The Expanding World of Tissue Engineering: The Building Blocks and New Applications of Tissue Engineered Constructs

PubMed Central

Zorlutuna, Pinar; Vrana, Nihal Engin; Khademhosseini, Ali

2013-01-01

The field of tissue engineering has been growing in the recent years as more products have made it to the market and as new uses for the engineered tissues have emerged, motivating many researchers to engage in this multidisciplinary field of research. Engineered tissues are now not only considered as end products for regenerative medicine, but also have emerged as enabling technologies for other fields of research ranging from drug discovery to biorobotics. This widespread use necessitates a variety of methodologies for production of tissue engineered constructs. In this review, these methods together with their non-clinical applications will be described. First, we will focus on novel materials used in tissue engineering scaffolds; such as recombinant proteins and synthetic, self assembling polypeptides. The recent advances in the modular tissue engineering area will be discussed. Then scaffold-free production methods, based on either cell sheets or cell aggregates will be described. Cell sources used in tissue engineering and new methods that provide improved control over cell behavior such as pathway engineering and biomimetic microenvironments for directing cell differentiation will be discussed. Finally, we will summarize the emerging uses of engineered constructs such as model tissues for drug discovery, cancer research and biorobotics applications. PMID:23268388

Chimeric TALE recombinases with programmable DNA sequence specificity.

PubMed

Mercer, Andrew C; Gaj, Thomas; Fuller, Roberta P; Barbas, Carlos F

2012-11-01

Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.

Modular Rocket Engine Control Software (MRECS)

NASA Technical Reports Server (NTRS)

Tarrant, C.; Crook, J.

1998-01-01

The Modular Rocket Engine Control Software (MRECS) Program is a technology demonstration effort designed to advance the state-of-the-art in launch vehicle propulsion systems. Its emphasis is on developing and demonstrating a modular software architecture for advanced engine control systems that will result in lower software maintenance (operations) costs. It effectively accommodates software requirement changes that occur due to hardware technology upgrades and engine development testing. Ground rules directed by MSFC were to optimize modularity and implement the software in the Ada programming language. MRECS system software and the software development environment utilize Commercial-Off-the-Shelf (COTS) products. This paper presents the objectives, benefits, and status of the program. The software architecture, design, and development environment are described. MRECS tasks are defined and timing relationships given. Major accomplishments are listed. MRECS offers benefits to a wide variety of advanced technology programs in the areas of modular software architecture, reuse software, and reduced software reverification time related to software changes. MRECS was recently modified to support a Space Shuttle Main Engine (SSME) hot-fire test. Cold Flow and Flight Readiness Testing were completed before the test was cancelled. Currently, the program is focused on supporting NASA MSFC in accomplishing development testing of the Fastrac Engine, part of NASA's Low Cost Technologies (LCT) Program. MRECS will be used for all engine development testing.

Recombinant Collagen Engineered to Bind to Discoidin Domain Receptor Functions as a Receptor Inhibitor*

PubMed Central

An, Bo; Abbonante, Vittorio; Xu, Huifang; Gavriilidou, Despoina; Yoshizumi, Ayumi; Bihan, Dominique; Farndale, Richard W.; Kaplan, David L.; Balduini, Alessandra; Leitinger, Birgit; Brodsky, Barbara

2016-01-01

A bacterial collagen-like protein Scl2 has been developed as a recombinant collagen model system to host human collagen ligand-binding sequences, with the goal of generating biomaterials with selective collagen bioactivities. Defined binding sites in human collagen for integrins, fibronectin, heparin, and MMP-1 have been introduced into the triple-helical domain of the bacterial collagen and led to the expected biological activities. The modular insertion of activities is extended here to the discoidin domain receptors (DDRs), which are collagen-activated receptor tyrosine kinases. Insertion of the DDR-binding sequence from human collagen III into bacterial collagen led to specific receptor binding. However, even at the highest testable concentrations, the construct was unable to stimulate DDR autophosphorylation. The recombinant collagen expressed in Escherichia coli does not contain hydroxyproline (Hyp), and complementary synthetic peptide studies showed that replacement of Hyp by Pro at the critical Gly-Val-Met-Gly-Phe-Hyp position decreased the DDR-binding affinity and consequently required a higher concentration for the induction of receptor activation. The ability of the recombinant bacterial collagen to bind the DDRs without inducing kinase activation suggested it could interfere with the interactions between animal collagen and the DDRs, and such an inhibitory role was confirmed in vitro and with a cell migration assay. This study illustrates that recombinant collagen can complement synthetic peptides in investigating structure-activity relationships, and this system has the potential for the introduction or inhibition of specific biological activities. PMID:26702058

Survey of Modular Military Vehicles: Benefits and Burdens

DTIC Science & Technology

2016-01-01

Survey of Modular Military Vehicles: BENEFITS and BURDENS Jean M. Dasch and David J. Gorsich Modularity in military vehicle design is generally...considered a positive attribute that promotes adaptability, resilience, and cost savings. The benefits and burdens of modularity are considered by...Engineering Center, vehicles were considered based on horizontal modularity , vertical modularity , and distributed modularity . Examples were given for each

Atomic force microscopy reveals the mechanical design of a modular protein

PubMed Central

Li, Hongbin; Oberhauser, Andres F.; Fowler, Susan B.; Clarke, Jane; Fernandez, Julio M.

2000-01-01

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering. PMID:10823913

Atomic force microscopy reveals the mechanical design of a modular protein.

PubMed

Li, H; Oberhauser, A F; Fowler, S B; Clarke, J; Fernandez, J M

2000-06-06

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.

7 CFR Exhibit B to Subpart A of... - Requirements for Modular/Panelized Housing Units

Code of Federal Regulations, 2013 CFR

2013-01-01

... Regional Letters of Acceptance (RLA), Truss Connector Bulletins (TCB): and, Mechanical Engineering... issued by HUD include: Structural Engineering Bulletins (SEB) on a national basis, Area Letters of... Category III housing (modular/panelized housing that does not have to have a Structural Engineering...

7 CFR Exhibit B to Subpart A of... - Requirements for Modular/Panelized Housing Units

Code of Federal Regulations, 2014 CFR

2014-01-01

... Regional Letters of Acceptance (RLA), Truss Connector Bulletins (TCB): and, Mechanical Engineering... issued by HUD include: Structural Engineering Bulletins (SEB) on a national basis, Area Letters of... Category III housing (modular/panelized housing that does not have to have a Structural Engineering...

7 CFR Exhibit B to Subpart A of... - Requirements for Modular/Panelized Housing Units

Code of Federal Regulations, 2012 CFR

2012-01-01

... Regional Letters of Acceptance (RLA), Truss Connector Bulletins (TCB): and, Mechanical Engineering... issued by HUD include: Structural Engineering Bulletins (SEB) on a national basis, Area Letters of... Category III housing (modular/panelized housing that does not have to have a Structural Engineering...

Modular Rocket Engine Control Software (MRECS)

NASA Technical Reports Server (NTRS)

Tarrant, Charlie; Crook, Jerry

1997-01-01

The Modular Rocket Engine Control Software (MRECS) Program is a technology demonstration effort designed to advance the state-of-the-art in launch vehicle propulsion systems. Its emphasis is on developing and demonstrating a modular software architecture for a generic, advanced engine control system that will result in lower software maintenance (operations) costs. It effectively accommodates software requirements changes that occur due to hardware. technology upgrades and engine development testing. Ground rules directed by MSFC were to optimize modularity and implement the software in the Ada programming language. MRECS system software and the software development environment utilize Commercial-Off-the-Shelf (COTS) products. This paper presents the objectives and benefits of the program. The software architecture, design, and development environment are described. MRECS tasks are defined and timing relationships given. Major accomplishment are listed. MRECS offers benefits to a wide variety of advanced technology programs in the areas of modular software, architecture, reuse software, and reduced software reverification time related to software changes. Currently, the program is focused on supporting MSFC in accomplishing a Space Shuttle Main Engine (SSME) hot-fire test at Stennis Space Center and the Low Cost Boost Technology (LCBT) Program.

Numerical simulations of human tibia osteosynthesis using modular plates based on Nitinol staples.

PubMed

Tarniţă, Daniela; Tarniţă, D N; Popa, D; Grecu, D; Tarniţă, Roxana; Niculescu, D; Cismaru, F

2010-01-01

The shape memory alloys exhibit a number of remarkable properties, which open new possibilities in engineering and more specifically in biomedical engineering. The most important alloy used in biomedical applications is NiTi. This alloy combines the characteristics of the shape memory effect and superelasticity with excellent corrosion resistance, wear characteristics, mechanical properties and a good biocompatibility. These properties make it an ideal biological engineering material, especially in orthopedic surgery and orthodontics. In this work, modular plates for the osteosynthesis of the long bones fractures are presented. The proposed modular plates are realized from identical modules, completely interchangeable, made of titanium or stainless steel having as connecting elements U-shaped staples made of Nitinol. Using computed tomography (CT) images to provide three-dimensional geometric details and SolidWorks software package, the three dimensional virtual models of the tibia bone and of the modular plates are obtained. The finite element models of the tibia bone and of the modular plate are generated. For numerical simulation, VisualNastran software is used. Finally, displacements diagram, von Misses strain diagram, for the modular plate and for the fractured tibia and modular plate ensemble are obtained.

A pancreas specificity results from the combination of polyomavirus and Moloney murine leukemia virus enhancer.

PubMed Central

Rochford, R; Campbell, B A; Villarreal, L P

1987-01-01

An infectious recombinant polyomavirus was constructed in which a regulatory region of its genome, the B enhancer region (nucleotides 5128-5265) has been replaced with the 72- or 73-base-pair repeat enhancer from the Moloney murine leukemia virus genome. We show that this recombinant polyomavirus displays a strong tissue specificity for the pancreas of mice. This organ was not permissive for either the parental polyomavirus, which is predominantly kidney and salivary gland specific, or the Moloney murine leukemia virus, which is lymphotropic. This result indicated that tissue specificity can be achieved by a combination of apparently modular elements. Some of the implications of a modular mechanism of tissue specificity are considered. Images PMID:3025873

Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5' Untranslated Region.

PubMed

Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

2015-01-01

Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species' C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5' untranslated region (5' UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5' UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5' UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5' UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5' UTR. By contrast to the recombination of the cVDPV with the 5' UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5' UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages.

A Modular Artificial Intelligence Inference Engine System (MAIS) for support of on orbit experiments

NASA Technical Reports Server (NTRS)

Hancock, Thomas M., III

1994-01-01

This paper describes a Modular Artificial Intelligence Inference Engine System (MAIS) support tool that would provide health and status monitoring, cognitive replanning, analysis and support of on-orbit Space Station, Spacelab experiments and systems.

Exploration of the Genetic Organization of Morphological Modularity on the Mouse Mandible Using a Set of Interspecific Recombinant Congenic Strains Between C57BL/6 and Mice of the Mus spretus Species

PubMed Central

Burgio, Gaëtan; Baylac, Michel; Heyer, Evelyne; Montagutelli, Xavier

2012-01-01

Morphological integration and modularity within semi-autonomous modules are essential mechanisms for the evolution of morphological traits. However, the genetic makeup responsible for the control of variational modularity is still relatively unknown. In our study, we tested the hypothesis that the genetic variation for mandible shape clustered into two morphogenetic components: the alveolar group and the ascending ramus. We used the mouse as a model system to investigate genetics determinants of mandible shape. To do this, we used a combination of geometric morphometric tools and a set of 18 interspecific recombinant congenic strains (IRCS) derived from the distantly related species, Mus spretus SEG/Pas and Mus musculus C57BL/6. Quantitative trait loci (QTL) analysis comparing mandible morphometry between the C57BL/6 and the IRCSs identified 42 putative SEG/Pas segments responsible for the genetic variation. The magnitude of the QTL effects was dependent on the proportion of SEG/Pas genome inherited. Using a multivariate correlation coefficient adapted for modularity assessment and a two-block partial least squares analysis to explore the morphological integration, we found that these QTL clustered into two well-integrated morphogenetic groups, corresponding to the ascending ramus and the alveolar region. Together, these results provide evidence that the mouse mandible is subjected to genetic coordination in a modular manner. PMID:23050236

Development of a modularized two-step (M2S) chromosome integration technique for integration of multiple transcription units in Saccharomyces cerevisiae.

PubMed

Li, Siwei; Ding, Wentao; Zhang, Xueli; Jiang, Huifeng; Bi, Changhao

2016-01-01

Saccharomyces cerevisiae has already been used for heterologous production of fuel chemicals and valuable natural products. The establishment of complicated heterologous biosynthetic pathways in S. cerevisiae became the research focus of Synthetic Biology and Metabolic Engineering. Thus, simple and efficient genomic integration techniques of large number of transcription units are demanded urgently. An efficient DNA assembly and chromosomal integration method was created by combining homologous recombination (HR) in S. cerevisiae and Golden Gate DNA assembly method, designated as modularized two-step (M2S) technique. Two major assembly steps are performed consecutively to integrate multiple transcription units simultaneously. In Step 1, Modularized scaffold containing a head-to-head promoter module and a pair of terminators was assembled with two genes. Thus, two transcription units were assembled with Golden Gate method into one scaffold in one reaction. In Step 2, the two transcription units were mixed with modules of selective markers and integration sites and transformed into S. cerevisiae for assembly and integration. In both steps, universal primers were designed for identification of correct clones. Establishment of a functional β-carotene biosynthetic pathway in S. cerevisiae within 5 days demonstrated high efficiency of this method, and a 10-transcriptional-unit pathway integration illustrated the capacity of this method. Modular design of transcription units and integration elements simplified assembly and integration procedure, and eliminated frequent designing and synthesis of DNA fragments in previous methods. Also, by assembling most parts in Step 1 in vitro, the number of DNA cassettes for homologous integration in Step 2 was significantly reduced. Thus, high assembly efficiency, high integration capacity, and low error rate were achieved.

Very high gravity ethanol and fatty acid production of Zymomonas mobilis without amino acid and vitamin.

PubMed

Wang, Haoyong; Cao, Shangzhi; Wang, William Tianshuo; Wang, Kaven Tianyv; Jia, Xianhui

2016-06-01

Very high gravity (VHG) fermentation is the mainstream technology in ethanol industry, which requires the strains be resistant to multiple stresses such as high glucose concentration, high ethanol concentration, high temperature and harsh acidic conditions. To our knowledge, it was not reported previously that any ethanol-producing microbe showed a high performance in VHG fermentations without amino acid and vitamin. Here we demonstrate the engineering of a xylose utilizing recombinant Zymomonas mobilis for VHG ethanol fermentations. The recombinant strain can produce ethanol up to 136 g/L without amino acid and vitamin with a theoretical yield of 90 %, which is significantly superior to that produced by all the reported ethanol-producing strains. The intracellular fatty acids of the bacterial were about 16 % of the bacterial dry biomass, with the ratio of ethanol:fatty acids was about 273:1 (g/g). The recombinant strain was achieved by a multivariate-modular strategy tackles with the multiple stresses which are closely linked to the ethanol productivity of Z. mobilis. The over-expression of metB/yfdZ operon enabled the growth of the recombinant Z. mobilis in a chemically defined medium without amino acid and vitamin; and the fatty acids overproduction significantly increased ethanol tolerance and ethanol production. The coupled production of ethanol with fatty acids of the Z. mobilis without amino acid and vitamin under VHG fermentation conditions may permit a significant reduction of the production cost of ethanol and microbial fatty acids.

Microscale Technologies and Modular Approaches for Tissue Engineering: Moving toward the Fabrication of Complex Functional Structures

PubMed Central

Gauvin, Robert; Khademhosseini, Ali

2011-01-01

Micro- and nanoscale technologies have emerged as powerful tools in the fabrication of engineered tissues and organs. Here we focus on the application of these techniques to improve engineered tissue architecture and function using modular and directed self-assembly and highlight the emergence of this new class of materials for biomedical applications. PMID:21627163

Single-Domain Antibodies and the Promise of Modular Targeting in Cancer Imaging and Treatment.

PubMed

Iezzi, María Elena; Policastro, Lucía; Werbajh, Santiago; Podhajcer, Osvaldo; Canziani, Gabriela Alicia

2018-01-01

Monoclonal antibodies and their fragments have significantly changed the outcome of cancer in the clinic, effectively inhibiting tumor cell proliferation, triggering antibody-dependent immune effector cell activation and complement mediated cell death. Along with a continued expansion in number, diversity, and complexity of validated tumor targets there is an increasing focus on engineering recombinant antibody fragments for lead development. Single-domain antibodies (sdAbs), in particular those engineered from the variable heavy-chain fragment (VHH gene) found in Camelidae heavy-chain antibodies (or IgG2 and IgG3), are the smallest fragments that retain the full antigen-binding capacity of the antibody with advantageous properties as drugs. For similar reasons, growing attention is being paid to the yet smaller variable heavy chain new antigen receptor (VNAR) fragments found in Squalidae. sdAbs have been selected, mostly from immune VHH libraries, to inhibit or modulate enzyme activity, bind soluble factors, internalize cell membrane receptors, or block cytoplasmic targets. This succinct review is a compilation of recent data documenting the application of engineered, recombinant sdAb in the clinic as epitope recognition "modules" to build monomeric, dimeric and multimeric ligands that target, tag and stall solid tumor growth in vivo . Size, affinity, specificity, and the development profile of sdAbs drugs are seemingly consistent with desirable clinical efficacy and safety requirements. But the hepatotoxicity of the tetrameric anti-DR5-VHH drug in patients with pre-existing anti-drug antibodies halted the phase I clinical trial and called for a thorough pre-screening of the immune and poly-specific reactivities of the sdAb leads.

Adapter-directed display: a modular design for shuttling display on phage surfaces.

PubMed

Wang, Kevin Caili; Wang, Xinwei; Zhong, Pingyu; Luo, Peter Peizhi

2010-02-05

A novel adapter-directed phage display system was developed with modular features. In this system, the target protein is expressed as a fusion protein consisting of adapter GR1 from the phagemid vector, while the recombinant phage coat protein is expressed as a fusion protein consisting of adapter GR2 in the helper phage vector. Surface display of the target protein is accomplished through specific heterodimerization of GR1 and GR2 adapters, followed by incorporation of the heterodimers into phage particles. A series of engineered helper phages were constructed to facilitate both display valency and formats, based on various phage coat proteins. As the target protein is independent of a specific phage coat protein, this modular system allows the target protein to be displayed on any given phage coat protein and allows various display formats from the same vector without the need for reengineering. Here, we demonstrate the shuttling display of a single-chain Fv antibody on phage surfaces between multivalent and monovalent formats, as well as the shuttling display of an antigen-binding fragment molecule on phage coat proteins pIII, pVII, and pVIII using the same phagemid vectors combined with different helper phage vectors. This adapter-directed display concept has been applied to eukaryotic yeast surface display and to a novel cross-species display that can shuttle between prokaryotic phage and eukaryotic yeast systems. Copyright 2009 Elsevier Ltd. All rights reserved.

The Current Status of Modular Coordination. A Research Correlation Conference of Building Research Institute, Division of Engineering and Industrial Research (Fall 1959).

ERIC Educational Resources Information Center

National Academy of Sciences - National Research Council, Washington, DC.

Publication of conference presentations include--(1) a brief review of current modular standard development, (2) the statistical status of modular practice, (3) availability of modular products, and (4) educational programs on modular coordination. Included are--(1) explanatory diagrams, (2) text of an open panel discussion, and (3) a list of…

Modular Knowledge Representation and Reasoning in the Semantic Web

NASA Astrophysics Data System (ADS)

Serafini, Luciano; Homola, Martin

Construction of modular ontologies by combining different modules is becoming a necessity in ontology engineering in order to cope with the increasing complexity of the ontologies and the domains they represent. The modular ontology approach takes inspiration from software engineering, where modularization is a widely acknowledged feature. Distributed reasoning is the other side of the coin of modular ontologies: given an ontology comprising of a set of modules, it is desired to perform reasoning by combination of multiple reasoning processes performed locally on each of the modules. In the last ten years, a number of approaches for combining logics has been developed in order to formalize modular ontologies. In this chapter, we survey and compare the main formalisms for modular ontologies and distributed reasoning in the Semantic Web. We select four formalisms build on formal logical grounds of Description Logics: Distributed Description Logics, ℰ-connections, Package-based Description Logics and Integrated Distributed Description Logics. We concentrate on expressivity and distinctive modeling features of each framework. We also discuss reasoning capabilities of each framework.

Modularity Induced Gating and Delays in Neuronal Networks

PubMed Central

Shein-Idelson, Mark; Cohen, Gilad; Hanein, Yael

2016-01-01

Neural networks, despite their highly interconnected nature, exhibit distinctly localized and gated activation. Modularity, a distinctive feature of neural networks, has been recently proposed as an important parameter determining the manner by which networks support activity propagation. Here we use an engineered biological model, consisting of engineered rat cortical neurons, to study the role of modular topology in gating the activity between cell populations. We show that pairs of connected modules support conditional propagation (transmitting stronger bursts with higher probability), long delays and propagation asymmetry. Moreover, large modular networks manifest diverse patterns of both local and global activation. Blocking inhibition decreased activity diversity and replaced it with highly consistent transmission patterns. By independently controlling modularity and disinhibition, experimentally and in a model, we pose that modular topology is an important parameter affecting activation localization and is instrumental for population-level gating by disinhibition. PMID:27104350

Synthetic Zinc Finger Proteins: The Advent of Targeted Gene Regulation and Genome Modification Technologies

PubMed Central

2015-01-01

Conspectus The understanding of gene regulation and the structure and function of the human genome increased dramatically at the end of the 20th century. Yet the technologies for manipulating the genome have been slower to develop. For instance, the field of gene therapy has been focused on correcting genetic diseases and augmenting tissue repair for more than 40 years. However, with the exception of a few very low efficiency approaches, conventional genetic engineering methods have only been able to add auxiliary genes to cells. This has been a substantial obstacle to the clinical success of gene therapies and has also led to severe unintended consequences in several cases. Therefore, technologies that facilitate the precise modification of cellular genomes have diverse and significant implications in many facets of research and are essential for translating the products of the Genomic Revolution into tangible benefits for medicine and biotechnology. To address this need, in the 1990s, we embarked on a mission to develop technologies for engineering protein–DNA interactions with the aim of creating custom tools capable of targeting any DNA sequence. Our goal has been to allow researchers to reach into genomes to specifically regulate, knock out, or replace any gene. To realize these goals, we initially focused on understanding and manipulating zinc finger proteins. In particular, we sought to create a simple and straightforward method that enables unspecialized laboratories to engineer custom DNA-modifying proteins using only defined modular components, a web-based utility, and standard recombinant DNA technology. Two significant challenges we faced were (i) the development of zinc finger domains that target sequences not recognized by naturally occurring zinc finger proteins and (ii) determining how individual zinc finger domains could be tethered together as polydactyl proteins to recognize unique locations within complex genomes. We and others have since used this modular assembly method to engineer artificial proteins and enzymes that activate, repress, or create defined changes to user-specified genes in human cells, plants, and other organisms. We have also engineered novel methods for externally controlling protein activity and delivery, as well as developed new strategies for the directed evolution of protein and enzyme function. This Account summarizes our work in these areas and highlights independent studies that have successfully used the modular assembly approach to create proteins with novel function. We also discuss emerging alternative methods for genomic targeting, including transcription activator-like effectors (TALEs) and CRISPR/Cas systems, and how they complement the synthetic zinc finger protein technology. PMID:24877793

A modular approach to creating large engineered cartilage surfaces.

PubMed

Ford, Audrey C; Chui, Wan Fung; Zeng, Anne Y; Nandy, Aditya; Liebenberg, Ellen; Carraro, Carlo; Kazakia, Galateia; Alliston, Tamara; O'Connell, Grace D

2018-01-23

Native articular cartilage has limited capacity to repair itself from focal defects or osteoarthritis. Tissue engineering has provided a promising biological treatment strategy that is currently being evaluated in clinical trials. However, current approaches in translating these techniques to developing large engineered tissues remains a significant challenge. In this study, we present a method for developing large-scale engineered cartilage surfaces through modular fabrication. Modular Engineered Tissue Surfaces (METS) uses the well-known, but largely under-utilized self-adhesion properties of de novo tissue to create large scaffolds with nutrient channels. Compressive mechanical properties were evaluated throughout METS specimens, and the tensile mechanical strength of the bonds between attached constructs was evaluated over time. Raman spectroscopy, biochemical assays, and histology were performed to investigate matrix distribution. Results showed that by Day 14, stable connections had formed between the constructs in the METS samples. By Day 21, bonds were robust enough to form a rigid sheet and continued to increase in size and strength over time. Compressive mechanical properties and glycosaminoglycan (GAG) content of METS and individual constructs increased significantly over time. The METS technique builds on established tissue engineering accomplishments of developing constructs with GAG composition and compressive properties approaching native cartilage. This study demonstrated that modular fabrication is a viable technique for creating large-scale engineered cartilage, which can be broadly applied to many tissue engineering applications and construct geometries. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5’ Untranslated Region

PubMed Central

Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

2015-01-01

Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species’ C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5’ untranslated region (5’ UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5’ UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5’ UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5’ UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5’ UTR. By contrast to the recombination of the cVDPV with the 5’ UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5’ UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages. PMID:26562151

Biomechanical, Physiological, and Agility Performance of Soldiers Carrying Loads: A Comparison of the Modular Lightweight Load Carrying Equipment and a Lightning Packs, LLC, Prototype

DTIC Science & Technology

2016-12-27

2015 Approved for public release; distribution is unlimited U.S. Army Natick Soldier Research, Development and Engineering Center...is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and...MODULAR LIGHTWEIGHT LOAD CARRYING EQUIPMENT) HUMAN FACTORS ENGINEERING U.S. Army Natick Soldier Research, Development and Engineering Center ATTN

Modular Software for Spacecraft Navigation Using the Global Positioning System (GPS)

NASA Technical Reports Server (NTRS)

Truong, S. H.; Hartman, K. R.; Weidow, D. A.; Berry, D. L.; Oza, D. H.; Long, A. C.; Joyce, E.; Steger, W. L.

1996-01-01

The Goddard Space Flight Center Flight Dynamics and Mission Operations Divisions have jointly investigated the feasibility of engineering modular Global Positioning SYSTEM (GPS) navigation software to support both real time flight and ground postprocessing configurations. The goals of this effort are to define standard GPS data interfaces and to engineer standard, reusable navigation software components that can be used to build a broad range of GPS navigation support applications. The paper discusses the GPS modular software (GMOD) system and operations concepts, major requirements, candidate software architecture, feasibility assessment and recommended software interface standards. In additon, ongoing efforts to broaden the scope of the initial study and to develop modular software to support autonomous navigation using GPS are addressed,

Single-Domain Antibodies and the Promise of Modular Targeting in Cancer Imaging and Treatment

PubMed Central

Iezzi, María Elena; Policastro, Lucía; Werbajh, Santiago; Podhajcer, Osvaldo; Canziani, Gabriela Alicia

2018-01-01

Monoclonal antibodies and their fragments have significantly changed the outcome of cancer in the clinic, effectively inhibiting tumor cell proliferation, triggering antibody-dependent immune effector cell activation and complement mediated cell death. Along with a continued expansion in number, diversity, and complexity of validated tumor targets there is an increasing focus on engineering recombinant antibody fragments for lead development. Single-domain antibodies (sdAbs), in particular those engineered from the variable heavy-chain fragment (VHH gene) found in Camelidae heavy-chain antibodies (or IgG2 and IgG3), are the smallest fragments that retain the full antigen-binding capacity of the antibody with advantageous properties as drugs. For similar reasons, growing attention is being paid to the yet smaller variable heavy chain new antigen receptor (VNAR) fragments found in Squalidae. sdAbs have been selected, mostly from immune VHH libraries, to inhibit or modulate enzyme activity, bind soluble factors, internalize cell membrane receptors, or block cytoplasmic targets. This succinct review is a compilation of recent data documenting the application of engineered, recombinant sdAb in the clinic as epitope recognition “modules” to build monomeric, dimeric and multimeric ligands that target, tag and stall solid tumor growth in vivo. Size, affinity, specificity, and the development profile of sdAbs drugs are seemingly consistent with desirable clinical efficacy and safety requirements. But the hepatotoxicity of the tetrameric anti-DR5-VHH drug in patients with pre-existing anti-drug antibodies halted the phase I clinical trial and called for a thorough pre-screening of the immune and poly-specific reactivities of the sdAb leads. PMID:29520274

Photo-cross-linkable methacrylated gelatin and hydroxyapatite hybrid hydrogel for modularly engineering biomimetic osteon.

PubMed

Zuo, Yicong; Liu, Xiaolu; Wei, Dan; Sun, Jing; Xiao, Wenqian; Zhao, Huan; Guo, Likun; Wei, Qingrong; Fan, Hongsong; Zhang, Xingdong

2015-05-20

Modular tissue engineering holds great potential in regenerating natural complex tissues by engineering three-dimensional modular scaffolds with predefined geometry and biological characters. In modular tissue-like construction, a scaffold with an appropriate mechanical rigidity for assembling fabrication and high biocompatibility for cell survival is the key to the successful bioconstruction. In this work, a series of composite hydrogels (GH0, GH1, GH2, and GH3) based on a combination of methacrylated gelatin (GelMA) and hydroxyapatite (HA) was exploited to enhance hydrogel mechanical rigidity and promote cell functional expression for osteon biofabrication. These composite hydrogels presented a lower swelling ratio, higher mechanical moduli, and better biocompatibility when compared to the pure GelMA hydrogel. Furthermore, on the basis of the composite hydrogel and photolithograph technology, we successfully constructed an osteon-like concentric double-ring structure in which the inner ring encapsulating human umbilical vascular endothelial cells (HUVECs) was designed to imitate blood vessel tubule while the outer ring encapsulating human osteoblast-like cells (MG63s) acts as part of bone. During the coculture period, MG63s and HUVECs exhibited not only satisfying growth status but also the enhanced genic expression of osteogenesis-related and angiogenesis-related differentiations. These results demonstrate this GelMA-HA composite hydrogel system is promising for modular tissue engineering.

Reviews of STS Instructional Units.

ERIC Educational Resources Information Center

S-STS Reporter, 1987

1987-01-01

Provides reviews of modular materials that contain a Science, Technology, Society (STS) theme. Specifies the criteria and distinguishing features of STS materials. Includes reviews of programs which address the topics of energy, genetics, human reproduction, and recombinant DNA research. (ML)

Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs.

PubMed

Zucchelli, Silvia; Patrucco, Laura; Persichetti, Francesca; Gustincich, Stefano; Cotella, Diego

2016-01-01

Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.

Modular Engine Instrumentation System

NASA Technical Reports Server (NTRS)

Rice, W. J.; Birchenough, A. G.

1982-01-01

System that provides information and measurements never obtained before in real time has been developed. System shows not only real-time measurements but also results of computations of key combustion parameters in meaningful and easily understood display. Standard commercially-available shaft encoder plus data from pressure transducer act as principal drivers to device. Eventually, modular system could be developed into onboard controller for automobile engines.

