradually employed in microalgal research. Further, to optimize and produce better algal platforms, use of systems biology network analysis and integration of omics data is required. This review discusses two important approaches: systems biology and gene editing strategies used on microalgal systems with a focus on biofuel production and sustainable solutions. It also emphasizes that the integration of such systems would contribute and compliment applied research on microalgae. Recent advances in microalgae are discussed, including systems biology, gene editing approaches in lipid bio-synthesis, and antenna engineering. Lastly, it has been attempted here to showcase how CRISPR/Cas systems are a better editing tool than existing techniques that can be utilized for gene modulation and engineering during biofuel production.

PLANT ISOFLAVONES: BIOSYNHTESIS, DETECTION AND BIOLOGICAL PROPERTIES

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V. D. Naumenko

2013-10-01

Full Text Available Biological properties, chemical structures and biosynthesis pathways of plant isoflavones, especially soybean isoflavones (daidzein, genistein and glycitein are reviewed. The structures of isoflavones, and their aglicone and glucosides (glycosides forms as well as isoflavone biosynthesis pathways are described. General information about the advanced methods for the detection of isoflavones and their conjugates are considered. The importance of the profiling of isoflavones, flavonoids and their conjugates by means of analytical tools and methods to dissolve some questions in biology and medicine is discussed. The review provides data on the major isoflavone content in some vegetable crops and in the tissues of different soybean varieties. Health benefits and treatment or preventive properties of isoflavones for cancer, cardiovascular, endocrine diseases and metabolic disorders are highlighted. The mechanisms that may explain their positive biological effects are considered. The information on the application of advanced technologies to create new plant forms producing isoflavonoids with a predicted level of isoflavones, which is the most favorable for the treatment is given. The possibilities to use the metabolic engineering for the increasing of accumulation and synthesis of isoflavones at the non-legume crops such as tobacco, Arabidopsis and maize are considered. The examples how the plant tissues, which are not naturally produced of the isoflavones, can obtain potential for the synthesis of biologically active compounds via inducing of the activity of the introduced enzyme isoflavon synthase, are given. Specific biochemical pathways for increasing the synthesis of isoflavone genistein in Arabidopsis thaliana tissues are discussed. It is concluded that plant genetic engineering which is focused on modification of the secondary metabolites contain in plant tissues, enables to create the new crop varieties with improved agronomic properties and

Genetic Engineering In BioButanol Production And Tolerance

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Ashok Rao

Full Text Available ABSTRACT The growing need to address current energy and environmental problems has sparked an interest in developing improved biological methods to produce liquid fuels from renewable sources. Higher-chain alcohols possess chemical properties that are more similar to gasoline. Ethanol and butanol are two products which are used as biofuel. Butanol production was more concerned than ethanol because of its high octane number. Unfortunately, these alcohols are not produced efficiently in natural microorganisms, and thus economical production in industrial volumes remains a challenge. The synthetic biology, however, offers additional tools to engineer synthetic pathways in user-friendly hosts to help increase titers and productivity of bio-butanol. Knock out and over-expression of genes is the major approaches towards genetic manipulation and metabolic engineering of microbes. Yet there are TargeTron Technology, Antisense RNA and CRISPR technology has a vital role in genome manipulation of C.acetobutylicum. This review concentrates on the recent developments for efficient production of butanol and butanol tolerance by various genetically engineered microbes.

Osteochondral tissue engineering: scaffolds, stem cells and applications

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Nooeaid, Patcharakamon; Salih, Vehid; Beier, Justus P; Boccaccini, Aldo R

2012-01-01

Osteochondral tissue engineering has shown an increasing development to provide suitable strategies for the regeneration of damaged cartilage and underlying subchondral bone tissue. For reasons of the limitation in the capacity of articular cartilage to self-repair, it is essential to develop approaches based on suitable scaffolds made of appropriate engineered biomaterials. The combination of biodegradable polymers and bioactive ceramics in a variety of composite structures is promising in this area, whereby the fabrication methods, associated cells and signalling factors determine the success of the strategies. The objective of this review is to present and discuss approaches being proposed in osteochondral tissue engineering, which are focused on the application of various materials forming bilayered composite scaffolds, including polymers and ceramics, discussing the variety of scaffold designs and fabrication methods being developed. Additionally, cell sources and biological protein incorporation methods are discussed, addressing their interaction with scaffolds and highlighting the potential for creating a new generation of bilayered composite scaffolds that can mimic the native interfacial tissue properties, and are able to adapt to the biological environment. PMID:22452848

Introduction to tissue engineering and application for cartilage engineering.