A Modular Aero-Propulsion System Simulation of a Large Commercial Aircraft Engine

NASA Technical Reports Server (NTRS)

DeCastro, Jonathan A.; Litt, Jonathan S.; Frederick, Dean K.

2008-01-01

A simulation of a commercial engine has been developed in a graphical environment to meet the increasing need across the controls and health management community for a common research and development platform. This paper describes the Commercial Modular Aero Propulsion System Simulation (C-MAPSS), which is representative of a 90,000-lb thrust class two spool, high bypass ratio commercial turbofan engine. A control law resembling the state-of-the-art on board modern aircraft engines is included, consisting of a fan-speed control loop supplemented by relevant engine limit protection regulator loops. The objective of this paper is to provide a top-down overview of the complete engine simulation package.

A Modular Lentiviral and Retroviral Construction System to Rapidly Generate Vectors for Gene Expression and Gene Knockdown In Vitro and In Vivo

PubMed Central

Geiling, Benjamin; Vandal, Guillaume; Posner, Ada R.; de Bruyns, Angeline; Dutchak, Kendall L.; Garnett, Samantha; Dankort, David

2013-01-01

The ability to express exogenous cDNAs while suppressing endogenous genes via RNAi represents an extremely powerful research tool with the most efficient non-transient approach being accomplished through stable viral vector integration. Unfortunately, since traditional restriction enzyme based methods for constructing such vectors are sequence dependent, their construction is often difficult and not amenable to mass production. Here we describe a non-sequence dependent Gateway recombination cloning system for the rapid production of novel lentiviral (pLEG) and retroviral (pREG) vectors. Using this system to recombine 3 or 4 modular plasmid components it is possible to generate viral vectors expressing cDNAs with or without inhibitory RNAs (shRNAmirs). In addition, we demonstrate a method to rapidly produce and triage novel shRNAmirs for use with this system. Once strong candidate shRNAmirs have been identified they may be linked together in tandem to knockdown expression of multiple targets simultaneously or to improve the knockdown of a single target. Here we demonstrate that these recombinant vectors are able to express cDNA and effectively knockdown protein expression using both cell culture and animal model systems. PMID:24146852

Modular Heat Exchanger With Integral Heat Pipe

NASA Technical Reports Server (NTRS)

Schreiber, Jeffrey G.

1992-01-01

Modular heat exchanger with integral heat pipe transports heat from source to Stirling engine. Alternative to heat exchangers depending on integrities of thousands of brazed joints, contains only 40 brazed tubes.

A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals

PubMed Central

Wang, Baojun; Barahona, Mauricio; Buck, Martin

2013-01-01

Cells perceive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate particular phenotypic responses. Here, we employ both single and mixed cell type populations, pre-programmed with engineered modular cell signalling and sensing circuits, as processing units to detect and integrate multiple environmental signals. Based on an engineered modular genetic AND logic gate, we report the construction of a set of scalable synthetic microbe-based biosensors comprising exchangeable sensory, signal processing and actuation modules. These cellular biosensors were engineered using distinct signalling sensory modules to precisely identify various chemical signals, and combinations thereof, with a quantitative fluorescent output. The genetic logic gate used can function as a biological filter and an amplifier to enhance the sensing selectivity and sensitivity of cell-based biosensors. In particular, an Escherichia coli consortium-based biosensor has been constructed that can detect and integrate three environmental signals (arsenic, mercury and copper ion levels) via either its native two-component signal transduction pathways or synthetic signalling sensors derived from other bacteria in combination with a cell-cell communication module. We demonstrate how a modular cell-based biosensor can be engineered predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-input signals. This study illustrates some of the key practical design principles required for the future application of these biosensors in broad environmental and healthcare areas. PMID:22981411

Directional selection can drive the evolution of modularity in complex traits

PubMed Central

Melo, Diogo; Marroig, Gabriel

2015-01-01

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection. PMID:25548154

Directional selection can drive the evolution of modularity in complex traits.

PubMed

Melo, Diogo; Marroig, Gabriel

2015-01-13

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

Mutants of Cre recombinase with improved accuracy

PubMed Central

Eroshenko, Nikolai; Church, George M.

2013-01-01

Despite rapid advances in genome engineering technologies, inserting genes into precise locations in the human genome remains an outstanding problem. It has been suggested that site-specific recombinases can be adapted towards use as transgene delivery vectors. The specificity of recombinases can be altered either with directed evolution or via fusions to modular DNA-binding domains. Unfortunately, both wildtype and altered variants often have detectable activities at off-target sites. Here we use bacterial selections to identify mutations in the dimerization surface of Cre recombinase (R32V, R32M, and 303GVSdup) that improve the accuracy of recombination. The mutants are functional in bacteria, in human cells, and in vitro (except for 303GVSdup, which we did not purify), and have improved selectivity against both model off-target sites and the entire E. coli genome. We propose that destabilizing binding cooperativity may be a general strategy for improving the accuracy of dimeric DNA-binding proteins. PMID:24056590

The Modular Aero-Propulsion System Simulation (MAPSS) Users' Guide

NASA Technical Reports Server (NTRS)

Parker, Khary I.; Melcher, Kevin J.

2004-01-01

The Modular Aero-Propulsion System Simulation is a flexible turbofan engine simulation environment that provides the user a platform to develop advanced control algorithms. It is capable of testing the performance of control designs on a validated and verified generic engine model. In addition, it is able to generate state-space linear models of the engine model to aid in controller design. The engine model used in MAPSS is a generic high-pressure ratio, dual-spool, lowbypass, military-type, variable cycle turbofan engine with a digital controller. MAPSS is controlled by a graphical user interface (GUI) and this guide explains how to use it to take advantage of the capabilities of MAPSS.

Engineering modular polyketide synthases for production of biofuels and industrial chemicals.

PubMed

Cai, Wenlong; Zhang, Wenjun

2018-04-01

Polyketide synthases (PKSs) are one of the most profound biosynthetic factories for producing polyketides with diverse structures and biological activities. These enzymes have been historically studied and engineered to make un-natural polyketides for drug discovery, and have also recently been explored for synthesizing biofuels and industrial chemicals due to their versatility and customizability. Here, we review recent advances in the mechanistic understanding and engineering of modular PKSs for producing polyketide-derived chemicals, and provide perspectives on this relatively new application of PKSs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering modular ester fermentative pathways in Escherichia coli.

PubMed

Layton, Donovan S; Trinh, Cong T

2014-11-01

Sensation profiles are observed all around us and are made up of many different molecules, such as esters. These profiles can be mimicked in everyday items for their uses in foods, beverages, cosmetics, perfumes, solvents, and biofuels. Here, we developed a systematic 'natural' way to derive these products via fermentative biosynthesis. Each ester fermentative pathway was designed as an exchangeable ester production module for generating two precursors- alcohols and acyl-CoAs that were condensed by an alcohol acyltransferase to produce a combinatorial library of unique esters. As a proof-of-principle, we coupled these ester modules with an engineered, modular, Escherichia coli chassis in a plug-and-play fashion to create microbial cell factories for enhanced anaerobic production of a butyrate ester library. We demonstrated tight coupling between the modular chassis and ester modules for enhanced product biosynthesis, an engineered phenotype useful for directed metabolic pathway evolution. Compared to the wildtype, the engineered cell factories yielded up to 48 fold increase in butyrate ester production from glucose. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

A Modular Aerospike Engine Design Using Additive Manufacturing

NASA Technical Reports Server (NTRS)

Peugeot, John; Garcia, Chance; Burkhardt, Wendel

2014-01-01

A modular aerospike engine concept has been developed with the objective of demonstrating the viability of the aerospike design using additive manufacturing techniques. The aerospike system is a self-compensating design that allows for optimal performance over the entire flight regime and allows for the lowest possible mass vehicle designs. At low altitudes, improvements in Isp can be traded against chamber pressure, staging, and payload. In upper stage applications, expansion ratio and engine envelope can be traded against nozzle efficiency. These features provide flexibility to the System Designer optimizing a complete vehicle stage. The aerospike concept is a good example of a component that has demonstrated improved performance capability, but traditionally has manufacturing requirements that are too expensive and complex to use in a production vehicle. In recent years, additive manufacturing has emerged as a potential method for improving the speed and cost of building geometrically complex components in rocket engines. It offers a reduction in tooling overhead and significant improvements in the integration of the designer and manufacturing method. In addition, the modularity of the engine design provides the ability to perform full scale testing on the combustion devices outside of the full engine configuration. The proposed design uses a hydrocarbon based gas-generator cycle, with plans to take advantage of existing powerhead hardware while focusing DDT&E resources on manufacturing and sub-system testing of the combustion devices. The major risks for the modular aerospike concept lie in the performance of the propellant feed system, the structural integrity of the additive manufactured components, and the aerodynamic efficiency of the exhaust flow.

Modular digital holographic fringe data processing system

NASA Technical Reports Server (NTRS)

Downward, J. G.; Vavra, P. C.; Schebor, F. S.; Vest, C. M.

1985-01-01

A software architecture suitable for reducing holographic fringe data into useful engineering data is developed and tested. The results, along with a detailed description of the proposed architecture for a Modular Digital Fringe Analysis System, are presented.

Selective CXCR4+ Cancer Cell Targeting and Potent Antineoplastic Effect by a Nanostructured Version of Recombinant Ricin.

PubMed

Díaz, Raquel; Pallarès, Victor; Cano-Garrido, Olivia; Serna, Naroa; Sánchez-García, Laura; Falgàs, Aïda; Pesarrodona, Mireia; Unzueta, Ugutz; Sánchez-Chardi, Alejandro; Sánchez, Julieta M; Casanova, Isolda; Vázquez, Esther; Mangues, Ramón; Villaverde, Antonio

2018-05-29

Under the unmet need of efficient tumor-targeting drugs for oncology, a recombinant version of the plant toxin ricin (the modular protein T22-mRTA-H6) is engineered to self-assemble as protein-only, CXCR4-targeted nanoparticles. The soluble version of the construct self-organizes as regular 11 nm planar entities that are highly cytotoxic in cultured CXCR4 + cancer cells upon short time exposure, with a determined IC50 in the nanomolar order of magnitude. The chemical inhibition of CXCR4 binding sites in exposed cells results in a dramatic reduction of the cytotoxic potency, proving the receptor-dependent mechanism of cytotoxicity. The insoluble version of T22-mRTA-H6 is, contrarily, moderately active, indicating that free, nanostructured protein is the optimal drug form. In animal models of acute myeloid leukemia, T22-mRTA-H6 nanoparticles show an impressive and highly selective therapeutic effect, dramatically reducing the leukemia cells affectation of clinically relevant organs. Functionalized T22-mRTA-H6 nanoparticles are then promising prototypes of chemically homogeneous, highly potent antitumor nanostructured toxins for precise oncotherapies based on self-mediated intracellular drug delivery. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineered Modular Recombinant Transporters: Application of New Platform for Targeted Radiotherapeutic Agents to {alpha}-Particle Emitting {sup 211}At

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenkranz, Andrey A.; Department of Biophysics, Biological Faculty, Moscow State University, Moscow; Vaidyanathan, Ganesan

2008-09-01

Purpose: To generate and evaluate a modular recombinant transporter (MRT) for targeting {sup 211}At to cancer cells overexpressing the epidermal growth factor receptor (EGFR). Methods and Materials: The MRT was produced with four functional modules: (1) human epidermal growth factor as the internalizable ligand, (2) the optimized nuclear localization sequence of simian vacuolating virus 40 (SV40) large T-antigen, (3) a translocation domain of diphtheria toxin as an endosomolytic module, and (4) the Escherichia coli hemoglobin-like protein (HMP) as a carrier module. MRT was labeled using N-succinimidyl 3-[{sup 211}At]astato-5-guanidinomethylbenzoate (SAGMB), its {sup 125}I analogue SGMIB, or with {sup 131}I using Iodogen.more » Binding, internalization, and clonogenic assays were performed with EGFR-expressing A431, D247 MG, and U87MG.wtEGFR human cancer cell lines. Results: The affinity of SGMIB-MRT binding to A431 cells, determined by Scatchard analysis, was 22 nM, comparable to that measured before labeling. The binding of SGMIB-MRT and its internalization by A431 cancer cells was 96% and 99% EGFR specific, respectively. Paired label assays demonstrated that compared with Iodogen-labeled MRT, SGMIB-MRT and SAGMB-MRT exhibited more than threefold greater peak levels and durations of intracellular retention of activity. SAGMB-MRT was 10-20 times more cytotoxic than [{sup 211}At]astatide for all three cell lines. Conclusion: The results of this study have demonstrated the initial proof of principle for the MRT approach for designing targeted {alpha}-particle emitting radiotherapeutic agents. The high cytotoxicity of SAGMB-MRT for cancer cells overexpressing EGFR suggests that this {sup 211}At-labeled conjugate has promise for the treatment of malignancies, such as glioma, which overexpress this receptor.« less

Fluid design studies of integrated modular engine system

NASA Technical Reports Server (NTRS)

Frankenfield, Bruce; Carek, Jerry

1993-01-01

A study was performed to develop a fluid system design and show the feasibility of constructing an integrated modular engine (IME) configuration, using an expander cycle engine. The primary design goal of the IME configuration was to improve the propulsion system reliability. The IME fluid system was designed as a single fault tolerant system, while minimizing the required fluid components. This study addresses the design of the high pressure manifolds, turbopumps and thrust chambers for the IME configuration. A physical layout drawing was made, which located each of the fluid system components, manifolds and thrust chambers. Finally, a comparison was made between the fluid system designs of an IME system and a non-network (clustered) engine system.

Differential pleiotropy and HOX functional organization.

PubMed

Sivanantharajah, Lovesha; Percival-Smith, Anthony

2015-02-01

Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment. Copyright © 2014 Elsevier Inc. All rights reserved.

Advanced rocket propulsion

NASA Technical Reports Server (NTRS)

Obrien, Charles J.

1993-01-01

Existing NASA research contracts are supporting development of advanced reinforced polymer and metal matrix composites for use in liquid rocket engines of the future. Advanced rocket propulsion concepts, such as modular platelet engines, dual-fuel dual-expander engines, and variable mixture ratio engines, require advanced materials and structures to reduce overall vehicle weight as well as address specific propulsion system problems related to elevated operating temperatures, new engine components, and unique operating processes. High performance propulsion systems with improved manufacturability and maintainability are needed for single stage to orbit vehicles and other high performance mission applications. One way to satisfy these needs is to develop a small engine which can be clustered in modules to provide required levels of total thrust. This approach should reduce development schedule and cost requirements by lowering hardware lead times and permitting the use of existing test facilities. Modular engines should also reduce operational costs associated with maintenance and parts inventories.

The Keller Plan: A Successful Experiment in Engineering Education.

ERIC Educational Resources Information Center

Koen, Billy; And Others

1985-01-01

Discusses the Keller Plan or personalized system of instruction (PSI), a mastery-oriented, self-paced, modular teaching strategy using student/peer proctors. Success for PSI in chemical engineering, operations research, electrical engineering, and nuclear engineering courses is explained. (DH)

Competency Based Modular Experiments in Polymer Science and Technology.

ERIC Educational Resources Information Center

Pearce, Eli M; And Others

1980-01-01

Describes a competency-based, modular laboratory course emphasizing the synthesis and characterization of polymers and directed toward senior undergraduate and/or first-year graduate students in science and engineering. One module, free-radical polymerization kinetics by dilatometry, is included as a sample. (CS)

Modular and Spatially Explicit: A Novel Approach to System Dynamics

EPA Science Inventory

The Open Modeling Environment (OME) is an open-source System Dynamics (SD) simulation engine which has been created as a joint project between Oregon State University and the US Environmental Protection Agency. It is designed around a modular implementation, and provides a standa...

Tunable mechanical stability and deformation response of a resilin-based elastomer.

PubMed

Li, Linqing; Teller, Sean; Clifton, Rodney J; Jia, Xinqiao; Kiick, Kristi L

2011-06-13

Resilin, the highly elastomeric protein found in specialized compartments of most arthropods, possesses superior resilience and excellent high-frequency responsiveness. Enabled by biosynthetic strategies, we have designed and produced a modular, recombinant resilin-like polypeptide bearing both mechanically active and biologically active domains to create novel biomaterial microenvironments for engineering mechanically active tissues such as blood vessels, cardiovascular tissues, and vocal folds. Preliminary studies revealed that these recombinant materials exhibit promising mechanical properties and support the adhesion of NIH 3T3 fibroblasts. In this Article, we detail the characterization of the dynamic mechanical properties of these materials, as assessed via dynamic oscillatory shear rheology at various protein concentrations and cross-linking ratios. Simply by varying the polypeptide concentration and cross-linker ratios, the storage modulus G' can be easily tuned within the range of 500 Pa to 10 kPa. Strain-stress cycles and resilience measurements were probed via standard tensile testing methods and indicated the excellent resilience (>90%) of these materials, even when the mechanically active domains are intercepted by nonmechanically active biological cassettes. Further evaluation, at high frequencies, of the mechanical properties of these materials were assessed by a custom-designed torsional wave apparatus (TWA) at frequencies close to human phonation, indicating elastic modulus values from 200 to 2500 Pa, which is within the range of experimental data collected on excised porcine and human vocal fold tissues. The results validate the outstanding mechanical properties of the engineered materials, which are highly comparable to the mechanical properties of targeted vocal fold tissues. The ease of production of these biologically active materials, coupled to their outstanding mechanical properties over a range of compositions, suggests their potential in tissue regeneration applications.

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology.

PubMed

Wang, Baojun; Kitney, Richard I; Joly, Nicolas; Buck, Martin

2011-10-18

Modular and orthogonal genetic logic gates are essential for building robust biologically based digital devices to customize cell signalling in synthetic biology. Here we constructed an orthogonal AND gate in Escherichia coli using a novel hetero-regulation module from Pseudomonas syringae. The device comprises two co-activating genes hrpR and hrpS controlled by separate promoter inputs, and a σ(54)-dependent hrpL promoter driving the output. The hrpL promoter is activated only when both genes are expressed, generating digital-like AND integration behaviour. The AND gate is demonstrated to be modular by applying new regulated promoters to the inputs, and connecting the output to a NOT gate module to produce a combinatorial NAND gate. The circuits were assembled using a parts-based engineering approach of quantitative characterization, modelling, followed by construction and testing. The results show that new genetic logic devices can be engineered predictably from novel native orthogonal biological control elements using quantitatively in-context characterized parts. © 2011 Macmillan Publishers Limited. All rights reserved.

Modular microfluidics for point-of-care protein purifications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Millet, L. J.; Lucheon, J. D.; Standaert, R. F.

Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured tomore » suit a variety of fluidic operations or biochemical processes. In conclusion, we demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.« less

Modular microfluidics for point-of-care protein purifications.

PubMed

Millet, L J; Lucheon, J D; Standaert, R F; Retterer, S T; Doktycz, M J

2015-04-21

Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. We demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.

Modular microfluidics for point-of-care protein purifications

DOE PAGES

Millet, L. J.; Lucheon, J. D.; Standaert, R. F.; ...

2015-01-01

Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured tomore » suit a variety of fluidic operations or biochemical processes. In conclusion, we demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.« less

An integrated knowledge system for wind tunnel testing - Project Engineers' Intelligent Assistant

NASA Technical Reports Server (NTRS)

Lo, Ching F.; Shi, George Z.; Hoyt, W. A.; Steinle, Frank W., Jr.

1993-01-01

The Project Engineers' Intelligent Assistant (PEIA) is an integrated knowledge system developed using artificial intelligence technology, including hypertext, expert systems, and dynamic user interfaces. This system integrates documents, engineering codes, databases, and knowledge from domain experts into an enriched hypermedia environment and was designed to assist project engineers in planning and conducting wind tunnel tests. PEIA is a modular system which consists of an intelligent user-interface, seven modules and an integrated tool facility. Hypermedia technology is discussed and the seven PEIA modules are described. System maintenance and updating is very easy due to the modular structure and the integrated tool facility provides user access to commercial software shells for documentation, reporting, or database updating. PEIA is expected to provide project engineers with technical information, increase efficiency and productivity, and provide a realistic tool for personnel training.

Joint Common Architecture Demonstration (JCA Demo) Final Report

DTIC Science & Technology

2016-07-28

approach for implementing open systems [16], formerly known as the Modular Open Systems Approach (MOSA). OSA is a business and technical strategy to... TECHNICAL REPORT RDMR-AD-16-01 JOINT COMMON ARCHITECTURE DEMONSTRATION (JCA DEMO) FINAL REPORT Scott A. Wigginton... Modular Avionics .......................................................................... 5 E. Model-Based Engineering

Designing ECM-mimetic Materials Using Protein Engineering

PubMed Central

Cai, Lei; Heilshorn, Sarah C.

2014-01-01

The natural extracellular matrix (ECM), with its multitude of evolved cell-instructive and cell-responsive properties, provides inspiration and guidelines for the design of engineered biomaterials. One strategy to create ECM-mimetic materials is the modular design of protein-based engineered ECM (eECM) scaffolds. This modular design strategy involves combining multiple protein domains with different functionalities into a single, modular polymer sequence, resulting in a multifunctional matrix with independent tunability of the individual domain functions. These eECMs often enable decoupled control over multiple material properties for fundamental studies of cell-matrix interactions. In addition, since the eECMs are frequently composed entirely of bioresorbable amino acids, these matrices have immense clinical potential for a variety of regenerative medicine applications. This brief review demonstrates how fundamental knowledge gained from structure-function studies of native proteins can be exploited in the design of novel protein-engineered biomaterials. While the field of protein-engineered biomaterials has existed for over 20 years, the community is only now beginning to fully explore the diversity of functional peptide modules that can be incorporated into these materials. We have chosen to highlight recent examples that either (1) demonstrate exemplary use as matrices with cell-instructive and cell-responsive properties or (2) demonstrate outstanding creativity in terms of novel molecular-level design and macro-level functionality. PMID:24365704

A modular toolset for recombination transgenesis and neurogenetic analysis of Drosophila.

PubMed

Wang, Ji-Wu; Beck, Erin S; McCabe, Brian D

2012-01-01

Transgenic Drosophila have contributed extensively to our understanding of nervous system development, physiology and behavior in addition to being valuable models of human neurological disease. Here, we have generated a novel series of modular transgenic vectors designed to optimize and accelerate the production and analysis of transgenes in Drosophila. We constructed a novel vector backbone, pBID, that allows both phiC31 targeted transgene integration and incorporates insulator sequences to ensure specific and uniform transgene expression. Upon this framework, we have built a series of constructs that are either backwards compatible with existing restriction enzyme based vectors or utilize Gateway recombination technology for high-throughput cloning. These vectors allow for endogenous promoter or Gal4 targeted expression of transgenic proteins with or without fluorescent protein or epitope tags. In addition, we have generated constructs that facilitate transgenic splice isoform specific RNA inhibition of gene expression. We demonstrate the utility of these constructs to analyze proteins involved in nervous system development, physiology and neurodegenerative disease. We expect that these reagents will facilitate the proficiency and sophistication of Drosophila genetic analysis in both the nervous system and other tissues.

Heterologous Protein Secretion in Lactobacilli with Modified pSIP Vectors

PubMed Central

Karlskås, Ingrid Lea; Maudal, Kristina; Axelsson, Lars; Rud, Ida; Eijsink, Vincent G. H.; Mathiesen, Geir

2014-01-01

We describe new variants of the modular pSIP-vectors for inducible gene expression and protein secretion in lactobacilli. The basic functionality of the pSIP system was tested in Lactobacillus strains representing 14 species using pSIP411, which harbors the broad-host-range Lactococcus lactis SH71rep replicon and a β-glucuronidase encoding reporter gene. In 10 species, the inducible gene expression system was functional. Based on these results, three pSIP vectors with different signal peptides were modified by replacing their narrow-host-range L. plantarum 256rep replicon with SH71rep and transformed into strains of five different species of Lactobacillus. All recombinant strains secreted the target protein NucA, albeit with varying production levels and secretion efficiencies. The Lp_3050 derived signal peptide generally resulted in the highest levels of secreted NucA. These modified pSIP vectors are useful tools for engineering a wide variety of Lactobacillus species. PMID:24614815

Engineering Protein Hydrogels Using SpyCatcher-SpyTag Chemistry.

PubMed

Gao, Xiaoye; Fang, Jie; Xue, Bin; Fu, Linglan; Li, Hongbin

2016-09-12

Constructing hydrogels from engineered proteins has attracted significant attention within the material sciences, owing to their myriad potential applications in biomedical engineering. Developing efficient methods to cross-link tailored protein building blocks into hydrogels with desirable mechanical, physical, and functional properties is of paramount importance. By making use of the recently developed SpyCatcher-SpyTag chemistry, we successfully engineered protein hydrogels on the basis of engineered tandem modular elastomeric proteins. Our resultant protein hydrogels are soft but stable, and show excellent biocompatibility. As the first step, we tested the use of these hydrogels as a drug carrier, as well as in encapsulating human lung fibroblast cells. Our results demonstrate the robustness of the SpyCatcher-SpyTag chemistry, even when the SpyTag (or SpyCatcher) is flanked by folded globular domains. These results demonstrate that SpyCatcher-SpyTag chemistry can be used to engineer protein hydrogels from tandem modular elastomeric proteins that can find applications in tissue engineering, in fundamental mechano-biological studies, and as a controlled drug release vehicle.

Recent Technology Advances in Distributed Engine Control

NASA Technical Reports Server (NTRS)

Culley, Dennis

2017-01-01

This presentation provides an overview of the work performed at NASA Glenn Research Center in distributed engine control technology. This is control system hardware technology that overcomes engine system constraints by modularizing control hardware and integrating the components over communication networks.

Reliability studies of Integrated Modular Engine system designs

NASA Technical Reports Server (NTRS)

Hardy, Terry L.; Rapp, Douglas C.

1993-01-01

A study was performed to evaluate the reliability of Integrated Modular Engine (IME) concepts. Comparisons were made between networked IME systems and non-networked discrete systems using expander cycle configurations. Both redundant and non-redundant systems were analyzed. Binomial approximation and Markov analysis techniques were employed to evaluate total system reliability. In addition, Failure Modes and Effects Analyses (FMEA), Preliminary Hazard Analyses (PHA), and Fault Tree Analysis (FTA) were performed to allow detailed evaluation of the IME concept. A discussion of these system reliability concepts is also presented.

Reliability studies of integrated modular engine system designs

NASA Technical Reports Server (NTRS)

Hardy, Terry L.; Rapp, Douglas C.

1993-01-01

A study was performed to evaluate the reliability of Integrated Modular Engine (IME) concepts. Comparisons were made between networked IME systems and non-networked discrete systems using expander cycle configurations. Both redundant and non-redundant systems were analyzed. Binomial approximation and Markov analysis techniques were employed to evaluate total system reliability. In addition, Failure Modes and Effects Analyses (FMEA), Preliminary Hazard Analyses (PHA), and Fault Tree Analysis (FTA) were performed to allow detailed evaluation of the IME concept. A discussion of these system reliability concepts is also presented.

Reliability studies of integrated modular engine system designs

NASA Astrophysics Data System (ADS)

Hardy, Terry L.; Rapp, Douglas C.

1993-06-01

A study was performed to evaluate the reliability of Integrated Modular Engine (IME) concepts. Comparisons were made between networked IME systems and non-networked discrete systems using expander cycle configurations. Both redundant and non-redundant systems were analyzed. Binomial approximation and Markov analysis techniques were employed to evaluate total system reliability. In addition, Failure Modes and Effects Analyses (FMEA), Preliminary Hazard Analyses (PHA), and Fault Tree Analysis (FTA) were performed to allow detailed evaluation of the IME concept. A discussion of these system reliability concepts is also presented.

Reliability studies of Integrated Modular Engine system designs

NASA Astrophysics Data System (ADS)

Hardy, Terry L.; Rapp, Douglas C.

1993-06-01

A study was performed to evaluate the reliability of Integrated Modular Engine (IME) concepts. Comparisons were made between networked IME systems and non-networked discrete systems using expander cycle configurations. Both redundant and non-redundant systems were analyzed. Binomial approximation and Markov analysis techniques were employed to evaluate total system reliability. In addition, Failure Modes and Effects Analyses (FMEA), Preliminary Hazard Analyses (PHA), and Fault Tree Analysis (FTA) were performed to allow detailed evaluation of the IME concept. A discussion of these system reliability concepts is also presented.

A Recombinant Platform for Prioritizing Aerolysin Molecular Grenades for Metastatic Prostate Cancer

DTIC Science & Technology

2016-12-01

the extracellular microenvironment at cancer sites. The objective for this proposal is to use a bio -engineering approach to produce recombinant pro...ominous diagnosis. The objective for this project is to use a bio -engineering approach to produce recombinant pro-toxins designed for specific cleavage

Predicted performance of an integrated modular engine system

NASA Technical Reports Server (NTRS)

Binder, Michael; Felder, James L.

1993-01-01

Space vehicle propulsion systems are traditionally comprised of a cluster of discrete engines, each with its own set of turbopumps, valves, and a thrust chamber. The Integrated Modular Engine (IME) concept proposes a vehicle propulsion system comprised of multiple turbopumps, valves, and thrust chambers which are all interconnected. The IME concept has potential advantages in fault-tolerance, weight, and operational efficiency compared with the traditional clustered engine configuration. The purpose of this study is to examine the steady-state performance of an IME system with various components removed to simulate fault conditions. An IME configuration for a hydrogen/oxygen expander cycle propulsion system with four sets of turbopumps and eight thrust chambers has been modeled using the Rocket Engine Transient Simulator (ROCETS) program. The nominal steady-state performance is simulated, as well as turbopump thrust chamber and duct failures. The impact of component failures on system performance is discussed in the context of the system's fault tolerant capabilities.

Nonhomologous Recombination between Defective Poliovirus and Coxsackievirus Genomes Suggests a New Model of Genetic Plasticity for Picornaviruses

PubMed Central

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line

2014-01-01

ABSTRACT Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3′ end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. PMID:25096874

Space station MSFC-DPD-235/DR no. CM-03 specification, modular space station project, Part 1 CEI

NASA Technical Reports Server (NTRS)

1971-01-01

Contract engineering item specifications for the modular space station are presented. These specifications resulted from the development and allocations of requirements which are concise statements of performance or constraints on performance. Specifications contain requirements for functional performance and for the verification of design solutions.

A Modular Approach for Teaching Partial Discharge Phenomenon through Experiment

ERIC Educational Resources Information Center

Chatterjee, B.; Dey, D.; Chakravorti, S.

2011-01-01

Partial discharge (PD) monitoring is an effective predictive maintenance tool for electrical power equipment. As a result, an understanding of the theory related to PD and the associated measurement techniques is now necessary knowledge for power engineers in their professional life. This paper presents a modular course on PD phenomenon in which…

PCL-HA microscaffolds for in vitro modular bone tissue engineering.

PubMed

Totaro, Alessandra; Salerno, Aurelio; Imparato, Giorgia; Domingo, Concepción; Urciuolo, Francesco; Netti, Paolo Antonio

2017-06-01

The evolution of microscaffolds and bone-bioactive surfaces is a pivotal point in modular bone tissue engineering. In this study, the design and fabrication of porous polycaprolactone (PCL) microscaffolds functionalized with hydroxyapatite (HA) nanoparticles by means of a bio-safe and versatile thermally-induced phase separation process is reported. The ability of the as-prepared nanocomposite microscaffolds to support the adhesion, growth and osteogenic differentiation of human mesenchymal stem cells (hMSCs) in standard and osteogenic media and using dynamic seeding/culture conditions was investigated. The obtained results demonstrated that the PCL-HA nanocomposite microparticles had an enhanced interaction with hMSCs and induced their osteogenic differentiation, even without the exogenous addition of osteogenic factors. In particular, calcium deposition, alizarin red assay, histological analysis, osteogenic gene expression and collagen I secretion were assessed. The results of these tests demonstrated the formation of bone microtissue precursors after 28 days of dynamic culture. These findings suggest that PCL-HA nanocomposite microparticles represent an excellent platform for in vitro modular bone tissue engineering. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Modular Engine Noise Component Prediction System (MCP) Program Users' Guide

NASA Technical Reports Server (NTRS)

Golub, Robert A. (Technical Monitor); Herkes, William H.; Reed, David H.

2004-01-01

This is a user's manual for Modular Engine Noise Component Prediction System (MCP). This computer code allows the user to predict turbofan engine noise estimates. The program is based on an empirical procedure that has evolved over many years at The Boeing Company. The data used to develop the procedure include both full-scale engine data and small-scale model data, and include testing done by Boeing, by the engine manufacturers, and by NASA. In order to generate a noise estimate, the user specifies the appropriate engine properties (including both geometry and performance parameters), the microphone locations, the atmospheric conditions, and certain data processing options. The version of the program described here allows the user to predict three components: inlet-radiated fan noise, aft-radiated fan noise, and jet noise. MCP predicts one-third octave band noise levels over the frequency range of 50 to 10,000 Hertz. It also calculates overall sound pressure levels and certain subjective noise metrics (e.g., perceived noise levels).

Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: Engineering a recombination-resistant genome

NASA Astrophysics Data System (ADS)

Yount, Boyd; Roberts, Rhonda S.; Lindesmith, Lisa; Baric, Ralph S.

2006-08-01

Live virus vaccines provide significant protection against many detrimental human and animal diseases, but reversion to virulence by mutation and recombination has reduced appeal. Using severe acute respiratory syndrome coronavirus as a model, we engineered a different transcription regulatory circuit and isolated recombinant viruses. The transcription network allowed for efficient expression of the viral transcripts and proteins, and the recombinant viruses replicated to WT levels. Recombinant genomes were then constructed that contained mixtures of the WT and mutant regulatory circuits, reflecting recombinant viruses that might occur in nature. Although viable viruses could readily be isolated from WT and recombinant genomes containing homogeneous transcription circuits, chimeras that contained mixed regulatory networks were invariantly lethal, because viable chimeric viruses were not isolated. Mechanistically, mixed regulatory circuits promoted inefficient subgenomic transcription from inappropriate start sites, resulting in truncated ORFs and effectively minimize viral structural protein expression. Engineering regulatory transcription circuits of intercommunicating alleles successfully introduces genetic traps into a viral genome that are lethal in RNA recombinant progeny viruses. regulation | systems biology | vaccine design

"Genetic Engineering" Gains Momentum (Science/Society Case Study).

ERIC Educational Resources Information Center

Moore, John W.; Moore, Elizabeth A., Eds.

1980-01-01

Reviews the benefits and hazards of genetic engineering, or "recombinant-DNA" research. Recent federal safety rules issued by NIH which ease the strict prohibitions on recombinant-DNA research are explained. (CS)

Clearing the skies over modular polyketide synthases.

PubMed

Sherman, David H; Smith, Janet L

2006-09-19

Modular polyketide synthases (PKSs) are large multifunctional proteins that synthesize complex polyketide metabolites in microbial cells. A series of recent studies confirm the close protein structural relationship between catalytic domains in the type I mammalian fatty acid synthase (FAS) and the basic synthase unit of the modular PKS. They also establish a remarkable similarity in the overall organization of the type I FAS and the PKS module. This information provides important new conclusions about catalytic domain architecture, function, and molecular recognition that are essential for future efforts to engineer useful polyketide metabolites with valuable biological activities.

Recombineering: A Homologous Recombination-Based Method of Genetic Engineering

PubMed Central

Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G.; Court, Donald L.

2009-01-01

Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in E. coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraints being imposed by restriction enzyme site location. Bacteriophage homologous recombination proteins catalyze these recombineering reactions using double- and single-strand linear DNA substrates, so-called targeting constructs, introduced by electroporation. Gene knockouts, deletions and point mutations are readily made, gene tags can be inserted, and regions of bacterial artificial chromosomes (BACs) or the E. coli genome can be subcloned by gene retrieval using recombineering. Most of these constructs can be made within about a week's time. PMID:19180090

Evolutionary and Developmental Modules

PubMed Central

Lacquaniti, Francesco; Ivanenko, Yuri P.; d’Avella, Andrea; Zelik, Karl E.; Zago, Myrka

2013-01-01

The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates. PMID:23730285

Evolutionary and developmental modules.

PubMed

Lacquaniti, Francesco; Ivanenko, Yuri P; d'Avella, Andrea; Zelik, Karl E; Zago, Myrka

2013-01-01

The identification of biological modules at the systems level often follows top-down decomposition of a task goal, or bottom-up decomposition of multidimensional data arrays into basic elements or patterns representing shared features. These approaches traditionally have been applied to mature, fully developed systems. Here we review some results from two other perspectives on modularity, namely the developmental and evolutionary perspective. There is growing evidence that modular units of development were highly preserved and recombined during evolution. We first consider a few examples of modules well identifiable from morphology. Next we consider the more difficult issue of identifying functional developmental modules. We dwell especially on modular control of locomotion to argue that the building blocks used to construct different locomotor behaviors are similar across several animal species, presumably related to ancestral neural networks of command. A recurrent theme from comparative studies is that the developmental addition of new premotor modules underlies the postnatal acquisition and refinement of several different motor behaviors in vertebrates.

Introduction of Sustainability Concepts into Industrial Engineering Education: A Modular Approach

ERIC Educational Resources Information Center

Nazzal, Dima; Zabinski, Joseph; Hugar, Alexander; Reinhart, Debra; Karwowski, Waldemar; Madani, Kaveh

2015-01-01

Sustainability in operations, production, and consumption continues to gain relevance for engineers. This trend will accelerate as demand for goods and services grows, straining resources and requiring ingenuity to replace boundless supply in meeting the needs of a more crowded, more prosperous world. Industrial engineers are uniquely positioned…

A Modular Toolset for Recombination Transgenesis and Neurogenetic Analysis of Drosophila

PubMed Central

Wang, Ji-Wu; Beck, Erin S.; McCabe, Brian D.

2012-01-01

Transgenic Drosophila have contributed extensively to our understanding of nervous system development, physiology and behavior in addition to being valuable models of human neurological disease. Here, we have generated a novel series of modular transgenic vectors designed to optimize and accelerate the production and analysis of transgenes in Drosophila. We constructed a novel vector backbone, pBID, that allows both phiC31 targeted transgene integration and incorporates insulator sequences to ensure specific and uniform transgene expression. Upon this framework, we have built a series of constructs that are either backwards compatible with existing restriction enzyme based vectors or utilize Gateway recombination technology for high-throughput cloning. These vectors allow for endogenous promoter or Gal4 targeted expression of transgenic proteins with or without fluorescent protein or epitope tags. In addition, we have generated constructs that facilitate transgenic splice isoform specific RNA inhibition of gene expression. We demonstrate the utility of these constructs to analyze proteins involved in nervous system development, physiology and neurodegenerative disease. We expect that these reagents will facilitate the proficiency and sophistication of Drosophila genetic analysis in both the nervous system and other tissues. PMID:22848718

[Vaccine application of recombinant herpesviruses].

PubMed

Yokoyama, N; Xuan, X; Mikami, T

2000-04-01

Recently, genetic engineering using recombinant DNA techniques has been applied to design new viral vaccines in order to reduce some problems which the present viral vaccines have. Up to now, many viruses have been investigated for development of recombinant attenuated vaccines or live viral vectors for delivery of foreign genes coding immunogenic antigens. In this article, we introduced the new vaccine strategy using genetically engineered herpesviruses.

Blade loss transient dynamics analysis, volume 2. Task 2: Theoretical and analytical development. Task 3: Experimental verification

NASA Technical Reports Server (NTRS)

Gallardo, V. C.; Storace, A. S.; Gaffney, E. F.; Bach, L. J.; Stallone, M. J.

1981-01-01

The component element method was used to develop a transient dynamic analysis computer program which is essentially based on modal synthesis combined with a central, finite difference, numerical integration scheme. The methodology leads to a modular or building-block technique that is amenable to computer programming. To verify the analytical method, turbine engine transient response analysis (TETRA), was applied to two blade-out test vehicles that had been previously instrumented and tested. Comparison of the time dependent test data with those predicted by TETRA led to recommendations for refinement or extension of the analytical method to improve its accuracy and overcome its shortcomings. The development of working equations, their discretization, numerical solution scheme, the modular concept of engine modelling, the program logical structure and some illustrated results are discussed. The blade-loss test vehicles (rig full engine), the type of measured data, and the engine structural model are described.

Gene and process level modulation to overcome the bottlenecks of recombinant proteins expression in Pichia pastoris.

PubMed

Prabhu, Ashish A; Boro, Bibari; Bharali, Biju; Chakraborty, Shuchishloka; Dasu, Veeranki V

2017-01-01

Process development involving system metabolic engineering and bioprocess engineering has become one of the major thrust for the development of therapeutic proteins or enzymes. Pichia pastoris has emerged as a prominent host for the production of therapeutic protein or enzymes. Regardless of producing high protein titers, various cellular and process level bottlenecks restrict the expression of recombinant proteins in P. pastoris. In the present review, we have summarized the recent developments in the expression of foreign proteins in P. pastoris. Further, we have discussed various cellular engineering strategies which include codon optimization, pathway engineering, signal peptide processing, development of protease deficient strain and glyco-engineered strains for the high yield protein secretion of recombinant protein. Bioprocess development of recombinant proteins in large-scale bioreactor including medium optimization, optimum feeding strategy and co-substrate feeding in fed-batch as well as continuous cultivation have been described. The recent advances in system and synthetic biology studies including metabolic flux analysis in understanding the phenotypic characteristics of recombinant Pichia and genome editing with CRISPR-CAS system have also been summarized. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Modular electron transfer circuits for synthetic biology

PubMed Central

Agapakis, Christina M

2010-01-01

Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production. PMID:21468209

Rapid enzyme regeneration results in the striking catalytic longevity of an engineered, single species, biocatalytic biofilm.

PubMed

Tong, Xiaoxue; Barberi, Tania Triscari; Botting, Catherine H; Sharma, Sunil V; Simmons, Mark J H; Overton, Tim W; Goss, Rebecca J M

2016-10-21

Engineering of single-species biofilms for enzymatic generation of fine chemicals is attractive. We have recently demonstrated the utility of an engineered Escherichia coli biofilm as a platform for synthesis of 5-halotryptophan. E. coli PHL644, expressing a recombinant tryptophan synthase, was employed to generate a biofilm. Its rapid deposition, and instigation of biofilm formation, was enforced by employing a spin-down method. The biofilm presents a large three-dimensional surface area, excellent for biocatalysis. The catalytic longevity of the engineered biofilm is striking, and we had postulated that this was likely to largely result from protection conferred to recombinant enzymes by biofilm's extracellular matrix. SILAC (stable isotopic labelled amino acids in cell cultures), and in particular dynamic SILAC, in which pulses of different isotopically labelled amino acids are administered to cells over a time course, has been used to follow the fate of proteins. To explore within our spin coated biofilm, whether the recombinant enzyme's longevity might be in part due to its regeneration, we introduced pulses of isotopically labelled lysine and phenylalanine into medium overlaying the biofilm and followed their incorporation over the course of biofilm development. Through SILAC analysis, we reveal that constant and complete regeneration of recombinant enzymes occurs within spin coated biofilms. The striking catalytic longevity within the biofilm results from more than just simple protection of active enzyme by the biofilm and its associated extracellular matrix. The replenishment of recombinant enzyme is likely to contribute significantly to the catalytic longevity observed for the engineered biofilm system. Here we provide the first evidence of a recombinant enzyme's regeneration in an engineered biofilm. The recombinant enzyme was constantly replenished over time as evidenced by dynamic SILAC, which suggests that the engineered E. coli biofilms are highly metabolically active, having a not inconsiderable energetic demand. The constant renewal of recombinant enzyme highlights the attractive possibility of utilising this biofilm system as a dynamic platform into which enzymes of interest can be introduced in a "plug-and-play" fashion and potentially be controlled through promoter switching for production of a series of desired fine chemicals.

An Introduction to the Fundamentals of Chemistry for the Marine Engineer.

ERIC Educational Resources Information Center

Schlenker, Richard M.

This document describes an introduction course in the fundamentals of chemistry for marine engineers. The course is modularized, audio tutorial allowing the student to progress at his own rate while integrating laboratory and lecture materials. (SL)

Oligonucleotide recombination enabled site-specific mutagenesis in bacteria

USDA-ARS?s Scientific Manuscript database

Recombineering refers to a strategy for engineering DNA sequences using a specialized mode of homologous recombination. This technology can be used for rapidly constructing precise changes in bacterial genome sequences in vivo. Oligo recombination is one type of recombineering that uses ssDNA olig...

Repurposing Mass-produced Internal Combustion Engines Quantifying the Value and Use of Low-cost Internal Combustion Piston Engines for Modular Applications in Energy and Chemical Engineering Industries

NASA Astrophysics Data System (ADS)

L'Heureux, Zara E.

This thesis proposes that internal combustion piston engines can help clear the way for a transformation in the energy, chemical, and refining industries that is akin to the transition computer technology experienced with the shift from large mainframes to small personal computers and large farms of individually small, modular processing units. This thesis provides a mathematical foundation, multi-dimensional optimizations, experimental results, an engine model, and a techno-economic assessment, all working towards quantifying the value of repurposing internal combustion piston engines for new applications in modular, small-scale technologies, particularly for energy and chemical engineering systems. Many chemical engineering and power generation industries have focused on increasing individual unit sizes and centralizing production. This "bigger is better" concept makes it difficult to evolve and incorporate change. Large systems are often designed with long lifetimes, incorporate innovation slowly, and necessitate high upfront investment costs. Breaking away from this cycle is essential for promoting change, especially change happening quickly in the energy and chemical engineering industries. The ability to evolve during a system's lifetime provides a competitive advantage in a field dominated by large and often very old equipment that cannot respond to technology change. This thesis specifically highlights the value of small, mass-manufactured internal combustion piston engines retrofitted to participate in non-automotive system designs. The applications are unconventional and stem first from the observation that, when normalized by power output, internal combustion engines are one hundred times less expensive than conventional, large power plants. This cost disparity motivated a look at scaling laws to determine if scaling across both individual unit size and number of units produced would predict the two order of magnitude difference seen here. For the first time, this thesis provides a mathematical analysis of scaling with a combination of both changing individual unit size and varying the total number of units produced. Different paths to meet a particular cumulative capacity are analyzed and show that total costs are path dependent and vary as a function of the unit size and number of units produced. The path dependence identified is fairly weak, however, and for all practical applications, the underlying scaling laws seem unaffected. This analysis continues to support the interest in pursuing designs built around small, modular infrastructure. Building on the observation that internal combustion engines are an inexpensive power-producing unit, the first optimization in this thesis focuses on quantifying the value of engine capacity committing to deliver power in the day-ahead electricity and reserve markets, specifically based on pricing from the New York Independent System Operator (NYISO). An optimization was written in Python to determine, based on engine cost, fuel cost, engine wear, engine lifetime, and electricity prices, when and how much of an engine's power should be committed to a particular energy market. The optimization aimed to maximize profit for the engine and generator (engine genset) system acting as a price-taker. The result is an annual profit on the order of \\$30 per kilowatt. The most value in the engine genset is in its commitments to the spinning reserve market, where power is often committed but not always called on to deliver. This analysis highlights the benefits of modularity in energy generation and provides one example where the system is so inexpensive and short-lived, that the optimization views the engine replacement cost as a consumable operating expense rather than a capital cost. Having the opportunity to incorporate incremental technological improvements in a system's infrastructure throughout its lifetime allows introduction of new technology with higher efficiencies and better designs. An alternative to traditionally large infrastructure that locks in a design and today's state-of-the-art technology for the next 50 - 70 years, is a system designed to incorporate new technology in a modular fashion. The modular engine genset system used for power generation is one example of how this works in practice. The largest single component of this thesis is modeling, designing, retrofitting, and testing a reciprocating piston engine used as a compressor. Motivated again by the low cost of an internal combustion engine, this work looks at how an engine (which is, in its conventional form, essentially a reciprocating compressor) can be cost-effectively retrofitted to perform as a small-scale gas compressor. In the laboratory, an engine compressor was built by retrofitting a one-cylinder, 79 cc engine. Various retrofitting techniques were incorporated into the system design, and the engine compressor performance was quantified in each iteration. Because the retrofitted engine is now a power consumer rather than a power-producing unit, the engine compressor is driven in the laboratory with an electric motor. Experimentally, compressed air engine exhaust (starting at elevated inlet pressures) surpassed 650 psia (about 45 bar), which makes this system very attractive for many applications in chemical engineering and refining industries. A model of the engine compressor system was written in Python and incorporates experimentally-derived parameters to quantify gas leakage, engine friction, and flow (including backflow) through valves. The model as a whole was calibrated and verified with experimental data and is used to explore engine retrofits beyond what was tested in the laboratory. Along with the experimental and modeling work, a techno-economic assessment is included to compare the engine compressor system with state-of-the-art, commercially-available compressors. Included in the financial analysis is a case study where an engine compressor system is modeled to achieve specific compression needs. The result of the assessment is that, indeed, the low engine cost, even with the necessary retrofits, provides a cost advantage over incumbent compression technologies. Lastly, this thesis provides an algorithm and case study for another application of small-scale units in energy infrastructure, specifically in energy storage. This study focuses on quantifying the value of small-scale, onsite energy storage in shaving peak power demands. This case study focuses on university-level power demands. The analysis finds that, because peak power is so costly, even small amounts of energy storage, when dispatched optimally, can provide significant cost reductions. This provides another example of the value of small-scale implementations, particularly in energy infrastructure. While the study focuses on flywheels and batteries as the energy storage medium, engine gensets could also be used to deliver power and shave peak power demands. The overarching goal of this thesis is to introduce small-scale, modular infrastructure, with a particular focus on the opportunity to retrofit and repurpose inexpensive, mass-manufactured internal combustion engines in new and unconventional applications. The modeling and experimental work presented in this dissertation show very compelling results for engines incorporated into both energy generation infrastructure and chemical engineering industries via compression technologies. The low engine cost provides an opportunity to add retrofits whilst remaining cost competitive with the incumbent technology. This work supports the claim that modular infrastructure, built on the indivisible unit of an internal combustion engine, can revolutionize many industries by providing a low-cost mechanism for rapid change and promoting small-scale designs.

Design and Implementation of Multi-Campus, Modular Master Classes in Biochemical Engineering

ERIC Educational Resources Information Center

Wuyts, Niek; Bruneel, Dorine; Meyers, Myriam; Van Hoof, Etienne; De Vos, Leander; Langie, Greet; Rediers, Hans

2015-01-01

The Master of Science in engineering technology: biochemical engineering is organised in KU Leuven at four geographically dispersed campuses. To sustain the Master's programmes at all campuses, it is clear that a unique education profile at each campus is crucial. In addition, a rationalisation is required by increased cooperation, increased…

Modular disposable can (MODCAN) crash cushion: A concept investigation

NASA Technical Reports Server (NTRS)

Knoell, A.; Wilson, A.

1976-01-01

A conceptual design investigation of an improved highway crash cushion system is presented. The system is referred to as a modular disposable can (MODCAN) crash system. It is composed of a modular arrangement of disposable metal beverage cans configured to serve as an effective highway impact attenuation system. Experimental data, design considerations, and engineering calculations supporting the design development are presented. Design performance is compared to that of a conventional steel drum system. It is shown that the MODCAN concepts offers the potential for smoother and safer occupant deceleration for a larger class of vehicle impact weights than the steel drum device.

Approximation of Engine Casing Temperature Constraints for Casing Mounted Electronics

NASA Technical Reports Server (NTRS)

Kratz, Jonathan L.; Culley, Dennis E.; Chapman, Jeffryes W.

2017-01-01

The performance of propulsion engine systems is sensitive to weight and volume considerations. This can severely constrain the configuration and complexity of the control system hardware. Distributed Engine Control technology is a response to these concerns by providing more flexibility in designing the control system, and by extension, more functionality leading to higher performing engine systems. Consequently, there can be a weight benefit to mounting modular electronic hardware on the engine core casing in a high temperature environment. This paper attempts to quantify the in-flight temperature constraints for engine casing mounted electronics. In addition, an attempt is made at studying heat soak back effects. The Commercial Modular Aero Propulsion System Simulation 40k (C-MAPSS40k) software is leveraged with real flight data as the inputs to the simulation. A two-dimensional (2-D) heat transfer model is integrated with the engine simulation to approximate the temperature along the length of the engine casing. This modification to the existing C-MAPSS40k software will provide tools and methodologies to develop a better understanding of the requirements for the embedded electronics hardware in future engine systems. Results of the simulations are presented and their implications on temperature constraints for engine casing mounted electronics is discussed.

Approximation of Engine Casing Temperature Constraints for Casing Mounted Electronics

NASA Technical Reports Server (NTRS)

Kratz, Jonathan; Culley, Dennis; Chapman, Jeffryes

2016-01-01

The performance of propulsion engine systems is sensitive to weight and volume considerations. This can severely constrain the configuration and complexity of the control system hardware. Distributed Engine Control technology is a response to these concerns by providing more flexibility in designing the control system, and by extension, more functionality leading to higher performing engine systems. Consequently, there can be a weight benefit to mounting modular electronic hardware on the engine core casing in a high temperature environment. This paper attempts to quantify the in-flight temperature constraints for engine casing mounted electronics. In addition, an attempt is made at studying heat soak back effects. The Commercial Modular Aero Propulsion System Simulation 40k (C-MAPSS40k) software is leveraged with real flight data as the inputs to the simulation. A two-dimensional (2-D) heat transfer model is integrated with the engine simulation to approximate the temperature along the length of the engine casing. This modification to the existing C-MAPSS40k software will provide tools and methodologies to develop a better understanding of the requirements for the embedded electronics hardware in future engine systems. Results of the simulations are presented and their implications on temperature constraints for engine casing mounted electronics is discussed.

Design control for clinical translation of 3D printed modular scaffolds.

PubMed

Hollister, Scott J; Flanagan, Colleen L; Zopf, David A; Morrison, Robert J; Nasser, Hassan; Patel, Janki J; Ebramzadeh, Edward; Sangiorgio, Sophia N; Wheeler, Matthew B; Green, Glenn E

2015-03-01

The primary thrust of tissue engineering is the clinical translation of scaffolds and/or biologics to reconstruct tissue defects. Despite this thrust, clinical translation of tissue engineering therapies from academic research has been minimal in the 27 year history of tissue engineering. Academic research by its nature focuses on, and rewards, initial discovery of new phenomena and technologies in the basic research model, with a view towards generality. Translation, however, by its nature must be directed at specific clinical targets, also denoted as indications, with associated regulatory requirements. These regulatory requirements, especially design control, require that the clinical indication be precisely defined a priori, unlike most academic basic tissue engineering research where the research target is typically open-ended, and furthermore requires that the tissue engineering therapy be constructed according to design inputs that ensure it treats or mitigates the clinical indication. Finally, regulatory approval dictates that the constructed system be verified, i.e., proven that it meets the design inputs, and validated, i.e., that by meeting the design inputs the therapy will address the clinical indication. Satisfying design control requires (1) a system of integrated technologies (scaffolds, materials, biologics), ideally based on a fundamental platform, as compared to focus on a single technology, (2) testing of design hypotheses to validate system performance as opposed to mechanistic hypotheses of natural phenomena, and (3) sequential testing using in vitro, in vivo, large preclinical and eventually clinical tests against competing therapies, as compared to single experiments to test new technologies or test mechanistic hypotheses. Our goal in this paper is to illustrate how design control may be implemented in academic translation of scaffold based tissue engineering therapies. Specifically, we propose to (1) demonstrate a modular platform approach founded on 3D printing for developing tissue engineering therapies and (2) illustrate the design control process for modular implementation of two scaffold based tissue engineering therapies: airway reconstruction and bone tissue engineering based spine fusion.

Design Control for Clinical Translation of 3D Printed Modular Scaffolds

PubMed Central

Hollister, Scott J.; Flanagan, Colleen L.; Zopf, David A.; Morrison, Robert J.; Nasser, Hassan; Patel, Janki J.; Ebramzadeh, Edward; Sangiorgio, Sophia N.; Wheeler, Matthew B.; Green, Glenn E.

2015-01-01

The primary thrust of tissue engineering is the clinical translation of scaffolds and/or biologics to reconstruct tissue defects. Despite this thrust, clinical translation of tissue engineering therapies from academic research has been minimal in the 27 year history of tissue engineering. Academic research by its nature focuses on, and rewards, initial discovery of new phenomena and technologies in the basic research model, with a view towards generality. Translation, however, by its nature must be directed at specific clinical targets, also denoted as indications, with associated regulatory requirements. These regulatory requirements, especially design control, require that the clinical indication be precisely defined a priori, unlike most academic basic tissue engineering research where the research target is typically open-ended, and furthermore requires that the tissue engineering therapy be constructed according to design inputs that ensure it treats or mitigates the clinical indication. Finally, regulatory approval dictates that the constructed system be verified, i.e., proven that it meets the design inputs, and validated, i.e., that by meeting the design inputs the therapy will address the clinical indication. Satisfying design control requires (1) a system of integrated technologies (scaffolds, materials, biologics), ideally based on a fundamental platform, as compared to focus on a single technology, (2) testing of design hypotheses to validate system performance as opposed to mechanistic hypotheses of natural phenomena, and (3) sequential testing using in vitro, in vivo, large preclinical and eventually clinical tests against competing therapies, as compared to single experiments to test new technologies or test mechanistic hypotheses. Our goal in this paper is to illustrate how design control may be implemented in academic translation of scaffold based tissue engineering therapies. Specifically, we propose to (1) demonstrate a modular platform approach founded on 3D printing for developing tissue engineering therapies and (2) illustrate the design control process for modular implementation of two scaffold based tissue engineering therapies: airway reconstruction and bone tissue engineering based spine fusion. PMID:25666115

User's Guide for the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS)

NASA Technical Reports Server (NTRS)

Frederick, Dean K.; DeCastro, Jonathan A.; Litt, Jonathan S.

2007-01-01

This report is a Users Guide for the NASA-developed Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) software, which is a transient simulation of a large commercial turbofan engine (up to 90,000-lb thrust) with a realistic engine control system. The software supports easy access to health, control, and engine parameters through a graphical user interface (GUI). C-MAPSS provides the user with a graphical turbofan engine simulation environment in which advanced algorithms can be implemented and tested. C-MAPSS can run user-specified transient simulations, and it can generate state-space linear models of the nonlinear engine model at an operating point. The code has a number of GUI screens that allow point-and-click operation, and have editable fields for user-specified input. The software includes an atmospheric model which allows simulation of engine operation at altitudes from sea level to 40,000 ft, Mach numbers from 0 to 0.90, and ambient temperatures from -60 to 103 F. The package also includes a power-management system that allows the engine to be operated over a wide range of thrust levels throughout the full range of flight conditions.

Engineering genetic circuit interactions within and between synthetic minimal cells

NASA Astrophysics Data System (ADS)

Adamala, Katarzyna P.; Martin-Alarcon, Daniel A.; Guthrie-Honea, Katriona R.; Boyden, Edward S.

2017-05-01

Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.

AN IMPROVEMENT TO THE MOUSE COMPUTERIZED UNCERTAINTY ANALYSIS SYSTEM

EPA Science Inventory

The original MOUSE (Modular Oriented Uncertainty System) system was designed to deal with the problem of uncertainties in Environmental engineering calculations, such as a set of engineering cast or risk analysis equations. It was especially intended for use by individuals with l...

Life with Four Billion Atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knight, Thomas

2013-04-10

Today it is commonplace to design and construct single silicon chips with billions of transistors. These are complex systems, difficult (but possible) to design, test, and fabricate. Remarkably, simple living systems can be assembled from a similar number of atoms, most of them in water molecules. In this talk I will present the current status of our attempts at full understanding and complexity reduction of one of the simplest living systems, the free-living bacterial species Mesoplasma florum. This 400 nm diameter cell thrives and replicates every 40 minutes with a genome of only 800 kilobases. Our recent experiments using transposonmore » gene knockouts identified 354 of 683 annotated genes as inessential in laboratory culture when inactivated individually. While a functional redesigned genome will certainly not remove all of those genes, this suggests that roughly half the genome can be removed in an intentional redesign. I will discuss our recent knockout results and methodology, and our future plans for Genome re-engineering using targeted knock-in/knock-out double recombination; whole cell metabolic models; comprehensive whole cell metabolite measurement techniques; creation of plug-and-play metabolic modules for the simplified organism; inherent and engineered biosafety control mechanisms. This redesign is part of a comprehensive plan to lay the foundations for a new discipline of engineering biology. Engineering biological systems requires a fundamentally different viewpoint from that taken by the science of biology. Key engineering principles of modularity, simplicity, separation of concerns, abstraction, flexibility, hierarchical design, isolation, and standardization are of critical importance. The essence of engineering is the ability to imagine, design, model, build, and characterize novel systems to achieve specific goals. Current tools and components for these tasks are primitive. Our approach is to create and distribute standard biological parts, organisms, assembly techniques, and measurement techniques as a way of enabling this new field.« less

Multimodular biocatalysts for natural product assembly

NASA Astrophysics Data System (ADS)

Schwarzer, Dirk; Marahiel, Mohamed A.

2001-03-01

Nonribosomal peptides and polyketides represent a large class of natural products that show an extreme structural diversity and broad pharmacological relevance. They are synthesized from simple building blocks such as amino or carboxy acids and malonate derivatives on multimodular enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively. Although utilizing different substrates, NRPSs and PKSs show striking similarities in the modular architecture of their catalytic domains and product assembly-line mechanism. Among these compounds are well known antibiotics (penicillin, vancomycin and erythromycin) as well as potent immunosuppressive agents (cyclosporin, rapamycin and FK 506). This review focuses on the modular organization of NRPSs, PKSs and mixed NRPS/PKS systems and how modules and domains that build up the biosynthetic templates can be exploited for the rational design of recombinant enzymes capable of synthesizing novel compounds.