Science.gov (United States)

de Isla, N; Huseltein, C; Jessel, N; Pinzano, A; Decot, V; Magdalou, J; Bensoussan, D; Stoltz, J-F

2010-01-01

Tissue engineering is a multidisciplinary field that applies the principles of engineering, life sciences, cell and molecular biology toward the development of biological substitutes that restore, maintain, and improve tissue function. In Western Countries, tissues or cells management for clinical uses is a medical activity governed by different laws. Three general components are involved in tissue engineering: (1) reparative cells that can form a functional matrix; (2) an appropriate scaffold for transplantation and support; and (3) bioreactive molecules, such as cytokines and growth factors that will support and choreograph formation of the desired tissue. These three components may be used individually or in combination to regenerate organs or tissues. Thus the growing development of tissue engineering needs to solve four main problems: cells, engineering development, grafting and safety studies.

Vitamin D and Depression: A Systematic Review and Meta-Analysis Comparing Studies with and without Biological Flaws

OpenAIRE

Simon Spedding

2014-01-01

Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The literature search was un...

Inverse Problems in Systems Biology: A Critical Review.

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Guzzi, Rodolfo; Colombo, Teresa; Paci, Paola

2018-01-01

Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable. So the addition of a certain limited noise does not fundamentally change the situation but can be used to solve the so-called ill-posed problem, as defined by Hadamard. It can be seen as an extra source of information. Recent studies have shown that complex systems, among others the systems biology, are poorly constrained and ill-conditioned because it is difficult to use experimental data to fully estimate their parameters. For these reasons was born the concept of sloppy models, a sequence of models of increasing complexity that become sloppy in the limit of microscopic accuracy. Furthermore the concept of sloppy models contains also the concept of un-identifiability, because the models are characterized by many parameters that are poorly constrained by experimental data. Then a strategy needs to be designed to infer, analyze, and understand biological systems. The aim of this work is to provide a critical review to the inverse problems in systems biology defining a strategy to determine the minimal set of information needed to overcome the problems arising from dynamic biological models that generally may have many unknown, non-measurable parameters.

Suitability of a PLCL fibrous scaffold for soft tissue engineering applications: A combined biological and mechanical characterisation.

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Laurent, Cédric P; Vaquette, Cédryck; Liu, Xing; Schmitt, Jean-François; Rahouadj, Rachid

2018-04-01

Poly(lactide-co-ε-caprolactone) (PLCL) has been reported to be a good candidate for tissue engineering because of its good biocompatibility. Particularly, a braided PLCL scaffold (PLL/PCL ratio = 85/15) has been recently designed and partially validated for ligament tissue engineering. In the present study, we assessed the in vivo biocompatibility of acellular and cellularised scaffolds in a rat model. We then determined its in vitro biocompatibility using stem cells issued from both bone marrow and Wharton Jelly. From a biological point of view, the scaffold was shown to be suitable for tissue engineering in all these cases. Secondly, while the initial mechanical properties of this scaffold have been previously reported to be adapted to load-bearing applications, we studied the evolution in time of the mechanical properties of PLCL fibres due to hydrolytic degradation. Results for isolated PLCL fibres were extrapolated to the fibrous scaffold using a previously developed numerical model. It was shown that no accumulation of plastic strain was to be expected for a load-bearing application such as anterior cruciate ligament tissue engineering. However, PLCL fibres exhibited a non-expected brittle behaviour after two months. This may involve a potential risk of premature failure of the scaffold, unless tissue growth compensates this change in mechanical properties. This combined study emphasises the need to characterise the properties of biomaterials in a pluridisciplinary approach, since biological and mechanical characterisations led in this case to different conclusions concerning the suitability of this scaffold for load-bearing applications.

Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production.