Achieving Energy Savings in Municipal Construction in Long Beach California

DOE Office of Scientific and Technical Information (OSTI.GOV)

None

Long Beach Gas and Oil (LBGO), the public gas utility in Long Beach, California, partnered with the U.S. Department of Energy (DOE) to develop and implement solutions to build a new, low-energy modular office building that is at least 50% below requirements set by Energy Standard 90.1-2007 of the American Society of Heating, Refrigerating, and Air-conditioning Engineers (ASHRAE), the American National Standards Institute (ANSI), and the Illuminating Engineering Society of America (IESNA) as part of DOE’s Commercial Building Partnerships (CBP) program. The LBGO building, which demonstrates that modular construction can be very energy efficient, is expected to exceed the ASHRAEmore » baseline by about 45%.« less

Synthetic biology of antimicrobial discovery

PubMed Central

Zakeri, Bijan; Lu, Timothy K.

2012-01-01

Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore, used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery. PMID:23654251

Synthetic biology of antimicrobial discovery.

PubMed

Zakeri, Bijan; Lu, Timothy K

2013-07-19

Antibiotic discovery has a storied history. From the discovery of penicillin by Sir Alexander Fleming to the relentless quest for antibiotics by Selman Waksman, the stories have become like folklore used to inspire future generations of scientists. However, recent discovery pipelines have run dry at a time when multidrug-resistant pathogens are on the rise. Nature has proven to be a valuable reservoir of antimicrobial agents, which are primarily produced by modularized biochemical pathways. Such modularization is well suited to remodeling by an interdisciplinary approach that spans science and engineering. Herein, we discuss the biological engineering of small molecules, peptides, and non-traditional antimicrobials and provide an overview of the growing applicability of synthetic biology to antimicrobials discovery.

Antares: A low cost modular launch vehicle for the future

NASA Technical Reports Server (NTRS)

1991-01-01

The single-stage-to-orbit launch vehicle Antares is a revolutionary concept based on identical modular units, enabling the Antares to efficiently launch communications satellites, as well as heavy payloads, into Earth orbit and beyond. The basic unit of the modular system, a single Antares vehicle, is aimed at launching approximately 10,000 kg (22,000 lb) into low Earth orbit (LEO). When coupled with a standard Centaur upper stage, it is capable of placing 4000 kg (8800 lb) into geosynchronous Earth orbit (GE0). The Antares incorporates a reusable engine, the Dual Mixture Ratio Engine (DMRE), as its propulsive device. This enables Antares to compete and excel in the satellite launch market by dramatically reducing launch costs. Inherent in the design is the capability to attach several of these vehicles together to provide heavy lift capability. Any number of these vehicles can be attached depending on the payload and mission requirements. With a seven-vehicle configuration, the Antares' modular concept provides a heavy lift capability of approximately 70,000 kg (154,000 lb) to LEO. This expandability allows for a wide range of payload options, such as large Earth satellites, Space Station Freedom material, and interplanetary spacecraft, and also offers a significant cost savings over a mixed fleet based on different launch vehicles.

Antares: A low cost modular launch vehicle for the future

NASA Astrophysics Data System (ADS)

The single-stage-to-orbit launch vehicle Antares is a revolutionary concept based on identical modular units, enabling the Antares to efficiently launch communications satellites, as well as heavy payloads, into Earth orbit and beyond. The basic unit of the modular system, a single Antares vehicle, is aimed at launching approximately 10,000 kg (22,000 lb) into low Earth orbit (LEO). When coupled with a standard Centaur upper stage, it is capable of placing 4000 kg (8800 lb) into geosynchronous Earth orbit (GE0). The Antares incorporates a reusable engine, the Dual Mixture Ratio Engine (DMRE), as its propulsive device. This enables Antares to compete and excel in the satellite launch market by dramatically reducing launch costs. Inherent in the design is the capability to attach several of these vehicles together to provide heavy lift capability. Any number of these vehicles can be attached depending on the payload and mission requirements. With a seven-vehicle configuration, the Antares' modular concept provides a heavy lift capability of approximately 70,000 kg (154,000 lb) to LEO. This expandability allows for a wide range of payload options, such as large Earth satellites, Space Station Freedom material, and interplanetary spacecraft, and also offers a significant cost savings over a mixed fleet based on different launch vehicles.

Modular Aero-Propulsion System Simulation

NASA Technical Reports Server (NTRS)

Parker, Khary I.; Guo, Ten-Huei

2006-01-01

The Modular Aero-Propulsion System Simulation (MAPSS) is a graphical simulation environment designed for the development of advanced control algorithms and rapid testing of these algorithms on a generic computational model of a turbofan engine and its control system. MAPSS is a nonlinear, non-real-time simulation comprising a Component Level Model (CLM) module and a Controller-and-Actuator Dynamics (CAD) module. The CLM module simulates the dynamics of engine components at a sampling rate of 2,500 Hz. The controller submodule of the CAD module simulates a digital controller, which has a typical update rate of 50 Hz. The sampling rate for the actuators in the CAD module is the same as that of the CLM. MAPSS provides a graphical user interface that affords easy access to engine-operation, engine-health, and control parameters; is used to enter such input model parameters as power lever angle (PLA), Mach number, and altitude; and can be used to change controller and engine parameters. Output variables are selectable by the user. Output data as well as any changes to constants and other parameters can be saved and reloaded into the GUI later.

Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges.

PubMed

Yuzawa, Satoshi; Keasling, Jay D; Katz, Leonard

2017-04-01

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. We have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

Marking Embryonic Stem Cells with a 2A Self-Cleaving Peptide: A NKX2-5 Emerald GFP BAC Reporter

PubMed Central

Hsiao, Edward C.; Yoshinaga, Yuko; Nguyen, Trieu D.; Musone, Stacy L.; Kim, Judy E.; Swinton, Paul; Espineda, Isidro; Manalac, Carlota; deJong, Pieter J.; Conklin, Bruce R.

2008-01-01

Background Fluorescent reporters are useful for assaying gene expression in living cells and for identifying and isolating pure cell populations from heterogeneous cultures, including embryonic stem (ES) cells. Multiple fluorophores and genetic selection markers exist; however, a system for creating reporter constructs that preserve the regulatory sequences near a gene's native ATG start site has not been widely available. Methodology Here, we describe a series of modular marker plasmids containing independent reporter, bacterial selection, and eukaryotic selection components, compatible with both Gateway recombination and lambda prophage bacterial artificial chromosome (BAC) recombineering techniques. A 2A self-cleaving peptide links the reporter to the native open reading frame. We use an emerald GFP marker cassette to create a human BAC reporter and ES cell reporter line for the early cardiac marker NKX2-5. NKX2-5 expression was detected in differentiating mouse ES cells and ES cell-derived mice. Conclusions Our results describe a NKX2-5 ES cell reporter line for studying early events in cardiomyocyte formation. The results also demonstrate that our modular marker plasmids could be used for generating reporters from unmodified BACs, potentially as part of an ES cell reporter library. PMID:18596956

Linear aerospike engine. [for reusable single-stage-to-orbit vehicle

NASA Technical Reports Server (NTRS)

Kirby, F. M.; Martinez, A.

1977-01-01

A description is presented of a dual-fuel modular split-combustor linear aerospike engine concept. The considered engine represents an approach to an integrated engine for a reusable single-stage-to-orbit (SSTO) vehicle. The engine burns two fuels (hydrogen and a hydrocarbon) with oxygen in separate combustors. Combustion gases expand on a linear aerospike nozzle. An engine preliminary design is discussed. Attention is given to the evaluation process for selecting the optimum number of modules or divisions of the engine, aspects of cooling and power cycle balance, and details of engine operation.

Modular extracellular sensor architecture for engineering mammalian cell-based devices.

PubMed

Daringer, Nichole M; Dudek, Rachel M; Schwarz, Kelly A; Leonard, Joshua N

2014-12-19

Engineering mammalian cell-based devices that monitor and therapeutically modulate human physiology is a promising and emerging frontier in clinical synthetic biology. However, realizing this vision will require new technologies enabling engineered circuitry to sense and respond to physiologically relevant cues. No existing technology enables an engineered cell to sense exclusively extracellular ligands, including proteins and pathogens, without relying upon native cellular receptors or signal transduction pathways that may be subject to crosstalk with native cellular components. To address this need, we here report a technology we term a Modular Extracellular Sensor Architecture (MESA). This self-contained receptor and signal transduction platform is maximally orthogonal to native cellular processes and comprises independent, tunable protein modules that enable performance optimization and straightforward engineering of novel MESA that recognize novel ligands. We demonstrate ligand-inducible activation of MESA signaling, optimization of receptor performance using design-based approaches, and generation of MESA biosensors that produce outputs in the form of either transcriptional regulation or transcription-independent reconstitution of enzymatic activity. This systematic, quantitative platform characterization provides a framework for engineering MESA to recognize novel ligands and for integrating these sensors into diverse mammalian synthetic biology applications.

Therapeutic Recombinant Monoclonal Antibodies

ERIC Educational Resources Information Center

Bakhtiar, Ray

2012-01-01

During the last two decades, the rapid growth of biotechnology-derived techniques has led to a myriad of therapeutic recombinant monoclonal antibodies with significant clinical benefits. Recombinant monoclonal antibodies can be obtained from a number of natural sources such as animal cell cultures using recombinant DNA engineering. In contrast to…

Modular uncooled video engines based on a DSP processor

NASA Astrophysics Data System (ADS)

Schapiro, F.; Milstain, Y.; Aharon, A.; Neboshchik, A.; Ben-Simon, Y.; Kogan, I.; Lerman, I.; Mizrahi, U.; Maayani, S.; Amsterdam, A.; Vaserman, I.; Duman, O.; Gazit, R.

2011-06-01

The market demand for low SWaP (Size, Weight and Power) uncooled engines keeps growing. Low SWaP is especially critical in battery-operated applications such as goggles and Thermal Weapon Sights. A new approach for the design of the engines was implemented by SCD to optimize size and power consumption at system level. The new approach described in the paper, consists of: 1. A modular hardware design that allows the user to define the exact level of integration needed for his system 2. An "open architecture" based on the OMAPTM530 DSP that allows the integrator to take advantage of unused hardware (FPGA) and software (DSP) resources, for implementation of additional algorithms or functionality. The approach was successfully implemented on the first generation of 25μm pitch BIRD detectors, and more recently on the new, 640 x480, 17 μm pitch detector.

Airbreathing Pulse Detonation Engine Performance

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.; Yungster, Shaye

2002-01-01

This paper presents performance results for pulse detonation engines taking into account the effects of dissociation and recombination. The amount of sensible heat recovered through recombination in the PDE chamber and exhaust process was found to be significant. These results have an impact on the specific thrust, impulse and fuel consumption of the PDE.

Precision genome engineering in lactic acid bacteria

PubMed Central

2014-01-01

Innovative new genome engineering technologies for manipulating chromosomes have appeared in the last decade. One of these technologies, recombination mediated genetic engineering (recombineering) allows for precision DNA engineering of chromosomes and plasmids in Escherichia coli. Single-stranded DNA recombineering (SSDR) allows for the generation of subtle mutations without the need for selection and without leaving behind any foreign DNA. In this review we discuss the application of SSDR technology in lactic acid bacteria, with an emphasis on key factors that were critical to move this technology from E. coli into Lactobacillus reuteri and Lactococcus lactis. We also provide a blueprint for how to proceed if one is attempting to establish SSDR technology in a lactic acid bacterium. The emergence of CRISPR-Cas technology in genome engineering and its potential application to enhancing SSDR in lactic acid bacteria is discussed. The ability to perform precision genome engineering in medically and industrially important lactic acid bacteria will allow for the genetic improvement of strains without compromising safety. PMID:25185700

CIFOG: Cosmological Ionization Fields frOm Galaxies

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

CIFOG is a versatile MPI-parallelised semi-numerical tool to perform simulations of the Epoch of Reionization. From a set of evolving cosmological gas density and ionizing emissivity fields, it computes the time and spatially dependent ionization of neutral hydrogen (HI), neutral (HeI) and singly ionized helium (HeII) in the intergalactic medium (IGM). The code accounts for HII, HeII, HeIII recombinations, and provides different descriptions for the photoionization rate that are used to calculate the residual HI fraction in ionized regions. This tool has been designed to be coupled to semi-analytic galaxy formation models or hydrodynamical simulations. The modular fashion of the code allows the user to easily introduce new descriptions for recombinations and the photoionization rate.

Modular Algorithm Testbed Suite (MATS): A Software Framework for Automatic Target Recognition

DTIC Science & Technology

2017-01-01

004 OFFICE OF NAVAL RESEARCH ATTN JASON STACK MINE WARFARE & OCEAN ENGINEERING PROGRAMS CODE 32, SUITE 1092 875 N RANDOLPH ST ARLINGTON VA 22203 ONR...naval mine countermeasures (MCM) operations by automating a large portion of the data analysis. Successful long-term implementation of ATR requires a...Modular Algorithm Testbed Suite; MATS; Mine Countermeasures Operations U U U SAR 24 Derek R. Kolacinski (850) 230-7218 THIS PAGE INTENTIONALLY LEFT

Breaching the Phalanx: Developing a More Engineer-Centric Modular BCT

DTIC Science & Technology

2007-06-05

Obersturmbannfuehrer Jaochim Peiper’s Kampfgruppe Peiper (of the I SS Panzer Corps).42 The 1111th Engineer commander visualized a defensive scheme for the...the engineer planner scheduled a planning session with the I MEF engineer staff. This planning session was held at Camp Pendleton in September...covered sleeping /work areas, ammo storage, etc.). As the units did not begin the invasion until 20 March, this meant the BCTs lived in abject squalor

Rational design of alpha-helical tandem repeat proteins with closed architectures

PubMed Central

Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

2015-01-01

Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

A Modular Framework for Modeling Hardware Elements in Distributed Engine Control Systems

NASA Technical Reports Server (NTRS)

Zinnecker, Alicia M.; Culley, Dennis E.; Aretskin-Hariton, Eliot D.

2014-01-01

Progress toward the implementation of distributed engine control in an aerospace application may be accelerated through the development of a hardware-in-the-loop (HIL) system for testing new control architectures and hardware outside of a physical test cell environment. One component required in an HIL simulation system is a high-fidelity model of the control platform: sensors, actuators, and the control law. The control system developed for the Commercial Modular Aero-Propulsion System Simulation 40k (C-MAPSS40k) provides a verifiable baseline for development of a model for simulating a distributed control architecture. This distributed controller model will contain enhanced hardware models, capturing the dynamics of the transducer and the effects of data processing, and a model of the controller network. A multilevel framework is presented that establishes three sets of interfaces in the control platform: communication with the engine (through sensors and actuators), communication between hardware and controller (over a network), and the physical connections within individual pieces of hardware. This introduces modularity at each level of the model, encouraging collaboration in the development and testing of various control schemes or hardware designs. At the hardware level, this modularity is leveraged through the creation of a Simulink(R) library containing blocks for constructing smart transducer models complying with the IEEE 1451 specification. These hardware models were incorporated in a distributed version of the baseline C-MAPSS40k controller and simulations were run to compare the performance of the two models. The overall tracking ability differed only due to quantization effects in the feedback measurements in the distributed controller. Additionally, it was also found that the added complexity of the smart transducer models did not prevent real-time operation of the distributed controller model, a requirement of an HIL system.

A Modular Framework for Modeling Hardware Elements in Distributed Engine Control Systems

NASA Technical Reports Server (NTRS)

Zinnecker, Alicia M.; Culley, Dennis E.; Aretskin-Hariton, Eliot D.

2015-01-01

Progress toward the implementation of distributed engine control in an aerospace application may be accelerated through the development of a hardware-in-the-loop (HIL) system for testing new control architectures and hardware outside of a physical test cell environment. One component required in an HIL simulation system is a high-fidelity model of the control platform: sensors, actuators, and the control law. The control system developed for the Commercial Modular Aero-Propulsion System Simulation 40k (C-MAPSS40k) provides a verifiable baseline for development of a model for simulating a distributed control architecture. This distributed controller model will contain enhanced hardware models, capturing the dynamics of the transducer and the effects of data processing, and a model of the controller network. A multilevel framework is presented that establishes three sets of interfaces in the control platform: communication with the engine (through sensors and actuators), communication between hardware and controller (over a network), and the physical connections within individual pieces of hardware. This introduces modularity at each level of the model, encouraging collaboration in the development and testing of various control schemes or hardware designs. At the hardware level, this modularity is leveraged through the creation of a SimulinkR library containing blocks for constructing smart transducer models complying with the IEEE 1451 specification. These hardware models were incorporated in a distributed version of the baseline C-MAPSS40k controller and simulations were run to compare the performance of the two models. The overall tracking ability differed only due to quantization effects in the feedback measurements in the distributed controller. Additionally, it was also found that the added complexity of the smart transducer models did not prevent real-time operation of the distributed controller model, a requirement of an HIL system.

A Modular Framework for Modeling Hardware Elements in Distributed Engine Control Systems

NASA Technical Reports Server (NTRS)

Zinnecker, Alicia Mae; Culley, Dennis E.; Aretskin-Hariton, Eliot D.

2014-01-01

Progress toward the implementation of distributed engine control in an aerospace application may be accelerated through the development of a hardware-in-the-loop (HIL) system for testing new control architectures and hardware outside of a physical test cell environment. One component required in an HIL simulation system is a high-fidelity model of the control platform: sensors, actuators, and the control law. The control system developed for the Commercial Modular Aero-Propulsion System Simulation 40k (40,000 pound force thrust) (C-MAPSS40k) provides a verifiable baseline for development of a model for simulating a distributed control architecture. This distributed controller model will contain enhanced hardware models, capturing the dynamics of the transducer and the effects of data processing, and a model of the controller network. A multilevel framework is presented that establishes three sets of interfaces in the control platform: communication with the engine (through sensors and actuators), communication between hardware and controller (over a network), and the physical connections within individual pieces of hardware. This introduces modularity at each level of the model, encouraging collaboration in the development and testing of various control schemes or hardware designs. At the hardware level, this modularity is leveraged through the creation of a Simulink (R) library containing blocks for constructing smart transducer models complying with the IEEE 1451 specification. These hardware models were incorporated in a distributed version of the baseline C-MAPSS40k controller and simulations were run to compare the performance of the two models. The overall tracking ability differed only due to quantization effects in the feedback measurements in the distributed controller. Additionally, it was also found that the added complexity of the smart transducer models did not prevent real-time operation of the distributed controller model, a requirement of an HIL system.

Stability Analysis of Distributed Engine Control Systems Under Communication Packet Drop (Postprint)

DTIC Science & Technology

2008-07-01

use, modify, reproduce, release, perform, display, or disclose the work. 14. ABSTRACT Currently, Full Authority Digital Engine Control ( FADEC ...based on a centralized architecture framework is being widely used for gas turbine engine control. However, current FADEC is not able to meet the...system (DEC). FADEC based on Distributed Control Systems (DCS) offers modularity, improved control systems prognostics and fault tolerance along with

Status, Vision, and Challenges of an Intelligent Distributed Engine Control Architecture (Postprint)

DTIC Science & Technology

2007-09-18

TERMS turbine engine control, engine health management, FADEC , Universal FADEC , Distributed Controls, UF, UF Platform, common FADEC , Generic FADEC ...Modular FADEC , Adaptive Control 16. SECURITY CLASSIFICATION OF: 19a. NAME OF RESPONSIBLE PERSON (Monitor) a. REPORT Unclassified b. ABSTRACT...Eventually the Full Authority Digital Electronic Control ( FADEC ) became the norm. Presently, this control system architecture accounts for 15 to 20% of

Fast and Efficient Feature Engineering for Multi-Cohort Analysis of EHR Data.

PubMed

Ozery-Flato, Michal; Yanover, Chen; Gottlieb, Assaf; Weissbrod, Omer; Parush Shear-Yashuv, Naama; Goldschmidt, Yaara

2017-01-01

We present a framework for feature engineering, tailored for longitudinal structured data, such as electronic health records (EHRs). To fast-track feature engineering and extraction, the framework combines general-use plug-in extractors, a multi-cohort management mechanism, and modular memoization. Using this framework, we rapidly extracted thousands of features from diverse and large healthcare data sources in multiple projects.

Photosynthetic conversion of CO2 to farnesyl diphosphate-derived phytochemicals (amorpha-4,11-diene and squalene) by engineered cyanobacteria.

PubMed

Choi, Sun Young; Lee, Hyun Jeong; Choi, Jaeyeon; Kim, Jiye; Sim, Sang Jun; Um, Youngsoon; Kim, Yunje; Lee, Taek Soon; Keasling, Jay D; Woo, Han Min

2016-01-01

Metabolic engineering of cyanobacteria has enabled photosynthetic conversion of CO2 to value-added chemicals as bio-solar cell factories. However, the production levels of isoprenoids in engineered cyanobacteria were quite low, compared to other microbial hosts. Therefore, modular optimization of multiple gene expressions for metabolic engineering of cyanobacteria is required for the production of farnesyl diphosphate-derived isoprenoids from CO2. Here, we engineered Synechococcus elongatus PCC 7942 with modular metabolic pathways consisting of the methylerythritol phosphate pathway enzymes and the amorphadiene synthase for production of amorpha-4,11-diene, resulting in significantly increased levels (23-fold) of amorpha-4,11-diene (19.8 mg/L) in the best strain relative to a parental strain. Replacing amorphadiene synthase with squalene synthase led to the synthesis of a high amount of squalene (4.98 mg/L/OD730). Overexpression of farnesyl diphosphate synthase is the most critical factor for the significant production, whereas overexpression of 1-deoxy-d-xylulose 5-phosphate reductase is detrimental to the cell growth and the production. Additionally, the cyanobacterial growth inhibition was alleviated by expressing a terpene synthase in S. elongatus PCC 7942 strain with the optimized MEP pathway only (SeHL33). This is the first demonstration of photosynthetic production of amorpha-4,11-diene from CO2 in cyanobacteria and production of squalene in S. elongatus PCC 7942. Our optimized modular OverMEP strain (SeHL33) with either co-expression of ADS or SQS demonstrated the highest production levels of amorpha-4,11-diene and squalene, which could expand the list of farnesyl diphosphate-derived isoprenoids from CO2 as bio-solar cell factories.

Identifying and engineering promoters for high level and sustainable therapeutic recombinant protein production in cultured mammalian cells.

PubMed

Ho, Steven C L; Yang, Yuansheng

2014-08-01

Promoters are essential on plasmid vectors to initiate transcription of the transgenes when generating therapeutic recombinant proteins expressing mammalian cell lines. High and sustained levels of gene expression are desired during therapeutic protein production while gene expression is useful for cell engineering. As many finely controlled promoters exhibit cell and product specificity, new promoters need to be identified, optimized and carefully evaluated before use. Suitable promoters can be identified using techniques ranging from simple molecular biology methods to modern high-throughput omics screenings. Promoter engineering is often required after identification to either obtain high and sustained expression or to provide a wider range of gene expression. This review discusses some of the available methods to identify and engineer promoters for therapeutic recombinant protein expression in mammalian cells.

Airbreathing Pulse Detonation Engine Performance

NASA Technical Reports Server (NTRS)

Povinelli, Louis A.; Yungster, Shaye

2002-01-01

This paper presents performance results for pulse detonation engines (PDE) taking into account the effects of dissociation and recombination. The amount of sensible heat recovered through recombination in the PDE chamber and exhaust process was found to be significant. These results have an impact on the specific thrust, impulse and fuel consumption of the PDE.

Introduction to COFFE: The Next-Generation HPCMP CREATE-AV CFD Solver

NASA Technical Reports Server (NTRS)

Glasby, Ryan S.; Erwin, J. Taylor; Stefanski, Douglas L.; Allmaras, Steven R.; Galbraith, Marshall C.; Anderson, W. Kyle; Nichols, Robert H.

2016-01-01

HPCMP CREATE-AV Conservative Field Finite Element (COFFE) is a modular, extensible, robust numerical solver for the Navier-Stokes equations that invokes modularity and extensibility from its first principles. COFFE implores a flexible, class-based hierarchy that provides a modular approach consisting of discretization, physics, parallelization, and linear algebra components. These components are developed with modern software engineering principles to ensure ease of uptake from a user's or developer's perspective. The Streamwise Upwind/Petrov-Galerkin (SU/PG) method is utilized to discretize the compressible Reynolds-Averaged Navier-Stokes (RANS) equations tightly coupled with a variety of turbulence models. The mathematics and the philosophy of the methodology that makes up COFFE are presented.

Design of a modular digital computer system, CDRL no. D001, final design plan

NASA Technical Reports Server (NTRS)

Easton, R. A.

1975-01-01

The engineering breadboard implementation for the CDRL no. D001 modular digital computer system developed during design of the logic system was documented. This effort followed the architecture study completed and documented previously, and was intended to verify the concepts of a fault tolerant, automatically reconfigurable, modular version of the computer system conceived during the architecture study. The system has a microprogrammed 32 bit word length, general register architecture and an instruction set consisting of a subset of the IBM System 360 instruction set plus additional fault tolerance firmware. The following areas were covered: breadboard packaging, central control element, central processing element, memory, input/output processor, and maintenance/status panel and electronics.

Modular assembly of thick multifunctional cardiac patches

PubMed Central

Fleischer, Sharon; Shapira, Assaf; Feiner, Ron; Dvir, Tal

2017-01-01

In cardiac tissue engineering cells are seeded within porous biomaterial scaffolds to create functional cardiac patches. Here, we report on a bottom-up approach to assemble a modular tissue consisting of multiple layers with distinct structures and functions. Albumin electrospun fiber scaffolds were laser-patterned to create microgrooves for engineering aligned cardiac tissues exhibiting anisotropic electrical signal propagation. Microchannels were patterned within the scaffolds and seeded with endothelial cells to form closed lumens. Moreover, cage-like structures were patterned within the scaffolds and accommodated poly(lactic-co-glycolic acid) (PLGA) microparticulate systems that controlled the release of VEGF, which promotes vascularization, or dexamethasone, an anti-inflammatory agent. The structure, morphology, and function of each layer were characterized, and the tissue layers were grown separately in their optimal conditions. Before transplantation the tissue and microparticulate layers were integrated by an ECM-based biological glue to form thick 3D cardiac patches. Finally, the patches were transplanted in rats, and their vascularization was assessed. Because of the simple modularity of this approach, we believe that it could be used in the future to assemble other multicellular, thick, 3D, functional tissues. PMID:28167795

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dong, Shuyun; Wang, Yang; Cassidy-Amstutz, Caleb

2011-10-28

Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and themore » cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.« less

Genome engineering for improved recombinant protein expression in Escherichia coli.

PubMed

Mahalik, Shubhashree; Sharma, Ashish K; Mukherjee, Krishna J

2014-12-19

A metabolic engineering perspective which views recombinant protein expression as a multistep pathway allows us to move beyond vector design and identify the downstream rate limiting steps in expression. In E.coli these are typically at the translational level and the supply of precursors in the form of energy, amino acids and nucleotides. Further recombinant protein production triggers a global cellular stress response which feedback inhibits both growth and product formation. Countering this requires a system level analysis followed by a rational host cell engineering to sustain expression for longer time periods. Another strategy to increase protein yields could be to divert the metabolic flux away from biomass formation and towards recombinant protein production. This would require a growth stoppage mechanism which does not affect the metabolic activity of the cell or the transcriptional or translational efficiencies. Finally cells have to be designed for efficient export to prevent buildup of proteins inside the cytoplasm and also simplify downstream processing. The rational and the high throughput strategies that can be used for the construction of such improved host cell platforms for recombinant protein expression is the focus of this review.

Bacteriophage recombination systems and biotechnical applications.

PubMed

Nafissi, Nafiseh; Slavcev, Roderick

2014-04-01

Bacteriophage recombination systems have been widely used in biotechnology for modifying prokaryotic species, for creating transgenic animals and plants, and more recently, for human cell gene manipulation. In contrast to homologous recombination, which benefits from the endogenous recombination machinery of the cell, site-specific recombination requires an exogenous source of recombinase in mammalian cells. The mechanism of bacteriophage evolution and their coexistence with bacterial cells has become a point of interest ever since bacterial viruses' life cycles were first explored. Phage recombinases have already been exploited as valuable genetic tools and new phage enzymes, and their potential application to genetic engineering and genome manipulation, vectorology, and generation of new transgene delivery vectors, and cell therapy are attractive areas of research that continue to be investigated. The significance and role of phage recombination systems in biotechnology is reviewed in this paper, with specific focus on homologous and site-specific recombination conferred by the coli phages, λ, and N15, the integrase from the Streptomyces phage, ΦC31, the recombination system of phage P1, and the recently characterized recombination functions of Yersinia phage, PY54. Key steps of the molecular mechanisms involving phage recombination functions and their application to molecular engineering, our novel exploitations of the PY54-derived recombination system, and its application to the development of new DNA vectors are discussed.

Quantifying Impact of Chromosome Copy Number on Recombination in Escherichia coli.

PubMed

Reynolds, T Steele; Gill, Ryan T

2015-07-17

The ability to precisely and efficiently recombineer synthetic DNA into organisms of interest in a quantitative manner is a key requirement in genome engineering. Even though considerable effort has gone into the characterization of recombination in Escherichia coli, there is still substantial variability in reported recombination efficiencies. We hypothesized that this observed variability could, in part, be explained by the variability in chromosome copy number as well as the location of the replication forks relative to the recombination site. During rapid growth, E. coli cells may contain several pairs of open replication forks. While recombineered forks are resolving and segregating within the population, changes in apparent recombineering efficiency should be observed. In the case of dominant phenotypes, we predicted and then experimentally confirmed that the apparent recombination efficiency declined during recovery until complete segregation of recombineered and wild-type genomes had occurred. We observed the reverse trend for recessive phenotypes. The observed changes in apparent recombination efficiency were found to be in agreement with mathematical calculations based on our proposed mechanism. We also provide a model that can be used to estimate the total segregated recombination efficiency based on an initial efficiency and growth rate. These results emphasize the importance of employing quantitative strategies in the design of genome-scale engineering efforts.

Project Antares: A low cost modular launch vehicle for the future

NASA Astrophysics Data System (ADS)

Aarnio, Steve; Anderson, Hobie; Arzaz, El Mehdi; Bailey, Michelle; Beeghly, Jeff; Cartwright, Curt; Chau, William; Dawdy, Andrew; Detert, Bruce; Ervin, Miles

1991-06-01

The single stage to orbit launch vehicle Antares is based upon the revolutionary concept of modularity, enabling the Antares to efficiently launch communications satellites, as well as heavy payloads, into Earth's orbit and beyond. The basic unit of the modular system, a single Antares vehicle, is aimed at launching approximately 10,000 kg into low Earth orbit (LEO). When coupled with a Centaur upper stage it is capable of placing 3500 kg into geostationary orbit. The Antares incorporates a reusable engine, the Dual Mixture Ratio Engine (DMRE), as its propulsive device. This enables Antares to compete and excel in the satellite launch market by dramatically reducing launch costs. Antares' projected launch costs are $1340 per kg to LEO which offers a tremendous savings over launch vehicles available today. Inherent in the design is the capability to attach several of these vehicles together to provide heavy lift capability. Any number of these vehicles, up to seven, can be attached depending on the payload and mission requirements. With a seven vehicle configuration Antares's modular concept provides a heavy lift capability of approximately 70,000 kg to LEO. This expandability allows for a wider range of payload options such as large Earth satellites, Space Station Freedom support, and interplanetary spacecraft, and also offers a significant cost savings over a mixed fleet based on different launch vehicles.

Project Antares: A low cost modular launch vehicle for the future

NASA Technical Reports Server (NTRS)

Aarnio, Steve; Anderson, Hobie; Arzaz, El Mehdi; Bailey, Michelle; Beeghly, Jeff; Cartwright, Curt; Chau, William; Dawdy, Andrew; Detert, Bruce; Ervin, Miles

1991-01-01

The single stage to orbit launch vehicle Antares is based upon the revolutionary concept of modularity, enabling the Antares to efficiently launch communications satellites, as well as heavy payloads, into Earth's orbit and beyond. The basic unit of the modular system, a single Antares vehicle, is aimed at launching approximately 10,000 kg into low Earth orbit (LEO). When coupled with a Centaur upper stage it is capable of placing 3500 kg into geostationary orbit. The Antares incorporates a reusable engine, the Dual Mixture Ratio Engine (DMRE), as its propulsive device. This enables Antares to compete and excel in the satellite launch market by dramatically reducing launch costs. Antares' projected launch costs are $1340 per kg to LEO which offers a tremendous savings over launch vehicles available today. Inherent in the design is the capability to attach several of these vehicles together to provide heavy lift capability. Any number of these vehicles, up to seven, can be attached depending on the payload and mission requirements. With a seven vehicle configuration Antares's modular concept provides a heavy lift capability of approximately 70,000 kg to LEO. This expandability allows for a wider range of payload options such as large Earth satellites, Space Station Freedom support, and interplanetary spacecraft, and also offers a significant cost savings over a mixed fleet based on different launch vehicles.

A highly efficient targeted recombination system for engineering linear chromosomes of industrial bacteria Streptomyces.

PubMed

Pan, Hung-Yin; Chen, Carton W; Huang, Chih-Hung

2018-04-17

Soil bacteria Streptomyces are the most important producers of secondary metabolites, including most known antibiotics. These bacteria and their close relatives are unique in possessing linear chromosomes, which typically harbor 20 to 30 biosynthetic gene clusters of tens to hundreds of kb in length. Many Streptomyces chromosomes are accompanied by linear plasmids with sizes ranging from several to several hundred kb. The large linear plasmids also often contain biosynthetic gene clusters. We have developed a targeted recombination procedure for arm exchanges between a linear plasmid and a linear chromosome. A chromosomal segment inserted in an artificially constructed plasmid allows homologous recombination between the two replicons at the homology. Depending on the design, the recombination may result in two recombinant replicons or a single recombinant chromosome with the loss of the recombinant plasmid that lacks a replication origin. The efficiency of such targeted recombination ranges from 9 to 83% depending on the locations of the homology (and thus the size of the chromosomal arm exchanged), essentially eliminating the necessity of selection. The targeted recombination is useful for the efficient engineering of the Streptomyces genome for large-scale deletion, addition, and shuffling.

Engineering of In Vitro 3D Capillary Beds by Self-Directed Angiogenic Sprouting

PubMed Central

Chan, Juliana M.; Zervantonakis, Ioannis K.; Rimchala, Tharathorn; Polacheck, William J.; Whisler, Jordan; Kamm, Roger D.

2012-01-01

In recent years, microfluidic systems have been used to study fundamental aspects of angiogenesis through the patterning of single-layered, linear or geometric vascular channels. In vivo, however, capillaries exist in complex, three-dimensional (3D) networks, and angiogenic sprouting occurs with a degree of unpredictability in all x,y,z planes. The ability to generate capillary beds in vitro that can support thick, biological tissues remains a key challenge to the regeneration of vital organs. Here, we report the engineering of 3D capillary beds in an in vitro microfluidic platform that is comprised of a biocompatible collagen I gel supported by a mechanical framework of alginate beads. The engineered vessels have patent lumens, form robust ∼1.5 mm capillary networks across the devices, and support the perfusion of 1 µm fluorescent beads through them. In addition, the alginate beads offer a modular method to encapsulate and co-culture cells that either promote angiogenesis or require perfusion for cell viability in engineered tissue constructs. This laboratory-constructed vascular supply may be clinically significant for the engineering of capillary beds and higher order biological tissues in a scalable and modular manner. PMID:23226527

Engineered cartilaginous tubes for tracheal tissue replacement via self-assembly and fusion of human mesenchymal stem cell constructs.

PubMed

Dikina, Anna D; Strobel, Hannah A; Lai, Bradley P; Rolle, Marsha W; Alsberg, Eben

2015-06-01

There is a critical need to engineer a neotrachea because currently there are no long-term treatments for tracheal stenoses affecting large portions of the airway. In this work, a modular tracheal tissue replacement strategy was developed. High-cell density, scaffold-free human mesenchymal stem cell-derived cartilaginous rings and tubes were successfully generated through employment of custom designed culture wells and a ring-to-tube assembly system. Furthermore, incorporation of transforming growth factor-β1-delivering gelatin microspheres into the engineered tissues enhanced chondrogenesis with regard to tissue size and matrix production and distribution in the ring- and tube-shaped constructs, as well as luminal rigidity of the tubes. Importantly, all engineered tissues had similar or improved biomechanical properties compared to rat tracheas, which suggests they could be transplanted into a small animal model for airway defects. The modular, bottom up approach used to grow stem cell-based cartilaginous tubes in this report is a promising platform to engineer complex organs (e.g., trachea), with control over tissue size and geometry, and has the potential to be used to generate autologous tissue implants for human clinical applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Modular Approach to Integrating Biofuels Education into ChE Curriculum Part I--Learning Materials

ERIC Educational Resources Information Center

He, Q. Peter; Wang, Jin; Zhang, Rong; Johnson, Donald; Knight, Andrew; Polala, Ravali

2016-01-01

In view of potential demand for skilled engineers and competent researchers in the biofuels field, we have identified a significant gap between advanced biofuels research and undergraduate biofuels education in chemical engineering. To help bridge this gap, we created educational materials that systematically integrate biofuels technologies into…

Biophysical properties of dermal building-blocks affects extra cellular matrix assembly in 3D endogenous macrotissue.

PubMed

Urciuolo, F; Garziano, A; Imparato, G; Panzetta, V; Fusco, S; Casale, C; Netti, P A

2016-01-29

The fabrication of functional tissue units is one of the major challenges in tissue engineering due to their in vitro use in tissue-on-chip systems, as well as in modular tissue engineering for the construction of macrotissue analogs. In this work, we aim to engineer dermal tissue micromodules obtained by culturing human dermal fibroblasts into porous gelatine microscaffold. We proved that such stromal cells coupled with gelatine microscaffolds are able to synthesize and to assemble an endogenous extracellular matrix (ECM) resulting in tissue micromodules, which evolve their biophysical features over the time. In particular, we found a time-dependent variation of oxygen consumption kinetic parameters, of newly formed ECM stiffness and of micromodules self-aggregation properties. As consequence when used as building blocks to fabricate larger tissues, the initial tissue micromodules state strongly affects the ECM organization and maturation in the final macrotissue. Such results highlight the role of the micromodules properties in controlling the formation of three-dimensional macrotissue in vitro, defining an innovative design criterion for selecting tissue-building blocks for modular tissue engineering.

Design of Modular, Shape-transitioning Inlets for a Conical Hypersonic Vehicle

NASA Technical Reports Server (NTRS)

Gollan, Rowan J.; Smart, Michael K.

2010-01-01

For a hypersonic vehicle, propelled by scramjet engines, integration of the engines and airframe is highly desirable. Thus, the forward capture shape of the engine inlet should conform to the vehicle body shape. Furthermore, the use of modular engines places a constraint on the shape of the inlet sidewalls. Finally, one may desire a combustor cross- section shape that is different from that of the inlet. These shape constraints for the inlet can be accommodated by employing a streamline-tracing and lofting technique. This design technique was developed by Smart for inlets with a rectangular-to-elliptical shape transition. In this paper, we generalise that technique to produce inlets that conform to arbitrary shape requirements. As an example, we show the design of a body-integrated hypersonic inlet on a winged-cone vehicle, typical of what might be used in a three-stage orbital launch system. The special challenge of inlet design for this conical vehicle at an angle-of-attack is also discussed. That challenge is that the bow shock sits relatively close to the vehicle body.

OpenWorm: an open-science approach to modeling Caenorhabditis elegans.

PubMed

Szigeti, Balázs; Gleeson, Padraig; Vella, Michael; Khayrulin, Sergey; Palyanov, Andrey; Hokanson, Jim; Currie, Michael; Cantarelli, Matteo; Idili, Giovanni; Larson, Stephen

2014-01-01

OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.

A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants[OPEN

PubMed Central

Gil-Humanes, Javier; Čegan, Radim; Kono, Thomas J.Y.; Konečná, Eva; Belanto, Joseph J.; Starker, Colby G.

2017-01-01

We report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A Web-based tool streamlines vector selection and construction. One advantage of our platform is the use of the Csy-type (CRISPR system yersinia) ribonuclease 4 (Csy4) and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing 12 gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the Trex2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), Medicago truncatula, wheat (Triticum aestivum), and barley (Hordeum vulgare). PMID:28522548

Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods.

PubMed

Oldfield, Lauren M; Grzesik, Peter; Voorhies, Alexander A; Alperovich, Nina; MacMath, Derek; Najera, Claudia D; Chandra, Diya Sabrina; Prasad, Sanjana; Noskov, Vladimir N; Montague, Michael G; Friedman, Robert M; Desai, Prashant J; Vashee, Sanjay

2017-10-17

Here, we present a transformational approach to genome engineering of herpes simplex virus type 1 (HSV-1), which has a large DNA genome, using synthetic genomics tools. We believe this method will enable more rapid and complex modifications of HSV-1 and other large DNA viruses than previous technologies, facilitating many useful applications. Yeast transformation-associated recombination was used to clone 11 fragments comprising the HSV-1 strain KOS 152 kb genome. Using overlapping sequences between the adjacent pieces, we assembled the fragments into a complete virus genome in yeast, transferred it into an Escherichia coli host, and reconstituted infectious virus following transfection into mammalian cells. The virus derived from this yeast-assembled genome, KOS YA , replicated with kinetics similar to wild-type virus. We demonstrated the utility of this modular assembly technology by making numerous modifications to a single gene, making changes to two genes at the same time and, finally, generating individual and combinatorial deletions to a set of five conserved genes that encode virion structural proteins. While the ability to perform genome-wide editing through assembly methods in large DNA virus genomes raises dual-use concerns, we believe the incremental risks are outweighed by potential benefits. These include enhanced functional studies, generation of oncolytic virus vectors, development of delivery platforms of genes for vaccines or therapy, as well as more rapid development of countermeasures against potential biothreats.

A multi-purpose toolkit to enable advanced genome engineering in plants

DOE PAGES

Cermak, Tomas; Curtin, Shaun J.; Gil-Humanes, Javier; ...

2017-05-18

Here, we report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on Transcription Activator-Like Effector Nucleases TALENs and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A web-based tool streamlines vector selection and construction. One advantagemore » of our platform is the use of the Csy-type (CRISPR system yersinia) ribonuclease 4 Csy4 and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing twelve gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the Trex2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), Medicago truncatula, wheat (Triticum aestivum), and barley (Hordeum vulgare).« less

A multi-purpose toolkit to enable advanced genome engineering in plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cermak, Tomas; Curtin, Shaun J.; Gil-Humanes, Javier

Here, we report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on Transcription Activator-Like Effector Nucleases TALENs and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A web-based tool streamlines vector selection and construction. One advantagemore » of our platform is the use of the Csy-type (CRISPR system yersinia) ribonuclease 4 Csy4 and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing twelve gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the Trex2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), Medicago truncatula, wheat (Triticum aestivum), and barley (Hordeum vulgare).« less

Genome-wide engineering of an infectious clone of herpes simplex virus type 1 using synthetic genomics assembly methods

PubMed Central

Grzesik, Peter; Voorhies, Alexander A.; Alperovich, Nina; MacMath, Derek; Najera, Claudia D.; Chandra, Diya Sabrina; Prasad, Sanjana; Noskov, Vladimir N.; Montague, Michael G.; Friedman, Robert M.; Desai, Prashant J.

2017-01-01

Here, we present a transformational approach to genome engineering of herpes simplex virus type 1 (HSV-1), which has a large DNA genome, using synthetic genomics tools. We believe this method will enable more rapid and complex modifications of HSV-1 and other large DNA viruses than previous technologies, facilitating many useful applications. Yeast transformation-associated recombination was used to clone 11 fragments comprising the HSV-1 strain KOS 152 kb genome. Using overlapping sequences between the adjacent pieces, we assembled the fragments into a complete virus genome in yeast, transferred it into an Escherichia coli host, and reconstituted infectious virus following transfection into mammalian cells. The virus derived from this yeast-assembled genome, KOSYA, replicated with kinetics similar to wild-type virus. We demonstrated the utility of this modular assembly technology by making numerous modifications to a single gene, making changes to two genes at the same time and, finally, generating individual and combinatorial deletions to a set of five conserved genes that encode virion structural proteins. While the ability to perform genome-wide editing through assembly methods in large DNA virus genomes raises dual-use concerns, we believe the incremental risks are outweighed by potential benefits. These include enhanced functional studies, generation of oncolytic virus vectors, development of delivery platforms of genes for vaccines or therapy, as well as more rapid development of countermeasures against potential biothreats. PMID:28928148

Targeted introgression of a wheat stem rust resistance gene by DNA marker-assisted chromosome engineering.

PubMed

Niu, Zhixia; Klindworth, Daryl L; Friesen, Timothy L; Chao, Shiaoman; Jin, Yue; Cai, Xiwen; Xu, Steven S

2011-04-01

Chromosome engineering is a useful strategy for transfer of alien genes from wild relatives into modern crops. However, this strategy has not been extensively used for alien gene introgression in most crops due to low efficiency of conventional cytogenetic techniques. Here, we report an improved scheme of chromosome engineering for efficient elimination of a large amount of goatgrass (Aegilops speltoides) chromatin surrounding Sr39, a gene that provides resistance to multiple stem rust races, including Ug99 (TTKSK) in wheat. The wheat ph1b mutation, which promotes meiotic pairing between homoeologous chromosomes, was employed to induce recombination between wheat chromosome 2B and goatgrass 2S chromatin using a backcross scheme favorable for inducing and detecting the homoeologous recombinants with small goatgrass chromosome segments. Forty recombinants with Sr39 with reduced surrounding goatgrass chromatin were quickly identified from 1048 backcross progenies through disease screening and molecular marker analysis. Four of the recombinants carrying Sr39 with a minimal amount of goatgrass chromatin (2.87-9.15% of the translocated chromosomes) were verified using genomic in situ hybridization. Approximately 97% of the goatgrass chromatin was eliminated in one of the recombinants, in which a tiny goatgrass chromosome segment containing Sr39 was retained in the wheat genome. Localization of the goatgrass chromatin in the recombinants led to rapid development of three molecular markers tightly linked to Sr39. The new wheat lines and markers provide useful resources for the ongoing global effort to combat Ug99. This study has demonstrated great potential of chromosome engineering in genome manipulation for plant improvement.

Targeted Introgression of a Wheat Stem Rust Resistance Gene by DNA Marker-Assisted Chromosome Engineering

PubMed Central

Niu, Zhixia; Klindworth, Daryl L.; Friesen, Timothy L.; Chao, Shiaoman; Jin, Yue; Cai, Xiwen; Xu, Steven S.

2011-01-01

Chromosome engineering is a useful strategy for transfer of alien genes from wild relatives into modern crops. However, this strategy has not been extensively used for alien gene introgression in most crops due to low efficiency of conventional cytogenetic techniques. Here, we report an improved scheme of chromosome engineering for efficient elimination of a large amount of goatgrass (Aegilops speltoides) chromatin surrounding Sr39, a gene that provides resistance to multiple stem rust races, including Ug99 (TTKSK) in wheat. The wheat ph1b mutation, which promotes meiotic pairing between homoeologous chromosomes, was employed to induce recombination between wheat chromosome 2B and goatgrass 2S chromatin using a backcross scheme favorable for inducing and detecting the homoeologous recombinants with small goatgrass chromosome segments. Forty recombinants with Sr39 with reduced surrounding goatgrass chromatin were quickly identified from 1048 backcross progenies through disease screening and molecular marker analysis. Four of the recombinants carrying Sr39 with a minimal amount of goatgrass chromatin (2.87–9.15% of the translocated chromosomes) were verified using genomic in situ hybridization. Approximately 97% of the goatgrass chromatin was eliminated in one of the recombinants, in which a tiny goatgrass chromosome segment containing Sr39 was retained in the wheat genome. Localization of the goatgrass chromatin in the recombinants led to rapid development of three molecular markers tightly linked to Sr39. The new wheat lines and markers provide useful resources for the ongoing global effort to combat Ug99. This study has demonstrated great potential of chromosome engineering in genome manipulation for plant improvement. PMID:21242535

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

PubMed Central

2012-01-01

Visualization and analysis of molecular networks are both central to systems biology. However, there still exists a large technological gap between them, especially when assessing multiple network levels or hierarchies. Here we present RedeR, an R/Bioconductor package combined with a Java core engine for representing modular networks. The functionality of RedeR is demonstrated in two different scenarios: hierarchical and modular organization in gene co-expression networks and nested structures in time-course gene expression subnetworks. Our results demonstrate RedeR as a new framework to deal with the multiple network levels that are inherent to complex biological systems. RedeR is available from http://bioconductor.org/packages/release/bioc/html/RedeR.html. PMID:22531049

Modular adeno-associated virus (rAAV) vectors used for cellular virus-directed enzyme prodrug therapy

PubMed Central

Hagen, Sven; Baumann, Tobias; Wagner, Hanna J.; Morath, Volker; Kaufmann, Beate; Fischer, Adrian; Bergmann, Stefan; Schindler, Patrick; Arndt, Katja M.; Müller, Kristian M.

2014-01-01

The pre-clinical and clinical development of viral vehicles for gene transfer increased in recent years, and a recombinant adeno-associated virus (rAAV) drug took center stage upon approval in the European Union. However, lack of standardization, inefficient purification methods and complicated retargeting limit general usability. We address these obstacles by fusing rAAV-2 capsids with two modular targeting molecules (DARPin or Affibody) specific for a cancer cell-surface marker (EGFR) while simultaneously including an affinity tag (His-tag) in a surface-exposed loop. Equipping these particles with genes coding for prodrug converting enzymes (thymidine kinase or cytosine deaminase) we demonstrate tumor marker specific transduction and prodrug-dependent apoptosis of cancer cells. Coding terminal and loop modifications in one gene enabled specific and scalable purification. Our genetic parts for viral production adhere to a standardized cloning strategy facilitating rapid prototyping of virus directed enzyme prodrug therapy (VDEPT). PMID:24457557

Synthetic biology: programming cells for biomedical applications.

PubMed

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.

Synthetic Engineering of Spider Silk Fiber as Implantable Optical Waveguides for Low-Loss Light Guiding.

PubMed

Qiao, Xin; Qian, Zhigang; Li, Junjie; Sun, Hongji; Han, Yao; Xia, Xiaoxia; Zhou, Jin; Wang, Chunlan; Wang, Yan; Wang, Changyong

2017-05-03

A variety of devices used for biomedical engineering have been fabricated using protein polymer because of their excellent properties, such as strength, toughness, biocompatibility, and biodegradability. In this study, we fabricated an optical waveguide using genetically engineered spider silk protein. This method has two significant advantages: (1) recombinant spider silk optical waveguide exhibits excellent optical and biological properties and (2) biosynthesis of spider silk protein can overcome the limitation to the research on spider silk optical waveguide due to the low yield of natural spider silk. In detail, two kinds of protein-based optical waveguides made from recombinant spider silk protein and regenerative silkworm silk protein were successfully prepared. Results suggested that the recombinant spider silk optical waveguide showed a smoother surface and a higher refractive index when compared with regenerative silkworm silk protein. The optical loss of recombinant spider silk optical waveguide was 0.8 ± 0.1 dB/cm in air and 1.9 ± 0.3 dB/cm in mouse muscles, which were significantly lower than those of regenerative silkworm silk optical waveguide. Moreover, recombinant spider silk optical waveguide can meet the demand to guide and efficiently deliver light through biological tissue. In addition, recombinant spider silk optical waveguide showed low toxicity to cells in vitro and low-level inflammatory reaction with surrounding tissue in vivo. Therefore, recombinant spider silk optical waveguide is a promising implantable device to guide and deliver light with low loss.

Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome

PubMed Central

2013-01-01

Background Phage-encoded serine integrases, such as φC31 integrase, are widely used for genome engineering. Fifteen such integrases have been described but their utility for genome engineering has not been compared in uniform assays. Results We have compared fifteen serine integrases for their utility for DNA manipulations in mammalian cells after first demonstrating that all were functional in E. coli. Chromosomal recombination reporters were used to show that seven integrases were active on chromosomally integrated DNA in human fibroblasts and mouse embryonic stem cells. Five of the remaining eight enzymes were active on extra-chromosomal substrates thereby demonstrating that the ability to mediate extra-chromosomal recombination is no guide to ability to mediate site-specific recombination on integrated DNA. All the integrases that were active on integrated DNA also promoted DNA integration reactions that were not mediated through conservative site-specific recombination or damaged the recombination sites but the extent of these aberrant reactions varied over at least an order of magnitude. Bxb1 integrase yielded approximately two-fold more recombinants and displayed about two fold less damage to the recombination sites than the next best recombinase; φC31 integrase. Conclusions We conclude that the Bxb1 and φC31 integrases are the reagents of choice for genome engineering in vertebrate cells and that DNA damage repair is a major limitation upon the utility of this class of site-specific recombinase. PMID:24139482

Avco Lycoming QCGAT program design cycle, demonstrated performance and emissions

NASA Technical Reports Server (NTRS)

Fogel, P.; Koschier, A.

1980-01-01

A high bypass ratio, twin spool turbofan engine of modular design which incorporates a front fan module driven by a modified LTS101 core engine was tested. The engine is housed in a nacelle incorporating full length fan ducting with sound treatment in both the inlet and fan discharge flow paths. Design goals of components and results of component tests are presented together with full engine test results. The rationale behind the combustor design selected for the engine is presented as well as the emissions test results. Total system (engine and nacelle) test results are included.

Army Engineers in a Joint and Multinational Environment

DTIC Science & Technology

2008-05-22

operatio 0 in a maneuver battalion in national ns. The battalion also lacked...construction management section (CMS) to fulfill these requirements and provide operatio mission guidance for the multinational units. The CMS, led by a lieuten...also deleting from the inventory the engineer group headquarters, relying 115 Andrew Feickert, “U.S. Army’s Modular Redesign: Issues for Congress

Modular Simulator System (MSS). System/Segment Specification for the Generic MSS - System Integration. Volume 1

DTIC Science & Technology

1993-08-20

UNLIMITED. SYSTEMS ENGINEERING DIVISION AERONAUTICAL SYSTEMS CENTER AIR FORCE MATERIEL COMMAND WRIGHT PATTERSON AFB OH 45433-7126 YOITCE When Government...BASINGER Progatl anager Team Leader Special Programs Divsion Special Programs Division JAMES J. O’CONNELL Chief, Systems Engineering Division Training...ADDRESS(ES) 10. SPONSORING/ MONITORING AGENCY REPORT NUMBER Aeronautical Systems Center Systems Engineering Division ASC-TR-94-50 10 Bldg 11 2240 B St

Modular design of metabolic network for robust production of n-butanol from galactose-glucose mixtures.

PubMed

Lim, Hyun Gyu; Lim, Jae Hyung; Jung, Gyoo Yeol

2015-01-01

Refactoring microorganisms for efficient production of advanced biofuel such as n-butanol from a mixture of sugars in the cheap feedstock is a prerequisite to achieve economic feasibility in biorefinery. However, production of biofuel from inedible and cheap feedstock is highly challenging due to the slower utilization of biomass-driven sugars, arising from complex assimilation pathway, difficulties in amplification of biosynthetic pathways for heterologous metabolite, and redox imbalance caused by consuming intracellular reducing power to produce quite reduced biofuel. Even with these problems, the microorganisms should show robust production of biofuel to obtain industrial feasibility. Thus, refactoring microorganisms for efficient conversion is highly desirable in biofuel production. In this study, we engineered robust Escherichia coli to accomplish high production of n-butanol from galactose-glucose mixtures via the design of modular pathway, an efficient and systematic way, to reconstruct the entire metabolic pathway with many target genes. Three modular pathways designed using the predictable genetic elements were assembled for efficient galactose utilization, n-butanol production, and redox re-balancing to robustly produce n-butanol from a sugar mixture of galactose and glucose. Specifically, the engineered strain showed dramatically increased n-butanol production (3.3-fold increased to 6.2 g/L after 48-h fermentation) compared to the parental strain (1.9 g/L) in galactose-supplemented medium. Moreover, fermentation with mixtures of galactose and glucose at various ratios from 2:1 to 1:2 confirmed that our engineered strain was able to robustly produce n-butanol regardless of sugar composition with simultaneous utilization of galactose and glucose. Collectively, modular pathway engineering of metabolic network can be an effective approach in strain development for optimal biofuel production with cost-effective fermentable sugars. To the best of our knowledge, this study demonstrated the first and highest n-butanol production from galactose in E. coli. Moreover, robust production of n-butanol with sugar mixtures with variable composition would facilitate the economic feasibility of the microbial process using a mixture of sugars from cheap biomass in the near future.

Systematic engineering of pentose phosphate pathway improves Escherichia coli succinate production.

PubMed

Tan, Zaigao; Chen, Jing; Zhang, Xueli

2016-01-01

Succinate biosynthesis of Escherichia coli is reducing equivalent-dependent and the EMP pathway serves as the primary reducing equivalent source under anaerobic condition. Compared with EMP, pentose phosphate pathway (PPP) is reducing equivalent-conserving but suffers from low efficacy. In this study, the ribosome binding site library and modified multivariate modular metabolic engineering (MMME) approaches are employed to overcome the low efficacy of PPP and thus increase succinate production. Altering expression levels of different PPP enzymes have distinct effects on succinate production. Specifically, increased expression of five enzymes, i.e., Zwf, Pgl, Gnd, Tkt, and Tal, contributes to increased succinate production, while the increased expression of two enzymes, i.e., Rpe and Rpi, significantly decreases succinate production. Modular engineering strategy is employed to decompose PPP into three modules according to position and function. Engineering of Zwf/Pgl/Gnd and Tkt/Tal modules effectively increases succinate yield and production, while engineering of Rpe/Rpi module decreases. Imbalance of enzymatic reactions in PPP is alleviated using MMME approach. Finally, combinational utilization of engineered PPP and SthA transhydrogenase enables succinate yield up to 1.61 mol/mol glucose, which is 94% of theoretical maximum yield (1.71 mol/mol) and also the highest succinate yield in minimal medium to our knowledge. In summary, we systematically engineered the PPP for improving the supply of reducing equivalents and thus succinate production. Besides succinate, these PPP engineering strategies and conclusions can also be applicable to the production of other reducing equivalent-dependent biorenewables.

Preliminary development of an advanced modular pressure relief cushion: Testing and user evaluation.

PubMed

Freeto, Tyler; Mitchell, Steven J; Bogie, Kath M

2018-02-01

Effective pressure relief cushions are identified as a core assistive technology need by the World Health Organization Global Cooperation on Assistive Technology. High quality affordable wheelchair cushions could provide effective pressure relief for many individuals with limited access to advanced assistive technology. Value driven engineering (VdE) principles were employed to develop a prototype modular cushion. Low cost dynamically responsive gel balls were arranged in a close packed array and seated in bilayer foam for containment and support. Two modular cushions, one with high compliance balls and one with moderate compliance balls were compared with High Profile and Low Profile Roho ® and Jay ® Medical 2 cushions. ISO 16480-2 biomechanical standardized tests were applied to assess cushion performance. A preliminary materials cost analysis was carried out. A prototype modular cushion was evaluated by 12 participants who reported satisfaction using a questionnaire based on the Quebec User Evaluation of Satisfaction with Assistive Technology (QUEST 2.0) instrument. Overall the modular cushions performed better than, or on par with, the most widely prescribed commercially available cushions under ISO 16480-2 testing. Users rated the modular cushion highly for overall appearance, size and dimensions, comfort, safety, stability, ease of adjustment and general ease of use. Cost-analysis indicated that every modular cushion component a could be replaced several times and still maintain cost-efficacy over the complete cushion lifecycle. A VdE modular cushion has the potential provide effective pressure relief for many users at a low lifetime cost. Copyright © 2017. Published by Elsevier Ltd.

Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

PubMed

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line; Delpeyroux, Francis

2014-08-05

Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3' end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. Importance: The multiplication of circulating vaccine-derived polioviruses (cVDPVs) in poorly immunized human populations can render these viruses pathogenic, causing poliomyelitis outbreaks. Most cVDPVs are intertypic recombinants between a poliovirus (PV) strain and another human enterovirus, such as type 17 coxsackie A viruses (CA17). For further studies of the genetic exchanges between PV and CA17, we have developed a model of recombination, making it possible to rescue defective PV RNA genomes with a short deletion by cotransfecting cells with the defective PV genome and CA17 genomic RNA. Numerous recombinants were found, including homologous PV/CA17 recombinants, but mostly nonhomologous recombinants presenting duplications of parental sequences preferentially located in particular regions. Long duplications were excised by passages in cultured cells or in mice, generating diverse homologous recombinants. Recombination leading to nonhomologous recombinants, which evolve into homologous recombinants, may therefore be seen as a model of genetic plasticity in enteroviruses and, possibly, in other RNA viruses. Copyright © 2014 Holmblat et al.

Cancer, viruses, and mass migration: Paul Berg's venture into eukaryotic biology and the advent of recombinant DNA research and technology, 1967-1980.