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Chen, Xianzhong; Zhou, Li; Tian, Kangming; Kumar, Ashwani; Singh, Suren; Prior, Bernard A; Wang, Zhengxiang

2013-12-01

In order to decrease carbon emissions and negative environmental impacts of various pollutants, more bulk and/or fine chemicals are produced by bioprocesses, replacing the traditional energy and fossil based intensive route. The Gram-negative rod-shaped bacterium, Escherichia coli has been studied extensively on a fundamental and applied level and has become a predominant host microorganism for industrial applications. Furthermore, metabolic engineering of E. coli for the enhanced biochemical production has been significantly promoted by the integrated use of recent developments in systems biology, synthetic biology and evolutionary engineering. In this review, we focus on recent efforts devoted to the use of genetically engineered E. coli as a sustainable platform for the production of industrially important biochemicals such as biofuels, organic acids, amino acids, sugar alcohols and biopolymers. In addition, representative secondary metabolites produced by E. coli will be systematically discussed and the successful strategies for strain improvements will be highlighted. Moreover, this review presents guidelines for future developments in the bio-based chemical production using E. coli as an industrial platform. Copyright © 2013 Elsevier Inc. All rights reserved.

Biological technologies for the remediation of co-contaminated soil.

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Ye, Shujing; Zeng, Guangming; Wu, Haipeng; Zhang, Chang; Dai, Juan; Liang, Jie; Yu, Jiangfang; Ren, Xiaoya; Yi, Huan; Cheng, Min; Zhang, Chen

2017-12-01

Compound contamination in soil, caused by unreasonable waste disposal, has attracted increasing attention on a global scale, particularly since multiple heavy metals and/or organic pollutants are entering natural ecosystem through human activities, causing an enormous threat. The remediation of co-contaminated soil is more complicated and difficult than that of single contamination, due to the disparate remediation pathways utilized for different types of pollutants. Several modern remediation technologies have been developed for the treatment of co-contaminated soil. Biological remediation technologies, as the eco-friendly methods, have received widespread concern due to soil improvement besides remediation. This review summarizes the application of biological technologies, which contains microbial technologies (function microbial remediation and composting or compost addition), biochar, phytoremediation technologies, genetic engineering technologies and biochemical technologies, for the remediation of co-contaminated soil with heavy metals and organic pollutants. Mechanisms of these technologies and their remediation efficiencies are also reviewed. Based on this study, this review also identifies the future research required in this field.

Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives

Directory of Open Access Journals (Sweden)

Jian Zha

2017-12-01

Full Text Available Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.

The Need for Integrated Approaches in Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

2016-08-15

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must b e considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

Passive Techniques for Fan Noise Reduction in New Turbofan Engines: Review

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M.Gorj-Bandpy

2013-03-01

Full Text Available Among the various environmental concerns, the aircraft noise item has been constantly growing in importance over the past years. Measures for its reduction at the source as well its mitigation around airports must take into account aspects of medicine and technical design as well as legal and land use planning aspects. Fan noise is one of the principal noise sources in turbofan aero-engines. In this paper a review of the main technologies employed for the reduction of fan noise turbofan engines is presented.

Biofabrication to build the biology-device interface

International Nuclear Information System (INIS)

Liu Yi; Kim, Eunkyoung; Culver, James N; Bentley, William E; Payne, Gregory F; Ghodssi, Reza; Rubloff, Gary W

2010-01-01

The last century witnessed spectacular advances in both microelectronics and biotechnology yet there was little synergy between the two. A challenge to their integration is that biological and electronic systems are constructed using divergent fabrication paradigms. Biology fabricates bottom-up with labile components, while microelectronic devices are fabricated top-down using methods that are 'bio-incompatible'. Biofabrication-the use of biological materials and mechanisms for construction-offers the opportunity to span these fabrication paradigms by providing convergent approaches for building the bio-device interface. Integral to biofabrication are stimuli-responsive materials (e.g. film-forming polysaccharides) that allow directed assembly under near physiological conditions in response to device-imposed signals. Biomolecular engineering, through recombinant technology, allows biological components to be endowed with information for assembly (e.g. encoded in a protein's amino acid sequence). Finally, self-assembly and enzymatic assembly provide the mechanisms for construction over a hierarchy of length scales. Here, we review recent advances in the use of biofabrication to build the bio-device interface. We anticipate that the biofabrication toolbox will expand over the next decade as more researchers enlist the unique construction capabilities of biology. Further, we look forward to observing the application of this toolbox to create devices that can better diagnose disease, detect pathogens and discover drugs. Finally, we expect that biofabrication will enable the effective interfacing of biology with electronics to create implantable devices for personalized and regenerative medicine. (topical review)