PubMed

Yi, Doogab

2008-01-01

The existing literature on the development of recombinant DNA technology and genetic engineering tends to focus on Stanley Cohen and Herbert Boyer's recombinant DNA cloning technology and its commercialization starting in the mid-1970s. Historians of science, however, have pointedly noted that experimental procedures for making recombinant DNA molecules were initially developed by Stanford biochemist Paul Berg and his colleagues, Peter Lobban and A. Dale Kaiser in the early 1970s. This paper, recognizing the uneasy disjuncture between scientific authorship and legal invention in the history of recombinant DNA technology, investigates the development of recombinant DNA technology in its full scientific context. I do so by focusing on Stanford biochemist Berg's research on the genetic regulation of higher organisms. As I hope to demonstrate, Berg's new venture reflected a mass migration of biomedical researchers as they shifted from studying prokaryotic organisms like bacteria to studying eukaryotic organisms like mammalian and human cells. It was out of this boundary crossing from prokaryotic to eukaryotic systems through virus model systems that recombinant DNA technology and other significant new research techniques and agendas emerged. Indeed, in their attempt to reconstitute 'life' as a research technology, Stanford biochemists' recombinant DNA research recast genes as a sequence that could be rewritten thorough biochemical operations. The last part of this paper shifts focus from recombinant DNA technology's academic origins to its transformation into a genetic engineering technology by examining the wide range of experimental hybridizations which occurred as techniques and knowledge circulated between Stanford biochemists and the Bay Area's experimentalists. Situating their interchange in a dense research network based at Stanford's biochemistry department, this paper helps to revise the canonized history of genetic engineering's origins that emerged during the patenting of Cohen-Boyer's recombinant DNA cloning procedures.

Use of a protein engineering strategy to overcome limitations in the production of "Difficult to Express" recombinant proteins.

PubMed

Hussain, Hirra; Fisher, David I; Abbott, W Mark; Roth, Robert G; Dickson, Alan J

2017-10-01

Certain recombinant proteins are deemed "difficult to express" in mammalian expression systems requiring significant cell and/or process engineering to abrogate expression bottlenecks. With increasing demand for the production of recombinant proteins in mammalian cells, low protein yields can have significant consequences for industrial processes. To investigate the molecular mechanisms that restrict expression of recombinant proteins, naturally secreted model proteins were analyzed from the tissue inhibitors of metalloproteinase (TIMP) protein family. In particular, TIMP-2 and TIMP-3 were subjected to detailed study. TIMP proteins share significant sequence homology (∼50% identity and ∼70% similarity in amino acid sequence). However, they show marked differences in secretion in mammalian expression systems despite this extensive sequence homology. Using these two proteins as models, this study characterized the molecular mechanisms responsible for poor recombinant protein production. Our results reveal that both TIMP-2 and TIMP-3 are detectable at mRNA and protein level within the cell but only TIMP-2 is secreted effectively into the extracellular medium. Analysis of protein localization and the nature of intracellular protein suggest TIMP-3 is severely limited in its post-translational processing. To overcome this challenge, modification of the TIMP-3 sequence to include a furin protease-cleavable pro-sequence resulted in secretion of the modified TIMP-3 protein, however, incomplete processing was observed. Based on the TIMP-3 data, the protein engineering approach was optimized and successfully applied in combination with cell engineering, the overexpression of furin, to another member of the TIMP protein family (the poorly expressed TIMP-4). Use of the described protein engineering strategy resulted in successful secretion of poorly (TIMP-4) and non-secreted (TIMP-3) targets, and presents a novel strategy to enhance the production of "difficult" recombinant targets. Biotechnol. Bioeng. 2017;114: 2348-2359. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A modular modulation method for achieving increases in metabolite production.

PubMed

Acerenza, Luis; Monzon, Pablo; Ortega, Fernando

2015-01-01

Increasing the production of overproducing strains represents a great challenge. Here, we develop a modular modulation method to determine the key steps for genetic manipulation to increase metabolite production. The method consists of three steps: (i) modularization of the metabolic network into two modules connected by linking metabolites, (ii) change in the activity of the modules using auxiliary rates producing or consuming the linking metabolites in appropriate proportions and (iii) determination of the key modules and steps to increase production. The mathematical formulation of the method in matrix form shows that it may be applied to metabolic networks of any structure and size, with reactions showing any kind of rate laws. The results are valid for any type of conservation relationships in the metabolite concentrations or interactions between modules. The activity of the module may, in principle, be changed by any large factor. The method may be applied recursively or combined with other methods devised to perform fine searches in smaller regions. In practice, it is implemented by integrating to the producer strain heterologous reactions or synthetic pathways producing or consuming the linking metabolites. The new procedure may contribute to develop metabolic engineering into a more systematic practice. © 2015 American Institute of Chemical Engineers.

Transposable elements as a molecular evolutionary force

NASA Technical Reports Server (NTRS)

Fedoroff, N. V.

1999-01-01

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

Re-engineering bacteria for ethanol production

DOEpatents

Yomano, Lorraine P; York, Sean W; Zhou, Shengde; Shanmugam, Keelnatham; Ingram, Lonnie O

2014-05-06

The invention provides recombinant bacteria, which comprise a full complement of heterologous ethanol production genes. Expression of the full complement of heterologous ethanol production genes causes the recombinant bacteria to produce ethanol as the primary fermentation product when grown in mineral salts medium, without the addition of complex nutrients. Methods for producing the recombinant bacteria and methods for producing ethanol using the recombinant bacteria are also disclosed.

Three Decades of Recombinant DNA.

ERIC Educational Resources Information Center

Palmer, Jackie

1985-01-01

Discusses highlights in the development of genetic engineering, examining techniques with recombinant DNA, legal and ethical issues, GenBank (a national database of nucleic acid sequences), and other topics. (JN)

Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking

PubMed Central

Miras, Manuel; Sempere, Raquel N.; Kraft, Jelena J.; Miller, W. Allen; Aranda, Miguel A.; Truniger, Veronica

2015-01-01

Summary Many plant viruses depend on functional RNA elements, called 3′-UTR cap-independent translation enhancers (3′-CITEs), for translation of their RNAs. In this manuscript we provide direct proof for the existing hypothesis that 3′-CITEs are modular and transferable by recombination in nature, and that this is associated with an advantage for the created virus. By characterizing a newly identified Melon necrotic spot virus (MNSV; Tombusviridae) isolate, which is able to overcome eukaryotic translation initiation factor 4E (eIF4E)-mediated resistance, we found that it contains a 55 nucleotide insertion in its 3′-UTR. We provide strong evidence that this insertion was acquired by interfamilial recombination with the 3′-UTR of an Asiatic Cucurbit aphid-borne yellows virus (CABYV; Luteoviridae). By constructing chimeric viruses, we showed that this recombined sequence is responsible for resistance breaking. Analysis of the translational efficiency of reporter constructs showed that this sequence functions as a novel 3′-CITE in both resistant and susceptible plants, being essential for translation control in resistant plants. In conclusion, we showed that a recombination event between two clearly identified viruses from different families led to the transfer of exactly the sequence corresponding to a functional RNA element, giving rise to a new isolate with the capacity to infect an otherwise non-susceptible host. PMID:24372390

Interfamilial recombination between viruses led to acquisition of a novel translation-enhancing RNA element that allows resistance breaking.

PubMed

Miras, Manuel; Sempere, Raquel N; Kraft, Jelena J; Miller, W Allen; Aranda, Miguel A; Truniger, Veronica

2014-04-01

Many plant viruses depend on functional RNA elements, called 3'-UTR cap-independent translation enhancers (3'-CITEs), for translation of their RNAs. In this manuscript we provide direct proof for the existing hypothesis that 3'-CITEs are modular and transferable by recombination in nature, and that this is associated with an advantage for the created virus. By characterizing a newly identified Melon necrotic spot virus (MNSV; Tombusviridae) isolate, which is able to overcome eukaryotic translation initiation factor 4E (eIF4E)-mediated resistance, we found that it contains a 55 nucleotide insertion in its 3'-UTR. We provide strong evidence that this insertion was acquired by interfamilial recombination with the 3'-UTR of an Asiatic Cucurbit aphid-borne yellows virus (CABYV; Luteoviridae). By constructing chimeric viruses, we showed that this recombined sequence is responsible for resistance breaking. Analysis of the translational efficiency of reporter constructs showed that this sequence functions as a novel 3'-CITE in both resistant and susceptible plants, being essential for translation control in resistant plants. In conclusion, we showed that a recombination event between two clearly identified viruses from different families led to the transfer of exactly the sequence corresponding to a functional RNA element, giving rise to a new isolate with the capacity to infect an otherwise nonsusceptible host. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

A Modular Approach to Arithmetic and Logic Unit Design on a Reconfigurable Hardware Platform for Educational Purpose

NASA Astrophysics Data System (ADS)

Oztekin, Halit; Temurtas, Feyzullah; Gulbag, Ali

The Arithmetic and Logic Unit (ALU) design is one of the important topics in Computer Architecture and Organization course in Computer and Electrical Engineering departments. There are ALU designs that have non-modular nature to be used as an educational tool. As the programmable logic technology has developed rapidly, it is feasible that ALU design based on Field Programmable Gate Array (FPGA) is implemented in this course. In this paper, we have adopted the modular approach to ALU design based on FPGA. All the modules in the ALU design are realized using schematic structure on Altera's Cyclone II Development board. Under this model, the ALU content is divided into four distinct modules. These are arithmetic unit except for multiplication and division operations, logic unit, multiplication unit and division unit. User can easily design any size of ALU unit since this approach has the modular nature. Then, this approach was applied to microcomputer architecture design named BZK.SAU.FPGA10.0 instead of the current ALU unit.

Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

PubMed

Echegaray, Sebastian; Bakr, Shaimaa; Rubin, Daniel L; Napel, Sandy

2017-10-06

The aim of this study was to develop an open-source, modular, locally run or server-based system for 3D radiomics feature computation that can be used on any computer system and included in existing workflows for understanding associations and building predictive models between image features and clinical data, such as survival. The QIFE exploits various levels of parallelization for use on multiprocessor systems. It consists of a managing framework and four stages: input, pre-processing, feature computation, and output. Each stage contains one or more swappable components, allowing run-time customization. We benchmarked the engine using various levels of parallelization on a cohort of CT scans presenting 108 lung tumors. Two versions of the QIFE have been released: (1) the open-source MATLAB code posted to Github, (2) a compiled version loaded in a Docker container, posted to DockerHub, which can be easily deployed on any computer. The QIFE processed 108 objects (tumors) in 2:12 (h/mm) using 1 core, and 1:04 (h/mm) hours using four cores with object-level parallelization. We developed the Quantitative Image Feature Engine (QIFE), an open-source feature-extraction framework that focuses on modularity, standards, parallelism, provenance, and integration. Researchers can easily integrate it with their existing segmentation and imaging workflows by creating input and output components that implement their existing interfaces. Computational efficiency can be improved by parallelizing execution at the cost of memory usage. Different parallelization levels provide different trade-offs, and the optimal setting will depend on the size and composition of the dataset to be processed.

Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

PubMed Central

Rakshambikai, Ramaswamy; Gnanavel, Mutharasu; Srinivasan, Narayanaswamy

2014-01-01

The highly modular nature of protein kinases generates diverse functional roles mediated by evolutionary events such as domain recombination, insertion and deletion of domains. Usually domain architecture of a kinase is related to the subfamily to which the kinase catalytic domain belongs. However outlier kinases with unusual domain architectures serve in the expansion of the functional space of the protein kinase family. For example, Src kinases are made-up of SH2 and SH3 domains in addition to the kinase catalytic domain. A kinase which lacks these two domains but retains sequence characteristics within the kinase catalytic domain is an outlier that is likely to have modes of regulation different from classical src kinases. This study defines two types of outlier kinases: hybrids and rogues depending on the nature of domain recombination. Hybrid kinases are those where the catalytic kinase domain belongs to a kinase subfamily but the domain architecture is typical of another kinase subfamily. Rogue kinases are those with kinase catalytic domain characteristic of a kinase subfamily but the domain architecture is typical of neither that subfamily nor any other kinase subfamily. This report provides a consolidated set of such hybrid and rogue kinases gleaned from six eukaryotic genomes–S.cerevisiae, D. melanogaster, C.elegans, M.musculus, T.rubripes and H.sapiens–and discusses their functions. The presence of such kinases necessitates a revisiting of the classification scheme of the protein kinase family using full length sequences apart from classical classification using solely the sequences of kinase catalytic domains. The study of these kinases provides a good insight in engineering signalling pathways for a desired output. Lastly, identification of hybrids and rogues in pathogenic protozoa such as P.falciparum sheds light on possible strategies in host-pathogen interactions. PMID:25255313

An Introduction to Boiler Water Chemistry for the Marine Engineer: A Text of Audio-Tutorial Instruction.

ERIC Educational Resources Information Center

Schlenker, Richard M.; And Others

Presented is a manuscript for an introductory boiler water chemistry course for marine engineer education. The course is modular, self-paced, audio-tutorial, contract graded and combined lecture-laboratory instructed. Lectures are presented to students individually via audio-tapes and 35 mm slides. The course consists of a total of 17 modules -…

Concepts for Developing and Utilizing Crowdsourcing for Neurotechnology Advancement

DTIC Science & Technology

2013-05-01

understanding of brain function and related neuroimaging tools, which is mostly limited to highly trained neuroscientists and engineers who wish to...Included are some programmatic suggestions, as well as exemplar applications to fit this end goal. 15. SUBJECT TERMS modular, EEG, neuroscience ... neuroscience -related problems among professionals in other fields, such as engineering and computer science, utilizing this approach to inspire true

Transition in Gas Turbine Engine Control System Architecture: Modular, Distributed, Embedded

DTIC Science & Technology

2009-08-01

Design + Development + Certification + Procurement + Life Cycle Cost = Net Savings for our Customers Approved for Public Release 16 Economic ...Supporting Small Quantity Electronics Need Broadly Applicable High Temperature Electronics Supply Base Approved for Public Release 17 Economic ...rc ec ures Approved for Public Release 18 Economic Drivers for New FADEC Designs FADEC Implementation Time Pacing Engine Development Issues • FADEC

Mechanical-Kinetic Modeling of a Molecular Walker from a Modular Design Principle

NASA Astrophysics Data System (ADS)

Hou, Ruizheng; Loh, Iong Ying; Li, Hongrong; Wang, Zhisong

2017-02-01

Artificial molecular walkers beyond burnt-bridge designs are complex nanomachines that potentially replicate biological walkers in mechanisms and functionalities. Improving the man-made walkers up to performance for widespread applications remains difficult, largely because their biomimetic design principles involve entangled kinetic and mechanical effects to complicate the link between a walker's construction and ultimate performance. Here, a synergic mechanical-kinetic model is developed for a recently reported DNA bipedal walker, which is based on a modular design principle, potentially enabling many directional walkers driven by a length-switching engine. The model reproduces the experimental data of the walker, and identifies its performance-limiting factors. The model also captures features common to the underlying design principle, including counterintuitive performance-construction relations that are explained by detailed balance, entropy production, and bias cancellation. While indicating a low directional fidelity for the present walker, the model suggests the possibility of improving the fidelity above 90% by a more powerful engine, which may be an improved version of the present engine or an entirely new engine motif, thanks to the flexible design principle. The model is readily adaptable to aid these experimental developments towards high-performance molecular walkers.

Parts plus pipes: synthetic biology approaches to metabolic engineering

PubMed Central

Boyle, Patrick M.; Silver, Pamela A.

2011-01-01

Synthetic biologists combine modular biological “parts” to create higher-order devices. Metabolic engineers construct biological “pipes” by optimizing the microbial conversion of basic substrates to desired compounds. Many scientists work at the intersection of these two philosophies, employing synthetic devices to enhance metabolic engineering efforts. These integrated approaches promise to do more than simply improve product yields; they can expand the array of products that are tractable to produce biologically. In this review, we explore the application of synthetic biology techniques to next-generation metabolic engineering challenges, as well as the emerging engineering principles for biological design. PMID:22037345

Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lian, Jiazhang; HamediRad, Mohammad; Zhao, Huimin

Thanks to its ease of use, modularity, and scalability, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been increasingly used in the design and engineering of Saccharomyces cerevisiae, one of the most popular hosts for industrial biotechnology. This review summarizes the recent development of this disruptive technology for metabolic engineering applications, including CRISPR-mediated gene knock-out and knock-in as well as transcriptional activation and interference. More importantly, multi-functional CRISPR systems that combine both gain- and loss-of-function modulations for combinatorial metabolic engineering are highlighted.

Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System

DOE PAGES

Lian, Jiazhang; HamediRad, Mohammad; Zhao, Huimin

2018-04-18

Thanks to its ease of use, modularity, and scalability, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been increasingly used in the design and engineering of Saccharomyces cerevisiae, one of the most popular hosts for industrial biotechnology. This review summarizes the recent development of this disruptive technology for metabolic engineering applications, including CRISPR-mediated gene knock-out and knock-in as well as transcriptional activation and interference. More importantly, multi-functional CRISPR systems that combine both gain- and loss-of-function modulations for combinatorial metabolic engineering are highlighted.

Program document for Energy Systems Optimization Program 2 (ESOP2). Volume 1: Engineering manual

NASA Technical Reports Server (NTRS)

Hamil, R. G.; Ferden, S. L.

1977-01-01

The Energy Systems Optimization Program, which is used to provide analyses of Modular Integrated Utility Systems (MIUS), is discussed. Modifications to the input format to allow modular inputs in specified blocks of data are described. An optimization feature which enables the program to search automatically for the minimum value of one parameter while varying the value of other parameters is reported. New program option flags for prime mover analyses and solar energy for space heating and domestic hot water are also covered.

Engineering Design Handbook: Timing Systems and Components

DTIC Science & Technology

1975-12-01

23-1 23-2 Modular Components 23-2 23—3 Integrated Circuits 23—2 23—4 Matching Techniques 23-5 23-5 DC and AC Systems 23-7 23-6 Hybrid...Assembly Illustrating Modular Design . . 23—4 23-3 Characteristics of the Source 23—6 23—4 Characteristics of the Load 23—6 23—5 Matching Source and...4-1 INTRODUCTION There is a continuous demand for increased precision and accuracy in frequency control. Today fast time pulses are used in

Fly-by-Wireless Update

NASA Technical Reports Server (NTRS)

Studor, George

2010-01-01

The presentation reviews what is meant by the term 'fly-by-wireless', common problems and motivation, provides recent examples, and examines NASA's future and basis for collaboration. The vision is to minimize cables and connectors and increase functionality across the aerospace industry by providing reliable, lower cost, modular, and higher performance alternatives to wired data connectivity to benefit the entire vehicle/program life-cycle. Focus areas are system engineering and integration methods to reduce cables and connectors, vehicle provisions for modularity and accessibility, and a 'tool box' of alternatives to wired connectivity.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuzawa, Satoshi; Keasling, Jay D.; Katz, Leonard

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. Finally, we have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

Tissue engineering skeletal muscle for orthopaedic applications

NASA Technical Reports Server (NTRS)

Payumo, Francis C.; Kim, Hyun D.; Sherling, Michael A.; Smith, Lee P.; Powell, Courtney; Wang, Xiao; Keeping, Hugh S.; Valentini, Robert F.; Vandenburgh, Herman H.

2002-01-01

With current technology, tissue-engineered skeletal muscle analogues (bioartificial muscles) generate too little active force to be clinically useful in orthopaedic applications. They have been engineered genetically with numerous transgenes (growth hormone, insulinlike growth factor-1, erythropoietin, vascular endothelial growth factor), and have been shown to deliver these therapeutic proteins either locally or systemically for months in vivo. Bone morphogenetic proteins belonging to the transforming growth factor-beta superfamily are osteoinductive molecules that drive the differentiation pathway of mesenchymal cells toward the chondroblastic or osteoblastic lineage, and stimulate bone formation in vivo. To determine whether skeletal muscle cells endogenously expressing bone morphogenetic proteins might serve as a vehicle for systemic bone morphogenetic protein delivery in vivo, proliferating skeletal myoblasts (C2C12) were transduced with a replication defective retrovirus containing the gene for recombinant human bone morphogenetic protein-6 (C2BMP-6). The C2BMP-6 cells constitutively expressed recombinant human bone morphogenetic protein-6 and synthesized bioactive recombinant human bone morphogenetic protein-6, based on increased alkaline phosphatase activity in coincubated mesenchymal cells. C2BMP-6 cells did not secrete soluble, bioactive recombinant human bone morphogenetic protein-6, but retained the bioactivity in the cell layer. Therefore, genetically-engineered skeletal muscle cells might serve as a platform for long-term delivery of osteoinductive bone morphogenetic proteins locally.

The role of engineered materials in superconducting tunnel junction X-ray detectors - Suppression of quasiparticle recombination losses via a phononic band gap

NASA Technical Reports Server (NTRS)

Rippert, Edward D.; Ketterson, John B.; Chen, Jun; Song, Shenian; Lomatch, Susanne; Maglic, Stevan R.; Thomas, Christopher; Cheida, M. A.; Ulmer, Melville P.

1992-01-01

An engineered structure is proposed that can alleviate quasi-particle recombination losses via the existence of a phononic band gap that overlaps the 2-Delta energy of phonons produced during recombination of quasi-particles. Attention is given to a 1D Kronig-Penny model for phonons normally incident to the layers of a multilayered superconducting tunnel junction as an idealized example. A device with a high density of Bragg resonances is identified as desirable; both Nb/Si and NbN/SiN superlattices have been produced, with the latter having generally superior performance.

The "Frankenplasmid" lab: an investigative exercise for teaching recombinant DNA methods.

PubMed

Dean, Derek M; Wilder, Jason A

2011-01-01

We describe an investigative laboratory module designed to give college undergraduates strong practical and theoretical experience with recombinant DNA methods within 3 weeks. After deducing restriction enzyme maps for two different plasmids, students ligate the plasmids together in the same reaction, transform E. coli with this mixture of ligated DNA, and plate the cells on media that specifically select for hybrid plasmids. The main goal of the assignment is for students to deduce the gene map of one hybrid "Frankenplasmid" using the LacZ phenotype of its transformants, PCR, and restriction mapping. Our protocol results in a number of possible outcomes, meaning that students are mapping truly unknown plasmids. The open-ended nature of this assignment results in an effective module that teaches recombinant DNA procedures while engaging students with its investigative approach, increasing complexity, and puzzle-like quality. Moreover, the modular design of the activity allows it to be adapted to a more limited schedule, introductory courses, or more advanced courses. Copyright © 2011 International Union of Biochemistry and Molecular Biology, Inc.

User's Guide for the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS): Version 2

NASA Technical Reports Server (NTRS)

Liu, Yuan; Frederick, Dean K.; DeCastro, Jonathan A.; Litt, Jonathan S.; Chan, William W.

2012-01-01

This report is a Users Guide for version 2 of the NASA-developed Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) software, which is a transient simulation of a large commercial turbofan engine (up to 90,000-lb thrust) with a realistic engine control system. The software supports easy access to health, control, and engine parameters through a graphical user interface (GUI). C-MAPSS v.2 has some enhancements over the original, including three actuators rather than one, the addition of actuator and sensor dynamics, and an improved controller, while retaining or improving on the convenience and user-friendliness of the original. C-MAPSS v.2 provides the user with a graphical turbofan engine simulation environment in which advanced algorithms can be implemented and tested. C-MAPSS can run user-specified transient simulations, and it can generate state-space linear models of the nonlinear engine model at an operating point. The code has a number of GUI screens that allow point-and-click operation, and have editable fields for user-specified input. The software includes an atmospheric model which allows simulation of engine operation at altitudes from sea level to 40,000 ft, Mach numbers from 0 to 0.90, and ambient temperatures from -60 to 103 F. The package also includes a power-management system that allows the engine to be operated over a wide range of thrust levels throughout the full range of flight conditions.

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering.

PubMed

Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M Teresa; Buchholz, Frank

2016-07-22

Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets.

21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

Code of Federal Regulations, 2014 CFR

2014-04-01

... SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS NEW ANIMAL DRUGS IN GENETICALLY ENGINEERED ANIMALS § 528.1070 Bc6 recombinant deoxyribonucleic acid construct. (a) Specifications and indications for...

21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

Code of Federal Regulations, 2012 CFR

2012-04-01

... SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS NEW ANIMAL DRUGS IN GENETICALLY ENGINEERED ANIMALS § 528.1070 Bc6 recombinant deoxyribonucleic acid construct. (a) Specifications and indications for...

21 CFR 528.1070 - Bc6 recombinant deoxyribonucleic acid construct.

Code of Federal Regulations, 2013 CFR

2013-04-01

... SERVICES (CONTINUED) ANIMAL DRUGS, FEEDS, AND RELATED PRODUCTS NEW ANIMAL DRUGS IN GENETICALLY ENGINEERED ANIMALS § 528.1070 Bc6 recombinant deoxyribonucleic acid construct. (a) Specifications and indications for...

Construction of hybrid peptide synthetases by module and domain fusions

PubMed Central

Mootz, Henning D.; Schwarzer, Dirk; Marahiel, Mohamed A.

2000-01-01

Nonribosomal peptide synthetases are modular enzymes that assemble peptides of diverse structures and important biological activities. Their modular organization provides a great potential for the rational design of novel compounds by recombination of the biosynthetic genes. Here we describe the extension of a dimodular system to trimodular ones based on whole-module fusion. The recombinant hybrid enzymes were purified to monitor product assembly in vitro. We started from the first two modules of tyrocidine synthetase, which catalyze the formation of the dipeptide dPhe-Pro, to construct such hybrid systems. Fusion of the second, proline-specific module with the ninth and tenth modules of the tyrocidine synthetases, specific for ornithine and leucine, respectively, resulted in dimodular hybrid enzymes exhibiting the combined substrate specificities. The thioesterase domain was fused to the terminal module. Upon incubation of these dimodular enzymes with the first tyrocidine module, TycA, incorporating dPhe, the predicted tripeptides dPhe-Pro-Orn and dPhe-Pro-Leu were obtained at rates of 0.15 min-1 and 2.1 min-1. The internal thioesterase domain was necessary and sufficient to release the products from the hybrid enzymes and thereby facilitate a catalytic turnover. Our approach of whole-module fusion is based on an improved definition of the fusion sites and overcomes the recently discovered editing function of the intrinsic condensation domains. The stepwise construction of hybrid peptide synthetases from catalytic subunits reinforces the inherent potential for the synthesis of novel, designed peptides. PMID:10811885

Construction of hybrid peptide synthetases by module and domain fusions.

PubMed

Mootz, H D; Schwarzer, D; Marahiel, M A

2000-05-23

Nonribosomal peptide synthetases are modular enzymes that assemble peptides of diverse structures and important biological activities. Their modular organization provides a great potential for the rational design of novel compounds by recombination of the biosynthetic genes. Here we describe the extension of a dimodular system to trimodular ones based on whole-module fusion. The recombinant hybrid enzymes were purified to monitor product assembly in vitro. We started from the first two modules of tyrocidine synthetase, which catalyze the formation of the dipeptide dPhe-Pro, to construct such hybrid systems. Fusion of the second, proline-specific module with the ninth and tenth modules of the tyrocidine synthetases, specific for ornithine and leucine, respectively, resulted in dimodular hybrid enzymes exhibiting the combined substrate specificities. The thioesterase domain was fused to the terminal module. Upon incubation of these dimodular enzymes with the first tyrocidine module, TycA, incorporating dPhe, the predicted tripeptides dPhe-Pro-Orn and dPhe-Pro-Leu were obtained at rates of 0.15 min(-1) and 2.1 min(-1). The internal thioesterase domain was necessary and sufficient to release the products from the hybrid enzymes and thereby facilitate a catalytic turnover. Our approach of whole-module fusion is based on an improved definition of the fusion sites and overcomes the recently discovered editing function of the intrinsic condensation domains. The stepwise construction of hybrid peptide synthetases from catalytic subunits reinforces the inherent potential for the synthesis of novel, designed peptides.

Bacterial production and structure-functional validation of a recombinant antigen-binding fragment (Fab) of an anti-cancer therapeutic antibody targeting epidermal growth factor receptor.

PubMed

Kim, Ji-Hun; Sim, Dae-Won; Park, Dongsun; Jung, Tai-Geun; Lee, Seonghwan; Oh, Taeheun; Ha, Jong-Ryul; Seok, Seung-Hyeon; Seo, Min-Duk; Kang, Ho Chul; Kim, Young Pil; Won, Hyung-Sik

2016-12-01

Fragment engineering of monoclonal antibodies (mAbs) has emerged as an excellent paradigm to develop highly efficient therapeutic and/or diagnostic agents. Engineered mAb fragments can be economically produced in bacterial systems using recombinant DNA technologies. In this work, we established recombinant production in Escherichia coli for monovalent antigen-binding fragment (Fab) adopted from a clinically used anticancer mAB drug cetuximab targeting epidermal growth factor receptor (EGFR). Recombinant DNA constructs were designed to express both polypeptide chains comprising Fab in a single vector and to secrete them to bacterial periplasmic space for efficient folding. Particularly, a C-terminal engineering to confer an interchain disulfide bond appeared to be able to enhance its heterodimeric integrity and EGFR-binding activity. Conformational relevance of the purified final product was validated by mass spectrometry and crystal structure at 1.9 Å resolution. Finally, our recombinant cetuximab-Fab was found to have strong binding affinity to EGFR overexpressed in human squamous carcinoma model (A431) cells. Its binding ability was comparable to that of cetuximab. Its EGFR-binding affinity was estimated at approximately 0.7 nM of Kd in vitro, which was quite stronger than the binding affinity of natural ligand EGF. Hence, the results validate that our construction could serve as an efficient platform to produce a recombinant cetuximab-Fab with a retained antigen-binding functionality.

A non-modular type B feruloyl esterase from Neurospora crassa exhibits concentration-dependent substrate inhibition.

PubMed Central

Crepin, Valerie F; Faulds, Craig B; Connerton, Ian F

2003-01-01

Feruloyl esterases, a subclass of the carboxylic acid esterases (EC 3.1.1.1), are able to hydrolyse the ester bond between the hydroxycinnamic acids and sugars present in the plant cell wall. The enzymes have been classified as type A or type B, based on their substrate specificity for aromatic moieties. We show that Neurospora crassa has the ability to produce multiple ferulic acid esterase activities depending upon the length of fermentation with either sugar beet pulp or wheat bran substrates. A gene identified on the basis of its expression on sugar beet pulp has been cloned and overexpressed in Pichia pastoris. The gene encodes a single-domain ferulic acid esterase, which represents the first report of a non-modular type B enzyme (fae-1 gene; GenBank accession no. AJ293029). The purified recombinant protein has been shown to exhibit concentration-dependent substrate inhibition (K(m) 0.048 mM, K (i) 2.5 mM and V(max) 8.2 units/mg against methyl 3,4-dihydroxycinnamate). The kinetic behaviour of the non-modular enzyme is discussed in terms of the diversity in the roles of the feruloyl esterases in the mobilization of plant cell wall materials and their respective modes of action. PMID:12435269

Engineer Company Force Structure Force Modularization in Support of Decisive Action. Does the Corps of Engineers Need to Re-Structure Engineer Construction Companies Again in order to Support Decisive Actions?

DTIC Science & Technology

2012-05-16

Regional Command RCP Route Clearance Platoon RSOI Reception, Staging, Onward Movement, Integration SBCT Stryker Brigade Combat Team TOE Table of...Point (ASPs), and field hospital platforms; prepare river crossing sites; and support port repair due to Hydraulic Excavator (HYEX), provides force...platforms, FARPS, supply routes, roads, control points, fire bases, tank ditches, ASPs, and field hospital platforms; prepare river crossing sites; and

Assessment of Augmented Electronic Fuel Controls for Modular Engine Diagnostics and Condition Monitoring

DTIC Science & Technology

1978-12-01

not retumn it to the originator. Unclassified READ INSTRUCTIONSJ EPORT DOCUMENTATION PAGE BEFORE COMPLETING FORMJ. GOVT ACCESSr - ECIPIENT’S CATALOG...responsible for low engine performance of an installed engine. In the case of the T700, a study was completed in Nov. 197 7 which def8 nod an analytical...ECM study has been completed . T" e results of the various systems considered areo presented below. &sateim A - Az exponsive system foaturing in- X ~(X

Recombinant DNA production of spider silk proteins

PubMed Central

Tokareva, Olena; Michalczechen-Lacerda, Valquíria A; Rech, Elíbio L; Kaplan, David L

2013-01-01

Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks. PMID:24119078

Automated Engineering Design (AED); An approach to automated documentation

NASA Technical Reports Server (NTRS)

Mcclure, C. W.

1970-01-01

The automated engineering design (AED) is reviewed, consisting of a high level systems programming language, a series of modular precoded subroutines, and a set of powerful software machine tools that effectively automate the production and design of new languages. AED is used primarily for development of problem and user-oriented languages. Software production phases are diagramed, and factors which inhibit effective documentation are evaluated.

The Modular Clock Algorithm for Blind Rendezvous

DTIC Science & Technology

2009-03-26

and Computer Engineering Graduate School of Engineering and Management Air Force Institute of Technology Air University Air Education and Training...capabilities in spectrum management and particularly in harvesting unused portions of pre-allocated band- width under DSA. The term “cognitive radio” was...of rendezvous and our role as the waiter . However, if the “child” refuses to move from non-common spectrum, rendezvous cannot occur. Bluetooth

Modular Engine Noise Component Prediction System (MCP) Technical Description and Assessment Document

NASA Technical Reports Server (NTRS)

Herkes, William H.; Reed, David H.

2005-01-01

This report describes an empirical prediction procedure for turbofan engine noise. The procedure generates predicted noise levels for several noise components, including inlet- and aft-radiated fan noise, and jet-mixing noise. This report discusses the noise source mechanisms, the development of the prediction procedures, and the assessment of the accuracy of these predictions. Finally, some recommendations for future work are presented.

Modular assembly of synthetic proteins that span the plasma membrane in mammalian cells.

PubMed

Qudrat, Anam; Truong, Kevin

2016-12-09

To achieve synthetic control over how a cell responds to other cells or the extracellular environment, it is important to reliably engineer proteins that can traffic and span the plasma membrane. Using a modular approach to assemble proteins, we identified the minimum necessary components required to engineer such membrane-spanning proteins with predictable orientation in mammalian cells. While a transmembrane domain (TM) fused to the N-terminus of a protein is sufficient to traffic it to the endoplasmic reticulum (ER), an additional signal peptidase cleavage site downstream of this TM enhanced sorting out of the ER. Next, a second TM in the synthetic protein helped anchor and accumulate the membrane-spanning protein on the plasma membrane. The orientation of the components of the synthetic protein were determined through measuring intracellular Ca 2+ signaling using the R-GECO biosensor and through measuring extracellular quenching of yellow fluorescent protein variants by saturating acidic and salt conditions. This work forms the basis of engineering novel proteins that span the plasma membrane to potentially control intracellular responses to extracellular conditions.

Engineering Globular Protein Vesicles through Tunable Self-Assembly of Recombinant Fusion Proteins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jang, Yeongseon; Choi, Won Tae; Heller, William T.

Vesicles assembled from folded, globular proteins have potential for functions different from traditional lipid or polymeric vesicles. However, they also present challenges in understanding the assembly process and controlling vesicle properties. From detailed investigation of the assembly behavior of recombinant fusion proteins, this work reports a simple strategy to engineer protein vesicles containing functional, globular domains. This is achieved through tunable self-assembly of recombinant globular fusion proteins containing leucine zippers and elastin-like polypeptides. The fusion proteins form complexes in solution via high affinity binding of the zippers, and transition through dynamic coacervates to stable hollow vesicles upon warming. The thermalmore » driving force, which can be tuned by protein concentration or temperature, controls both vesicle size and whether vesicles are single or bi-layered. Lastly, these results provide critical information to engineer globular protein vesicles via self-assembly with desired size and membrane structure.« less

Engineering Globular Protein Vesicles through Tunable Self-Assembly of Recombinant Fusion Proteins

DOE PAGES

Jang, Yeongseon; Choi, Won Tae; Heller, William T.; ...

2017-07-27

Vesicles assembled from folded, globular proteins have potential for functions different from traditional lipid or polymeric vesicles. However, they also present challenges in understanding the assembly process and controlling vesicle properties. From detailed investigation of the assembly behavior of recombinant fusion proteins, this work reports a simple strategy to engineer protein vesicles containing functional, globular domains. This is achieved through tunable self-assembly of recombinant globular fusion proteins containing leucine zippers and elastin-like polypeptides. The fusion proteins form complexes in solution via high affinity binding of the zippers, and transition through dynamic coacervates to stable hollow vesicles upon warming. The thermalmore » driving force, which can be tuned by protein concentration or temperature, controls both vesicle size and whether vesicles are single or bi-layered. Lastly, these results provide critical information to engineer globular protein vesicles via self-assembly with desired size and membrane structure.« less

Integrated Control System Engineering Support.

DTIC Science & Technology

1984-12-01

interference susceptibility. " Study multiplex bus loading requirements. Flight Control Software 0 " Demonstrate efficiencies of modular software and...Major technical thrusts include the development of: (a) task-tailored mutimode con- trol laws incorporating direct force and weapon line pointing

Evaluation of Novel Design Strategies for Developing Zinc Finger Nucleases Tools for Treating Human Diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bach, Christian; Sherman, William; Pallis, Jani

Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless undesired locations. This cytotoxicity is associated with the binding ability of engineered zinc finger domains to bind dissimilar DNA sequences with high affinity. In general, binding preferences of transcription factors are associated with significant degenerated diversity and complexity which convolutes the design and engineering of precise DNA binding domains. Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable toolsmore » to precisely modify the human genome. Our findings indicate preservation of general modularity and significant alteration of the rank-specific binding preferences of the three-finger binding domain of transcription factor SP1 when exchanging amino acids in the 2nd finger.« less

Control and protection system for an installation for the combined production of electrical and thermal energy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agazzone, U.; Ausiello, F.P.

1981-06-23

A power-generating installation comprises a plurality of modular power plants each comprised of an internal combustion engine connected to an electric machine. The electric machine is used to start the engine and thereafter operates as a generator supplying power to an electrical network common to all the modular plants. The installation has a control and protection system comprising a plurality of control modules each associated with a respective plant, and a central unit passing control signals to the modules to control starting and stopping of the individual power plants. Upon the detection of abnormal operation or failure of its associatedmore » power plant, each control module transmits an alarm signal back to the central unit which thereupon stops, or prevents the starting, of the corresponding power plant. Parameters monitored by each control module include generated current and inter-winding leakage current of the electric machine.« less

Evaluation of Novel Design Strategies for Developing Zinc Finger Nucleases Tools for Treating Human Diseases

DOE PAGES

Bach, Christian; Sherman, William; Pallis, Jani; ...

2014-01-01

Zinc finger nucleases (ZFNs) are associated with cell death and apoptosis by binding at countless undesired locations. This cytotoxicity is associated with the binding ability of engineered zinc finger domains to bind dissimilar DNA sequences with high affinity. In general, binding preferences of transcription factors are associated with significant degenerated diversity and complexity which convolutes the design and engineering of precise DNA binding domains. Evolutionary success of natural zinc finger proteins, however, evinces that nature created specific evolutionary traits and strategies, such as modularity and rank-specific recognition to cope with binding complexity that are critical for creating clinical viable toolsmore » to precisely modify the human genome. Our findings indicate preservation of general modularity and significant alteration of the rank-specific binding preferences of the three-finger binding domain of transcription factor SP1 when exchanging amino acids in the 2nd finger.« less

Design of a Modular 5-kW Power Processing Unit for the Next-Generation 40-cm Ion Engine

NASA Technical Reports Server (NTRS)

Pinero, Luis R.; Bond, Thomas; Okada, Don; Pyter, Janusz; Wiseman, Steve

2002-01-01

NASA Glenn Research Center is developing a 5/10-kW ion engine for a broad range of mission applications. Simultaneously, a 5-kW breadboard poster processing unit is being designed and fabricated. The design includes a beam supply consisting of four 1.1 kW power modules connected in parallel, equally sharing the output current. A novel phase-shifted/pulse-width-modulated dual full-bridge topology was chosen for its soft-switching characteristics. The proposed modular approach allows scalability to higher powers as well as the possibility of implementing an N+1 redundant beam supply. Efficiencies in excess of 96% were measured during testing of a breadboard beam power module. A specific mass of 3.0 kg/kW is expected for a flight PRO. This represents a 50% reduction from the state of the art NSTAR power processor.

Genome engineering and gene expression control for bacterial strain development.

PubMed

Song, Chan Woo; Lee, Joungmin; Lee, Sang Yup

2015-01-01

In recent years, a number of techniques and tools have been developed for genome engineering and gene expression control to achieve desired phenotypes of various bacteria. Here we review and discuss the recent advances in bacterial genome manipulation and gene expression control techniques, and their actual uses with accompanying examples. Genome engineering has been commonly performed based on homologous recombination. During such genome manipulation, the counterselection systems employing SacB or nucleases have mainly been used for the efficient selection of desired engineered strains. The recombineering technology enables simple and more rapid manipulation of the bacterial genome. The group II intron-mediated genome engineering technology is another option for some bacteria that are difficult to be engineered by homologous recombination. Due to the increasing demands on high-throughput screening of bacterial strains having the desired phenotypes, several multiplex genome engineering techniques have recently been developed and validated in some bacteria. Another approach to achieve desired bacterial phenotypes is the repression of target gene expression without the modification of genome sequences. This can be performed by expressing antisense RNA, small regulatory RNA, or CRISPR RNA to repress target gene expression at the transcriptional or translational level. All of these techniques allow efficient and rapid development and screening of bacterial strains having desired phenotypes, and more advanced techniques are expected to be seen. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering bacteria to solve the Burnt Pancake Problem

PubMed Central

Haynes, Karmella A; Broderick, Marian L; Brown, Adam D; Butner, Trevor L; Dickson, James O; Harden, W Lance; Heard, Lane H; Jessen, Eric L; Malloy, Kelly J; Ogden, Brad J; Rosemond, Sabriya; Simpson, Samantha; Zwack, Erin; Campbell, A Malcolm; Eckdahl, Todd T; Heyer, Laurie J; Poet, Jeffrey L

2008-01-01

Background We investigated the possibility of executing DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA. Results Inversions (or "flips") of the DNA fragment pancakes are driven by the Salmonella typhimurium Hin/hix DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in E. coli. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of in vivo flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes. Conclusion The Hin/hix system is a proof-of-concept demonstration of in vivo computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/hix may provide a flexible new tool for manipulating transgenic DNA in vivo. PMID:18492232

Harnessing recombination to speed adaptive evolution in Escherichia coli.

PubMed

Winkler, James; Kao, Katy C

2012-09-01

Evolutionary engineering typically involves asexual propagation of a strain to improve a desired phenotype. However, asexual populations suffer from extensive clonal interference, a phenomenon where distinct lineages of beneficial clones compete and are often lost from the population given sufficient time. Improved adaptive mutants can likely be generated by genetic exchange between lineages, thereby reducing clonal interference. We present a system that allows continuous in situ recombination by using an Esherichia coli F-based conjugation system lacking surface exclusion. Evolution experiments revealed that Hfr-mediated recombination significantly speeds adaptation in certain circumstances. These results show that our system is stable, effective, and suitable for use in evolutionary engineering applications. Copyright © 2012 Elsevier Inc. All rights reserved.

Nucleotide sequences encoding a thermostable alkaline protease

DOEpatents

Wilson, David B.; Lao, Guifang

1998-01-01

Nucleotide sequences, derived from a thermophilic actinomycete microorganism, which encode a thermostable alkaline protease are disclosed. Also disclosed are variants of the nucleotide sequences which encode a polypeptide having thermostable alkaline proteolytic activity. Recombinant thermostable alkaline protease or recombinant polypeptide may be obtained by culturing in a medium a host cell genetically engineered to contain and express a nucleotide sequence according to the present invention, and recovering the recombinant thermostable alkaline protease or recombinant polypeptide from the culture medium.

Modular assembly of proteins on nanoparticles.

PubMed

Ma, Wenwei; Saccardo, Angela; Roccatano, Danilo; Aboagye-Mensah, Dorothy; Alkaseem, Mohammad; Jewkes, Matthew; Di Nezza, Francesca; Baron, Mark; Soloviev, Mikhail; Ferrari, Enrico

2018-04-16

Generally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold-sulfur bonds (Au-S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.

Cell type-specific manipulation with GFP-dependent Cre recombinase.

PubMed

Tang, Jonathan C Y; Rudolph, Stephanie; Dhande, Onkar S; Abraira, Victoria E; Choi, Seungwon; Lapan, Sylvain W; Drew, Iain R; Drokhlyansky, Eugene; Huberman, Andrew D; Regehr, Wade G; Cepko, Constance L

2015-09-01

There are many transgenic GFP reporter lines that allow the visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. We developed a method that exploits GFP for gene manipulation, Cre recombinase dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation and AAV viral vectors, we delivered CRE-DOG to multiple GFP mouse lines, which led to effective recombination selectively in GFP-labeled cells. Furthermore, CRE-DOG enabled optogenetic control of these neurons. Beyond providing a new set of tools for manipulation of gene expression selectively in GFP(+) cells, we found that GFP can be used to reconstitute the activity of a protein not known to have a modular structure, suggesting that this strategy might be applicable to a wide range of proteins.

Use of virion DNA as a cloning vector for the construction of mutant and recombinant herpesviruses.

PubMed

Duboise, S M; Guo, J; Desrosiers, R C; Jung, J U

1996-10-15

We have developed improved procedures for the isolation of deletion mutant, point mutant, and recombinant herpesvirus saimiri. These procedures take advantage of the absence of NotI and AscI restriction enzyme sites within the viral genome and use reporter genes for the identification of recombinant viruses. Genes for secreted engineered alkaline phosphatase and green fluorescent protein were placed under simian virus 40 early promoter control and flanked by NotI and AscI restriction sites. When permissive cells were cotransfected with herpesvirus saimiri virion DNA and one of the engineered reporter genes cloned within herpesvirus saimiri sequences, recombinant viruses were readily identified and purified on the basis of expression of the reporter gene. Digestion of recombinant virion DNA with NotI or AscI was used to delete the reporter gene from the recombinant herpesvirus saimiri. Replacement of the reporter gene can be achieved by NotI or AscI digestion of virion DNA and ligation with a terminally matched fragment or, alternatively, by homologous recombination in cotransfected cells. Any gene can, in theory, be cloned directly into the virion DNA when flanked by the appropriate NotI or AscI sites. These procedures should be widely applicable in their general form to most or all herpesviruses that replicate permissively in cultured cells.

Improved eco-friendly recombinant Anabaena sp. strain PCC7120 with enhanced nitrogen biofertilizer potential.

PubMed

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

Photosynthetic, nitrogen-fixing Anabaena strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of Anabaena sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the hetR gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields.

Improved Eco-Friendly Recombinant Anabaena sp. Strain PCC7120 with Enhanced Nitrogen Biofertilizer Potential▿

PubMed Central

Chaurasia, Akhilesh Kumar; Apte, Shree Kumar

2011-01-01

Photosynthetic, nitrogen-fixing Anabaena strains are native to tropical paddy fields and contribute to the carbon and nitrogen economy of such soils. Genetic engineering was employed to improve the nitrogen biofertilizer potential of Anabaena sp. strain PCC7120. Constitutive enhanced expression of an additional integrated copy of the hetR gene from a light-inducible promoter elevated HetR protein expression and enhanced functional heterocyst frequency in the recombinant strain. The recombinant strain displayed consistently higher nitrogenase activity than the wild-type strain and appeared to be in homeostasis with compatible modulation of photosynthesis and respiration. The enhanced combined nitrogen availability from the recombinant strain positively catered to the nitrogen demand of rice seedlings in short-term hydroponic experiments and supported better growth. The engineered strain is stable, eco-friendly, and useful for environmental application as nitrogen biofertilizer in paddy fields. PMID:21057013

Construction of live vaccines by using genetically engineered poxviruses: biological activity of recombinant vaccinia virus expressing influenza virus hemagglutinin.

PubMed Central

Panicali, D; Davis, S W; Weinberg, R L; Paoletti, E

1983-01-01

Recombinant vaccinia viruses containing the cloned hemagglutinin (HA) gene from influenza virus were constructed. The biological activity of these poxvirus vectors was demonstrated both in vitro and in vivo. Expression of HA in cells infected with recombinant vaccinia was detected by using specific anti-HA antiserum and 125I-labeled protein A, showing that HA synthesized under the regulation of vaccinia virus was antigenic. Immunization of rabbits with these recombinant poxviruses resulted in the production of antibodies reactive with authentic influenza HA as detected by radioimmunoassay, by inhibition of HA erythrocyte agglutination, and by neutralization of influenza virus infectivity. The production of antibodies directed against influenza HA suggested that the HA gene expressed in vaccinia is immunogenic. These data indicate the potential of genetically engineered poxviruses for use as generic live vaccine vehicles that have both human and veterinary applications. Images PMID:6310573

Efficient engineering of a bacteriophage genome using the type I-E CRISPR-Cas system.

PubMed

Kiro, Ruth; Shitrit, Dror; Qimron, Udi

2014-01-01

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) system has recently been used to engineer genomes of various organisms, but surprisingly, not those of bacteriophages (phages). Here we present a method to genetically engineer the Escherichia coli phage T7 using the type I-E CRISPR-Cas system. T7 phage genome is edited by homologous recombination with a DNA sequence flanked by sequences homologous to the desired location. Non-edited genomes are targeted by the CRISPR-Cas system, thus enabling isolation of the desired recombinant phages. This method broadens CRISPR Cas-based editing to phages and uses a CRISPR-Cas type other than type II. The method may be adjusted to genetically engineer any bacteriophage genome.

Genetic engineering approach to develop next-generation reagents for endotoxin quantification.

PubMed

Mizumura, Hikaru; Ogura, Norihiko; Aketagawa, Jun; Aizawa, Maki; Kobayashi, Yuki; Kawabata, Shun-Ichiro; Oda, Toshio

2017-02-01

The bacterial endotoxin test, which uses amebocyte lysate reagents of horseshoe crab origin, is a sensitive, reproducible and simple assay to measure endotoxin concentration. To develop sustainable raw materials for lysate reagents that do not require horseshoe crabs, three recombinant protease zymogens (factor C, derived from mammalian cells; factor B; and the proclotting enzyme derived from insect cells) were prepared using a genetic engineering technique. Recombinant cascade reagents (RCRs) were then prepared to reconstruct the reaction cascade in the amebocyte lysate reagent. The protease activity of the RCR containing recombinant factor C was much greater than that of recombinant factor C alone, indicating the efficiency of signal amplification in the cascade. Compared with the RCR containing the insect cell-derived factor C, those containing mammalian cell-derived factor C, which features different glycosylation patterns, were less susceptible to interference by the injectable drug components. The standard curve of the RCR containing mammalian cell-derived recombinant factor C had a steeper slope than the curves for those containing natural lysate reagents, suggesting a greater sensitivity to endotoxin. The present study supports the future production of recombinant reagents that do not require the use of natural resources.

Genetic engineering approach to develop next-generation reagents for endotoxin quantification

PubMed Central

Ogura, Norihiko; Aketagawa, Jun; Aizawa, Maki; Kobayashi, Yuki; Kawabata, Shun-ichiro; Oda, Toshio

2016-01-01

The bacterial endotoxin test, which uses amebocyte lysate reagents of horseshoe crab origin, is a sensitive, reproducible and simple assay to measure endotoxin concentration. To develop sustainable raw materials for lysate reagents that do not require horseshoe crabs, three recombinant protease zymogens (factor C, derived from mammalian cells; factor B; and the proclotting enzyme derived from insect cells) were prepared using a genetic engineering technique. Recombinant cascade reagents (RCRs) were then prepared to reconstruct the reaction cascade in the amebocyte lysate reagent. The protease activity of the RCR containing recombinant factor C was much greater than that of recombinant factor C alone, indicating the efficiency of signal amplification in the cascade. Compared with the RCR containing the insect cell-derived factor C, those containing mammalian cell-derived factor C, which features different glycosylation patterns, were less susceptible to interference by the injectable drug components. The standard curve of the RCR containing mammalian cell-derived recombinant factor C had a steeper slope than the curves for those containing natural lysate reagents, suggesting a greater sensitivity to endotoxin. The present study supports the future production of recombinant reagents that do not require the use of natural resources. PMID:27913792

Surface-initiated polymerization within mesoporous silica spheres for the modular design of charge-neutral polymer particles.

PubMed

Müllner, Markus; Cui, Jiwei; Noi, Ka Fung; Gunawan, Sylvia T; Caruso, Frank

2014-06-03

We report a templating approach for the preparation of functional polymer replica particles via surface-initiated polymerization in mesoporous silica templates. Subsequent removal of the template resulted in discrete polymer particles. Furthermore, redox-responsive replica particles could be engineered to disassemble in a reducing environment. Particles, made of poly(methacryloyloxyethyl phosphorylcholine) (PMPC) or poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA), exhibited very low association to human cancer cells (below 5%), which renders the reported charge-neutral polymer particles a modular and versatile class of highly functional carriers with potential applications in drug delivery.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

Research on collaborative innovation mechanism of green construction supply chain based on united agency

NASA Astrophysics Data System (ADS)

Zhang, Min; He, Weiyi

2018-06-01

Under the guidance of principal-agent theory and modular theory, the collaborative innovation of green technology-based companies, design contractors and project builders based on united agency will provide direction for the development of green construction supply chain in the future. After analyzing the existing independent agencies, this paper proposes the industry-university-research bilateral collaborative innovation network architecture and modularization with the innovative function of engineering design in the context of non-standard transformation interfaces, analyzes the innovation responsibility center, and gives some countermeasures and suggestions to promote the performance of bilateral cooperative innovation network.

Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering

PubMed Central

Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M. Teresa; Buchholz, Frank

2016-01-01

Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets. PMID:27444945

TVC actuator model. [for the space shuttle main engine

NASA Technical Reports Server (NTRS)

Baslock, R. W.

1977-01-01

A prototype Space Shuttle Main Engine (SSME) Thrust Vector Control (TVC) Actuator analog model was successfully completed. The prototype, mounted on five printed circuit (PC) boards, was delivered to NASA, checked out and tested using a modular replacement technique on an analog computer. In all cases, the prototype model performed within the recording techniques of the analog computer which is well within the tolerances of the specifications.

The final days of Solar Max - Lessons learned from engineering evaluation tests

NASA Technical Reports Server (NTRS)

Donnelly, Michael L.; Croft, John W.; Ward, David K.; Thames, Michael A.

1990-01-01

End-of-life engineering evaluation tests were performed on Solar Max between October and November 1989. The tests included four-wheel control law operation; reaction wheel rundowns; modular power subsystem standard power regulator unit voltage-temperature level tests; battery rundown/2nd plateau determination; high gain antenna retraction and jettison; and solar array jettison. This paper presents these tests, their results, and the lessons learned from them.

Developing an Integration Infrastructure for Distributed Engine Control Technologies

NASA Technical Reports Server (NTRS)

Culley, Dennis; Zinnecker, Alicia; Aretskin-Hariton, Eliot; Kratz, Jonathan

2014-01-01

Turbine engine control technology is poised to make the first revolutionary leap forward since the advent of full authority digital engine control in the mid-1980s. This change aims squarely at overcoming the physical constraints that have historically limited control system hardware on aero-engines to a federated architecture. Distributed control architecture allows complex analog interfaces existing between system elements and the control unit to be replaced by standardized digital interfaces. Embedded processing, enabled by high temperature electronics, provides for digitization of signals at the source and network communications resulting in a modular system at the hardware level. While this scheme simplifies the physical integration of the system, its complexity appears in other ways. In fact, integration now becomes a shared responsibility among suppliers and system integrators. While these are the most obvious changes, there are additional concerns about performance, reliability, and failure modes due to distributed architecture that warrant detailed study. This paper describes the development of a new facility intended to address the many challenges of the underlying technologies of distributed control. The facility is capable of performing both simulation and hardware studies ranging from component to system level complexity. Its modular and hierarchical structure allows the user to focus their interaction on specific areas of interest.

A novel nanobody-based target module for retargeting of T lymphocytes to EGFR-expressing cancer cells via the modular UniCAR platform

PubMed Central

Albert, Susann; Arndt, Claudia; Feldmann, Anja; Bachmann, Dominik; Koristka, Stefanie; Ludwig, Florian; Ziller-Walter, Pauline; Kegler, Alexandra; Gärtner, Sebastian; Schmitz, Marc; Ehninger, Armin; Cartellieri, Marc; Ehninger, Gerhard; Pietzsch, Hans-Jürgen; Steinbach, Jörg; Bachmann, Michael

2017-01-01

ABSTRACT Recent treatments of leukemias with chimeric antigen receptor (CAR) expressing T cells underline their impressive therapeutic potential. However, once adoptively transferred into patients, there is little scope left to shut them down after elimination of tumor cells or in case adverse side effects occur. This becomes of special relevance if they are directed against commonly expressed tumor associated antigens (TAAs) such as receptors of the ErbB family. To overcome this limitation, we recently established a modular CAR platform technology termed UniCAR. UniCARs are not directed against TAAs but instead against a unique peptide epitope on engineered recombinant targeting modules (TMs), which guide them to the target. In the absence of a TM UniCAR T cells are inactive. Thus an interruption of any UniCAR activity requires an elimination of unbound TM and the TM complexed with UniCAR T cells. Elimination of the latter one requires a disassembly of the UniCAR-TM complexes. Here, we describe a first nanobody (nb)-based TM directed against EGFR. The novel TM efficiently retargets UniCAR T cells to EGFR positive tumors and mediates highly efficient target-specific and target-dependent tumor cell lysis both in vitro and in vivo. After radiolabeling of the novel TM with 64Cu and 68Ga, we analyzed its biodistribution and clearance as well as the stability of the UniCAR-TM complexes. As expected unbound TM is rapidly eliminated while the elimination of the TM complexed with UniCAR T cells is delayed. Nonetheless, we show that UniCAR-TM complexes dissociate in vitro and in vivo in a concentration-dependent manner in line with the concept of a repeated stop and go retargeting of tumor cells via the UniCAR technology. PMID:28507794

Nucleotide sequences encoding a thermostable alkaline protease

DOEpatents

Wilson, D.B.; Lao, G.

1998-01-06

Nucleotide sequences, derived from a thermophilic actinomycete microorganism, which encode a thermostable alkaline protease are disclosed. Also disclosed are variants of the nucleotide sequences which encode a polypeptide having thermostable alkaline proteolytic activity. Recombinant thermostable alkaline protease or recombinant polypeptide may be obtained by culturing in a medium a host cell genetically engineered to contain and express a nucleotide sequence according to the present invention, and recovering the recombinant thermostable alkaline protease or recombinant polypeptide from the culture medium. 3 figs.

Performance modeling and techno-economic analysis of a modular concentrated solar power tower with latent heat storage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rea, Jonathan E.; Oshman, Christopher J.; Olsen, Michele L.

In this paper, we present performance simulations and techno-economic analysis of a modular dispatchable solar power tower. Using a heliostat field and power block three orders of magnitude smaller than conventional solar power towers, our unique configuration locates thermal storage and a power block directly on a tower receiver. To make the system dispatchable, a valved thermosyphon controls heat flow from a latent heat thermal storage tank to a Stirling engine. The modular design results in minimal balance of system costs and enables high deployment rates with a rapid realization of economies of scale. In this new analysis, we combinemore » performance simulations with techno-economic analysis to evaluate levelized cost of electricity, and find that the system has potential for cost-competitiveness with natural gas peaking plants and alternative dispatchable renewables.« less

A spatially localized architecture for fast and modular DNA computing

NASA Astrophysics Data System (ADS)

Chatterjee, Gourab; Dalchau, Neil; Muscat, Richard A.; Phillips, Andrew; Seelig, Georg

2017-09-01

Cells use spatial constraints to control and accelerate the flow of information in enzyme cascades and signalling networks. Synthetic silicon-based circuitry similarly relies on spatial constraints to process information. Here, we show that spatial organization can be a similarly powerful design principle for overcoming limitations of speed and modularity in engineered molecular circuits. We create logic gates and signal transmission lines by spatially arranging reactive DNA hairpins on a DNA origami. Signal propagation is demonstrated across transmission lines of different lengths and orientations and logic gates are modularly combined into circuits that establish the universality of our approach. Because reactions preferentially occur between neighbours, identical DNA hairpins can be reused across circuits. Co-localization of circuit elements decreases computation time from hours to minutes compared to circuits with diffusible components. Detailed computational models enable predictive circuit design. We anticipate our approach will motivate using spatial constraints for future molecular control circuit designs.

Ribo-attenuators: novel elements for reliable and modular riboswitch engineering.

PubMed

Folliard, Thomas; Mertins, Barbara; Steel, Harrison; Prescott, Thomas P; Newport, Thomas; Jones, Christopher W; Wadhams, George; Bayer, Travis; Armitage, Judith P; Papachristodoulou, Antonis; Rothschild, Lynn J

2017-07-04

Riboswitches are structural genetic regulatory elements that directly couple the sensing of small molecules to gene expression. They have considerable potential for applications throughout synthetic biology and bio-manufacturing as they are able to sense a wide range of small molecules and regulate gene expression in response. Despite over a decade of research they have yet to reach this considerable potential as they cannot yet be treated as modular components. This is due to several limitations including sensitivity to changes in genetic context, low tunability, and variability in performance. To overcome the associated difficulties with riboswitches, we have designed and introduced a novel genetic element called a ribo-attenuator in Bacteria. This genetic element allows for predictable tuning, insulation from contextual changes, and a reduction in expression variation. Ribo-attenuators allow riboswitches to be treated as truly modular and tunable components, thus increasing their reliability for a wide range of applications.

Challenges and opportunities in synthetic biology for chemical engineers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, YZ; Lee, JK; Zhao, HM

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. (C) 2012 Elsevier Ltd. All rights reserved.

Challenges and opportunities in synthetic biology for chemical engineers

PubMed Central

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

Challenges and opportunities in synthetic biology for chemical engineers.

PubMed

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.

Effects of pre-existing anti-carrier immunity and antigenic element multiplicity on efficacy of a modular virus-like particle vaccine.

PubMed

Chuan, Yap P; Rivera-Hernandez, Tania; Wibowo, Nani; Connors, Natalie K; Wu, Yang; Hughes, Fiona K; Lua, Linda H L; Middelberg, Anton P J

2013-09-01

Modularization of a peptide antigen for presentation on a microbially synthesized murine polyomavirus (MuPyV) virus-like particle (VLP) offers a new alternative for rapid and low-cost vaccine delivery at a global scale. In this approach, heterologous modules containing peptide antigenic elements are fused to and displayed on the VLP carrier, allowing enhancement of peptide immunogenicity via ordered and densely repeated presentation of the modules. This study addresses two key engineering questions pertaining to this platform, exploring the effects of (i) pre-existing carrier-specific immunity on modular VLP vaccine effectiveness and (ii) increase in the antigenic element number per VLP on peptide-specific immune response. These effects were studied in a mouse model and with modular MuPyV VLPs presenting a group A streptococcus (GAS) peptide antigen, J8i. The data presented here demonstrate that immunization with a modular VLP could induce high levels of J8i-specific antibodies despite a strong pre-existing anti-carrier immune response. Doubling of the J8i antigenic element number per VLP did not enhance J8i immunogenicity at a constant peptide dose. However, the strategy, when used in conjunction with increased VLP dose, could effectively increase the peptide dose up to 10-fold, leading to a significantly higher J8i-specific antibody titer. This study further supports feasibility of the MuPyV modular VLP vaccine platform by showing that, in the absence of adjuvant, modularized GAS antigenic peptide at a dose as low as 150 ng was sufficient to raise a high level of peptide-specific IgGs indicative of bactericidal activity. Copyright © 2013 Wiley Periodicals, Inc.

Orbit Transfer Rocket Engine Technology Program: Advanced engine study, task D.1/D.3

NASA Technical Reports Server (NTRS)

Martinez, A.; Erickson, C.; Hines, B.

1986-01-01

Concepts for space maintainability of OTV engines were examined. An engine design was developed which was driven by space maintenance requirements and by a failure mode and effects (FME) analysis. Modularity within the engine was shown to offer cost benefits and improved space maintenance capabilities. Space operable disconnects were conceptualized for both engine change-out and for module replacement. Through FME mitigation the modules were conceptualized to contain the least reliable and most often replaced engine components. A preliminary space maintenance plan was developed around a controls and condition monitoring system using advanced sensors, controls, and condition monitoring concepts. A complete engine layout was prepared satisfying current vehicle requirements and utilizing projected component advanced technologies. A technology plan for developing the required technology was assembled.

Computer program for a four-cylinder-Stirling-engine controls simulation

NASA Technical Reports Server (NTRS)

Daniels, C. J.; Lorenzo, C. F.

1982-01-01

A four cylinder Stirling engine, transient engine simulation computer program is presented. The program is intended for controls analysis. The associated engine model was simplified to shorten computer calculation time. The model includes engine mechanical drive dynamics and vehicle load effects. The computer program also includes subroutines that allow: (1) acceleration of the engine by addition of hydrogen to the system, and (2) braking of the engine by short circuiting of the working spaces. Subroutines to calculate degraded engine performance (e.g., due to piston ring and piston rod leakage) are provided. Input data required to run the program are described and flow charts are provided. The program is modular to allow easy modification of individual routines. Examples of steady state and transient results are presented.

Recombination Catalysts for Hypersonic Fuels

NASA Technical Reports Server (NTRS)

Chinitz, W.

1998-01-01

The goal of commercially-viable access to space will require technologies that reduce propulsion system weight and complexity, while extracting maximum energy from the products of combustion. This work is directed toward developing effective nozzle recombination catalysts for the supersonic and hypersonic aeropropulsion engines used to provide such access to space. Effective nozzle recombination will significantly reduce rk=le length (hence, propulsion system weight) and reduce fuel requirements, further decreasing the vehicle's gross lift-off weight. Two such catalysts have been identified in this work, barium and antimony compounds, by developing chemical kinetic reaction mechanisms for these materials and determining the engine performance enhancement for a typical flight trajectory. Significant performance improvements are indicated, using only 2% (mole or mass) of these compounds in the combustor product gas.

ADVANCED SEISMIC BASE ISOLATION METHODS FOR MODULAR REACTORS

DOE Office of Scientific and Technical Information (OSTI.GOV)

E. Blanford; E. Keldrauk; M. Laufer

2010-09-20

Advanced technologies for structural design and construction have the potential for major impact not only on nuclear power plant construction time and cost, but also on the design process and on the safety, security and reliability of next generation of nuclear power plants. In future Generation IV (Gen IV) reactors, structural and seismic design should be much more closely integrated with the design of nuclear and industrial safety systems, physical security systems, and international safeguards systems. Overall reliability will be increased, through the use of replaceable and modular equipment, and through design to facilitate on-line monitoring, in-service inspection, maintenance, replacement,more » and decommissioning. Economics will also receive high design priority, through integrated engineering efforts to optimize building arrangements to minimize building heights and footprints. Finally, the licensing approach will be transformed by becoming increasingly performance based and technology neutral, using best-estimate simulation methods with uncertainty and margin quantification. In this context, two structural engineering technologies, seismic base isolation and modular steel-plate/concrete composite structural walls, are investigated. These technologies have major potential to (1) enable standardized reactor designs to be deployed across a wider range of sites, (2) reduce the impact of uncertainties related to site-specific seismic conditions, and (3) alleviate reactor equipment qualification requirements. For Gen IV reactors the potential for deliberate crashes of large aircraft must also be considered in design. This report concludes that base-isolated structures should be decoupled from the reactor external event exclusion system. As an example, a scoping analysis is performed for a rectangular, decoupled external event shell designed as a grillage. This report also reviews modular construction technology, particularly steel-plate/concrete construction using factory prefabricated structural modules, for application to external event shell and base isolated structures.« less

New strategies for genetic engineering Pseudomonas syringae using recombination

USDA-ARS?s Scientific Manuscript database

Here we report that DNA oligonucleotides (oligos) introduced directly into bacteria by electroporation can recombine with the bacterial chromosome. This phenomenon was identified in Pseudomonas syringae and we subsequently found that Escherichia coli, Salmonella typhimurium and Shigella flexneri are...

Dual transcriptional-translational cascade permits cellular level tuneable expression control

PubMed Central

Morra, Rosa; Shankar, Jayendra; Robinson, Christopher J.; Halliwell, Samantha; Butler, Lisa; Upton, Mathew; Hay, Sam; Micklefield, Jason; Dixon, Neil

2016-01-01

The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The discovery, design and reengineering of riboswitches offer an alternative means by which to control gene expression. Here we report the development and characterization of a novel tunable recombinant expression system, termed RiboTite, which operates at both the transcriptional and translational level. Using standard inducible promoters and orthogonal riboswitches, a multi-layered modular genetic control circuit was developed to control the expression of both bacteriophage T7 RNA polymerase and recombinant gene(s) of interest. The system was benchmarked against a number of commonly used E. coli expression systems, and shows tight basal control, precise analogue tunability of gene expression at the cellular level, dose-dependent regulation of protein production rates over extended growth periods and enhanced cell viability. This novel system expands the number of E. coli expression systems for use in recombinant protein production and represents a major performance enhancement over and above the most widely used expression systems. PMID:26405200

Generation of recombinant rotaviruses expressing fluorescent proteins using an optimized reverse genetics system.

PubMed

Komoto, Satoshi; Fukuda, Saori; Ide, Tomihiko; Ito, Naoto; Sugiyama, Makoto; Yoshikawa, Tetsushi; Murata, Takayuki; Taniguchi, Koki

2018-04-18

An entirely plasmid-based reverse genetics system for rotaviruses was established very recently. We improved the reverse genetics system to generate recombinant rotavirus by transfecting only 11 cDNA plasmids for its 11 gene segments under the condition of increasing the ratio of the cDNA plasmids for NSP2 and NSP5 genes. Utilizing this highly efficient system, we then engineered infectious recombinant rotaviruses expressing bioluminescent (NanoLuc luciferase) and fluorescent (EGFP and mCherry) reporters. These recombinant rotaviruses expressing reporters remained genetically stable during serial passages. Our reverse genetics approach and recombinant rotaviruses carrying reporter genes will be great additions to the tool kit for studying the molecular virology of rotavirus, and for developing future next-generation vaccines and expression vectors. IMPORTANCE Rotavirus is one of the most important pathogens causing severe gastroenteritis in young children worldwide. In this paper, we describe a robust and simple reverse genetics system based on only rotavirus cDNAs, and its application for engineering infectious recombinant rotaviruses harboring bioluminescent (NanoLuc) and fluorescent (EGFP and mCherry) protein genes. This highly efficient reverse genetics system and recombinant RVAs expressing reporters could be powerful tools for the study of different aspects of rotavirus replication. Furthermore, they may be useful for next-generation vaccine production for this medically important virus. Copyright © 2018 American Society for Microbiology.

Evaluating 3D-printed biomaterials as scaffolds for vascularized bone tissue engineering.

PubMed

Wang, Martha O; Vorwald, Charlotte E; Dreher, Maureen L; Mott, Eric J; Cheng, Ming-Huei; Cinar, Ali; Mehdizadeh, Hamidreza; Somo, Sami; Dean, David; Brey, Eric M; Fisher, John P

2015-01-07

There is an unmet need for a consistent set of tools for the evaluation of 3D-printed constructs. A toolbox developed to design, characterize, and evaluate 3D-printed poly(propylene fumarate) scaffolds is proposed for vascularized engineered tissues. This toolbox combines modular design and non-destructive fabricated design evaluation, evaluates biocompatibility and mechanical properties, and models angiogenesis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

PubMed Central

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs. PMID:28670307

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

PubMed

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of "microbial ecological power" observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to "discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems," we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs.

MODULAR FIELD-BIOREACTOR FOR ACID MINE DRAINAGE TREATMENT

EPA Science Inventory

The presentation focuses on the improvements to engineered features of a passive technology that has been used for remediation of acid rock drainage (ARD). This passive remedial technology, a sulfate-reducing bacteria (SRB) bioreactor, takes advantage of the ability of SRB that,...

Crew appliance concepts. Volume 5, appendix C: Modular space station appliances supporting engineering data

NASA Technical Reports Server (NTRS)

Proctor, B. W.; Reysa, R. P.; Russell, D. J.

1975-01-01

Housekeeping, off-duty, and medical data concerning the appliances considered for the space station are presented. Appliance functions analyzed include: cleanup, collection, processing and storage of refuse; crew entertainment and physical exercise, and the autoclaves and ergometers.

Modular evolution of phosphorylation-based signalling systems

PubMed Central

Jin, Jing; Pawson, Tony

2012-01-01

Phosphorylation sites are formed by protein kinases (‘writers’), frequently exert their effects following recognition by phospho-binding proteins (‘readers’) and are removed by protein phosphatases (‘erasers’). This writer–reader–eraser toolkit allows phosphorylation events to control a broad range of regulatory processes, and has been pivotal in the evolution of new functions required for the development of multi-cellular animals. The proteins that comprise this system of protein kinases, phospho-binding targets and phosphatases are typically modular in organization, in the sense that they are composed of multiple globular domains and smaller peptide motifs with binding or catalytic properties. The linkage of these binding and catalytic modules in new ways through genetic recombination, and the selection of particular domain combinations, has promoted the evolution of novel, biologically useful processes. Conversely, the joining of domains in aberrant combinations can subvert cell signalling and be causative in diseases such as cancer. Major inventions such as phosphotyrosine (pTyr)-mediated signalling that flourished in the first multi-cellular animals and their immediate predecessors resulted from stepwise evolutionary progression. This involved changes in the binding properties of interaction domains such as SH2 and their linkage to new domain types, and alterations in the catalytic specificities of kinases and phosphatases. This review will focus on the modular aspects of signalling networks and the mechanism by which they may have evolved. PMID:22889906

Recombinant lactobacillus for fermentation of xylose to lactic acid and lactate

DOEpatents

Picataggio, Stephen K.; Zhang, Min; Franden, Mary Ann; Mc Millan, James D.; Finkelstein, Mark

1998-01-01

A recombinant Lactobacillus MONT4 is provided which has been genetically engineered with xylose isomerase and xylulokinase genes from Lactobacillus pentosus to impart to the Lactobacillus MONT4 the ability to ferment lignocellulosic biomass containing xylose to lactic acid.

Development of an optical character recognition pipeline for handwritten form fields from an electronic health record.

PubMed

Rasmussen, Luke V; Peissig, Peggy L; McCarty, Catherine A; Starren, Justin

2012-06-01

Although the penetration of electronic health records is increasing rapidly, much of the historical medical record is only available in handwritten notes and forms, which require labor-intensive, human chart abstraction for some clinical research. The few previous studies on automated extraction of data from these handwritten notes have focused on monolithic, custom-developed recognition systems or third-party systems that require proprietary forms. We present an optical character recognition processing pipeline, which leverages the capabilities of existing third-party optical character recognition engines, and provides the flexibility offered by a modular custom-developed system. The system was configured and run on a selected set of form fields extracted from a corpus of handwritten ophthalmology forms. The processing pipeline allowed multiple configurations to be run, with the optimal configuration consisting of the Nuance and LEADTOOLS engines running in parallel with a positive predictive value of 94.6% and a sensitivity of 13.5%. While limitations exist, preliminary experience from this project yielded insights on the generalizability and applicability of integrating multiple, inexpensive general-purpose third-party optical character recognition engines in a modular pipeline.

Development of an optical character recognition pipeline for handwritten form fields from an electronic health record

PubMed Central

Peissig, Peggy L; McCarty, Catherine A; Starren, Justin

2011-01-01

Background Although the penetration of electronic health records is increasing rapidly, much of the historical medical record is only available in handwritten notes and forms, which require labor-intensive, human chart abstraction for some clinical research. The few previous studies on automated extraction of data from these handwritten notes have focused on monolithic, custom-developed recognition systems or third-party systems that require proprietary forms. Methods We present an optical character recognition processing pipeline, which leverages the capabilities of existing third-party optical character recognition engines, and provides the flexibility offered by a modular custom-developed system. The system was configured and run on a selected set of form fields extracted from a corpus of handwritten ophthalmology forms. Observations The processing pipeline allowed multiple configurations to be run, with the optimal configuration consisting of the Nuance and LEADTOOLS engines running in parallel with a positive predictive value of 94.6% and a sensitivity of 13.5%. Discussion While limitations exist, preliminary experience from this project yielded insights on the generalizability and applicability of integrating multiple, inexpensive general-purpose third-party optical character recognition engines in a modular pipeline. PMID:21890871

Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins.

PubMed

Delic, Marizela; Göngrich, Rebecca; Mattanovich, Diethard; Gasser, Brigitte

2014-07-20

Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.

[Culture conditions of engineered strain of L-asparaginase and the recombinant plasmid stability].

PubMed

Wang, Y; Qian, S; Ye, J; Meng, G; Zhang, S

1999-12-01

The growth curves of engineered strain JM105(pASN) were different in LB and M-3 media. The expression level and activity of L-asparaginase were affected apparently by both biomass and induction time. Glucose repression of production of L-asparaginase was found. The stability of the recombinant plasmid pASN in different host strains and in LB and M-3 media was determined. After cultivation inLB broth and M-3 media at 30 degrees C for more than 50 generations without antibiotic selection, then induced at 42 degrees C for up to 5 h, the engineered strains were proved to be stable, except for DHA alpha (pASN).

Expanding the Scope of Site-Specific Recombinases for Genetic and Metabolic Engineering

PubMed Central

Gaj, Thomas; Sirk, Shannon J.; Barbas, Carlos F.

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. PMID:23982993

Recombinant DNA production of spider silk proteins.

PubMed

Tokareva, Olena; Michalczechen-Lacerda, Valquíria A; Rech, Elíbio L; Kaplan, David L

2013-11-01

Spider dragline silk is considered to be the toughest biopolymer on Earth due to an extraordinary combination of strength and elasticity. Moreover, silks are biocompatible and biodegradable protein-based materials. Recent advances in genetic engineering make it possible to produce recombinant silks in heterologous hosts, opening up opportunities for large-scale production of recombinant silks for various biomedical and material science applications. We review the current strategies to produce recombinant spider silks. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Modular flow chamber for engineering bone marrow architecture and function.

PubMed

Di Buduo, Christian A; Soprano, Paolo M; Tozzi, Lorenzo; Marconi, Stefania; Auricchio, Ferdinando; Kaplan, David L; Balduini, Alessandra

2017-11-01

The bone marrow is a soft, spongy, gelatinous tissue found in the hollow cavities of flat and long bones that support hematopoiesis in order to maintain the physiologic turnover of all blood cells. Silk fibroin, derived from Bombyx mori silkworm cocoons, is a promising biomaterial for bone marrow engineering, because of its tunable architecture and mechanical properties, the capacity of incorporating labile compounds without loss of bioactivity and demonstrated ability to support blood cell formation. In this study, we developed a bone marrow scaffold consisting of a modular flow chamber made of polydimethylsiloxane, holding a silk sponge, prepared with salt leaching methods and functionalized with extracellular matrix components. The silk sponge was able to support efficient platelet formation when megakaryocytes were seeded in the system. Perfusion of the chamber allowed the recovery of functional platelets based on multiple activation tests. Further, inhibition of AKT signaling molecule, which has been shown to be crucial in regulating physiologic platelet formation, significantly reduced the number of collected platelets, suggesting the applicability of this tissue model for evaluation of the effects of bone marrow exposure to compounds that may affect platelet formation. In conclusion, we have bioengineered a novel modular system that, along with multi-porous silk sponges, can provide a useful technology for reproducing a simplified bone marrow scaffold for blood cell production ex vivo. Copyright © 2017 Elsevier Ltd. All rights reserved.

L-Cysteine Production in Escherichia coli Based on Rational Metabolic Engineering and Modular Strategy.

PubMed

Liu, Han; Fang, Guochen; Wu, Hui; Li, Zhimin; Ye, Qin

2018-05-01

L-cysteine is an amino acid with important physiological functions and has a wide range of applications in medicine, food, animal feed, and cosmetics industry. In this study, the L-cysteine synthesis in Escherichia coliEscherichia coli is divided into four modules: the transport module, sulfur module, precursor module, and degradation module. The engineered strain LH03 (overexpression of the feedback-insensitive cysE and the exporter ydeD in JM109) accumulated 45.8 mg L -1 of L-cysteine in 48 hr with yield of 0.4% g/g glucose. Further modifications of strains and culture conditions which based on the rational metabolic engineering and modular strategy improved the L-cysteine biosynthesis significantly. The engineered strain LH06 (with additional overexpression of serA, serC, and serB and double mutant of tnaA and sdaA in LH03) produced 620.9 mg L -1 of L-cysteine with yield of 6.0% g/g glucose, which increased the production by 12 times and the yield by 14 times more than those of LH03 in the original condition. In fed-batch fermentation performed in a 5-L reactor, the concentration of L-cysteine achieved 5.1 g L -1 in 32 hr. This work demonstrates that the combination of rational metabolic engineering and module strategy is a promising approach for increasing the L-cysteine production in E. coli. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recombinant lactobacillus for fermentation of xylose to lactic acid and lactate

DOEpatents

Picataggio, S.K.; Zhang, M.; Franden, M.A.; McMillan, J.D.; Finkelstein, M.

1998-08-25

A recombinant Lactobacillus MONT4 is provided which has been genetically engineered with xylose isomerase and xylulokinase genes from Lactobacillus pentosus to impart to the Lactobacillus MONT4 the ability to ferment lignocellulosic biomass containing xylose to lactic acid. 4 figs.

Engineer Medium and Feed for Modulating N-Glycosylation of Recombinant Protein Production in CHO Cell Culture.

PubMed

Fan, Yuzhou; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

2017-01-01

Chinese hamster ovary (CHO) cells have become the primary expression system for the production of complex recombinant proteins due to their long-term success in industrial scale production and generating appropriate protein N-glycans similar to that of humans. Control and optimization of protein N-glycosylation is crucial, as the structure of N-glycans can largely influence both biological and physicochemical properties of recombinant proteins. Protein N-glycosylation in CHO cell culture can be controlled and tuned by engineering medium, feed, culture process, as well as genetic elements of the cell. In this chapter, we will focus on how to carry out experiments for N-glycosylation modulation through medium and feed optimization. The workflow and typical methods involved in the experiment process will be presented.

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

PubMed Central

2011-01-01

Background Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. Results We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism’s metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. Conclusions After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis. PMID:22784571

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

PubMed

Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

2011-01-01

Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

Modular closed-loop control of diabetes.

PubMed

Patek, S D; Magni, L; Dassau, E; Karvetski, C; Toffanin, C; De Nicolao, G; Del Favero, S; Breton, M; Man, C Dalla; Renard, E; Zisser, H; Doyle, F J; Cobelli, C; Kovatchev, B P

2012-11-01

Modularity plays a key role in many engineering systems, allowing for plug-and-play integration of components, enhancing flexibility and adaptability, and facilitating standardization. In the control of diabetes, i.e., the so-called "artificial pancreas," modularity allows for the step-wise introduction of (and regulatory approval for) algorithmic components, starting with subsystems for assured patient safety and followed by higher layer components that serve to modify the patient's basal rate in real time. In this paper, we introduce a three-layer modular architecture for the control of diabetes, consisting in a sensor/pump interface module (IM), a continuous safety module (CSM), and a real-time control module (RTCM), which separates the functions of insulin recommendation (postmeal insulin for mitigating hyperglycemia) and safety (prevention of hypoglycemia). In addition, we provide details of instances of all three layers of the architecture: the APS© serving as the IM, the safety supervision module (SSM) serving as the CSM, and the range correction module (RCM) serving as the RTCM. We evaluate the performance of the integrated system via in silico preclinical trials, demonstrating 1) the ability of the SSM to reduce the incidence of hypoglycemia under nonideal operating conditions and 2) the ability of the RCM to reduce glycemic variability.

The development of a lightweight modular compliant surface bio-inspired robot

NASA Astrophysics Data System (ADS)

Stone, David L.; Cranney, John

2004-09-01

The DARPA Sponsored Compliant Surface Robotics (CSR) program pursues development of a high mobility, lightweight, modular, morphable robot for military forces in the field and for other industrial uses. The USTLAB effort builds on proof of concept feasibility studies and demonstration of a 4, 6, or 8 wheeled modular vehicle with articulated leg-wheel assemblies. In Phase I, basic open plant stability was proven for climbing over obstacles of ~18 inches high and traversing ~75 degree inclines (up, down, or sideways) in a platform of approximately 15 kilograms. At the completion of Phase II, we have completed mechanical and electronics engineering design and achieved changes which currently enable future work in active articulation, enabling autonomous reconfiguration for a wide variety of terrains, including upside down operations (in case of flip over), and we have reduced platform weight by one third. Currently the vehicle weighs 10 kilograms and will grow marginally as additional actuation, MEMS based organic sensing, payload, and autonomous processing is added. The CSR vehicle"s modular spider-like configuration facilitates adaptation to many uses and compliance over rugged terrain. The developmental process and the vehicle characteristics will be discussed.

The application of SMA spring actuators to a lightweight modular compliant surface bioinspired robot

NASA Astrophysics Data System (ADS)

Stone, David L.; Cranney, John; Liang, Robert; Taya, Minoru

2004-07-01

The DARPA Sponsored Compliant Surface Robotics (CSR) program pursues development of a high mobility, lightweight, modular, morph-able robot for military forces in the field and for other industrial uses. The USTLAB and University of Washington Center for Intelligent Materials and Systems (CIMS) effort builds on USTLAB proof of concept feasibility studies and demonstration of a 4, 6, or 8 wheeled modular vehicle with articulated leg-wheel assemblies. A collaborative effort between USTLAB and UW-CIMS explored the application of Shape Memory Alloy Nickel Titanium Alloy springs to a leg extension actuator capable of actuating with 4.5 Newton force over a 50 mm stroke. At the completion of Phase II, we have completed mechanical and electronics engineering design and achieved conventional actuation which currently enable active articulation, enabling autonomous reconfiguration for a wide variety of terrains, including upside down operations (in case of flip over), have developed a leg extension actuator demonstration model, and we have positioned our team to pursue a small vehicle with leg extension actuators in follow on work. The CSR vehicle's modular spider-like configuration facilitates adaptation to many uses and compliance over rugged terrain. The developmental process, actuator and vehicle characteristics will be discussed.

Cell Engineering and Molecular Pharming for Biopharmaceuticals

PubMed Central

Abdullah, M.A; Rahmah, Anisa ur; Sinskey, A.J; Rha, C.K

2008-01-01

Biopharmaceuticals are often produced by recombinant E. coli or mammalian cell lines. This is usually achieved by the introduction of a gene or cDNA coding for the protein of interest into a well-characterized strain of producer cells. Naturally, each recombinant production system has its own unique advantages and disadvantages. This paper examines the current practices, developments, and future trends in the production of biopharmaceuticals. Platform technologies for rapid screening and analyses of biosystems are reviewed. Strategies to improve productivity via metabolic and integrated engineering are also highlighted. PMID:19662143

Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli.

PubMed

Thomason, Lynn C; Costantino, Nina; Court, Donald L

2016-09-13

Recombineering, in vivo genetic engineering with bacteriophage homologous recombination systems, is a powerful technique for making genetic modifications in bacteria. Two systems widely used in Escherichia coli are the Red system from phage λ and RecET from the defective Rac prophage. We investigated the in vivo dependence of recombineering on DNA replication of the recombining substrate using plasmid targets. For λ Red recombination, when DNA replication of a circular target plasmid is prevented, recombination with single-stranded DNA oligonucleotides is greatly reduced compared to that under replicating conditions. For RecET recombination, when DNA replication of the targeted plasmid is prevented, the recombination frequency is also reduced, to a level identical to that seen for the Red system in the absence of replication. The very low level of oligonucleotide recombination observed in the absence of any phage recombination functions is the same in the presence or absence of DNA replication. In contrast, both the Red and RecET systems recombine a nonreplicating linear dimer plasmid with high efficiency to yield a circular monomer. Therefore, the DNA replication requirement is substrate dependent. Our data are consistent with recombination by both the Red and RecET systems occurring predominately by single-strand annealing rather than by strand invasion. Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli. Copyright © 2016 Thomason et al.

A Closer Look at 804: A Summary of Considerations for DoD Program Managers

DTIC Science & Technology

2011-12-01

aimed at changing the culture from one that is fo- cused typically on a single delivery to a new model that comprises multiple deliveries to es...under the Agency CIOs, and de - velop flexible budget models that align with modular development. • Launch an interactive platform for pre-RFP agency...permission@sei.cmu.edu. TM Carnegie Mellon Software Engineering Institute (stylized), Carnegie Mellon Software Engineering Institute (and de - sign), Simplex

LEGO® Bricks as Building Blocks for Centimeter-Scale Biological Environments: The Case of Plants

PubMed Central

Lind, Kara R.; Sizmur, Tom; Benomar, Saida; Miller, Anthony; Cademartiri, Ludovico

2014-01-01

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil. PMID:24963716

LEGO® bricks as building blocks for centimeter-scale biological environments: the case of plants.

PubMed

Lind, Kara R; Sizmur, Tom; Benomar, Saida; Miller, Anthony; Cademartiri, Ludovico

2014-01-01

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.

A FIELD STUDY WITH GENETICALLY ENGINEERED ALFALFA INOCULATED WITH RECOMBINANT SINORHIZOBIUM MELILOTI: EFFECTS ON THE SOIL ECOSYSTEM

EPA Science Inventory

The agricultural use of genetically engineered plants and microorganisms has become increasingly common. Because genetically engineered plants and microorganisms can produce compounds foreign to their environment, there is concern that they may become established outside of thei...

Genetically Engineered Virulent Phage Banks in the Detection and Control of Emergent Pathogenic Bacteria

PubMed Central

Blois, Hélène; Iris, François

2010-01-01

Natural outbreaks of multidrug-resistant microorganisms can cause widespread devastation, and several can be used or engineered as agents of bioterrorism. From a biosecurity standpoint, the capacity to detect and then efficiently control, within hours, the spread and the potential pathological effects of an emergent outbreak, for which there may be no effective antibiotics or vaccines, become key challenges that must be met. We turned to phage engineering as a potentially highly flexible and effective means to both detect and eradicate threats originating from emergent (uncharacterized) bacterial strains. To this end, we developed technologies allowing us to (1) concurrently modify multiple regions within the coding sequence of a gene while conserving intact the remainder of the gene, (2) reversibly interrupt the lytic cycle of an obligate virulent phage (T4) within its host, (3) carry out efficient insertion, by homologous recombination, of any number of engineered genes into the deactivated genomes of a T4 wild-type phage population, and (4) reactivate the lytic cycle, leading to the production of engineered infective virulent recombinant progeny. This allows the production of very large, genetically engineered lytic phage banks containing, in an E. coli host, a very wide spectrum of variants for any chosen phage-associated function, including phage host-range. Screening of such a bank should allow the rapid isolation of recombinant T4 particles capable of detecting (ie, diagnosing), infecting, and destroying hosts belonging to gram-negative bacterial species far removed from the original E. coli host. PMID:20569057

FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori

USDA-ARS?s Scientific Manuscript database

A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they h...

Enhanced functional recombinant factor VII production by HEK 293 cells stably transfected with VKORC1 where the gamma-carboxylase inhibitor calumenin is stably suppressed by shRNA transfection.

PubMed

Wajih, Nadeem; Owen, John; Wallin, Reidar

2008-01-01

Recombinant members of the vitamin K-dependent protein family (factors IX and VII and protein C) have become important pharmaceuticals in treatment of bleeding disorders and sepsis. However, because the in vivo gamma-carboxylation system in stable cell lines used for transfection has a limited capacity of post translational gamma-carboxylation, the recovery of fully gamma-carboxylated and functional proteins is low. In this work we have engineered recombinant factor VII producing HEK 293 cells to stably overexpress VKORC1, the reduced vitamin K gamma-carboxylase cofactor and in addition stably silenced the gamma-carboxylase inhibitory protein calumenin. Stable cell lines transfected with only a factor VII cDNA had a 9% production of functional recombinant factor VII. On the other hand, these recombinant factor VII producing cells when engineered to overexpress VKORC1 and having calumenin stably suppressed more than 80% by shRNA expression, produced 68% functional factor VII. The technology presented should be applicable to all vertebrae members of the vitamin K-dependent protein family and should lower the production cost of the clinically used factors VII, IX and protein C.

Genetically Programmable Thermoresponsive Plasmonic Gold/Silk-Elastin Protein Core/Shell Nanoparticles

PubMed Central

2015-01-01

The design and development of future molecular photonic/electronic systems pose the challenge of integrating functional molecular building blocks in a controlled, tunable, and reproducible manner. The modular nature and fidelity of the biosynthesis method provides a unique chemistry approach to one-pot synthesis of environmental factor-responsive chimeric proteins capable of energy conversion between the desired forms. In this work, facile tuning of dynamic thermal response in plasmonic nanoparticles was facilitated by genetic engineering of the structure, size, and self-assembly of the shell silk-elastin-like protein polymers (SELPs). Recombinant DNA techniques were implemented to synthesize a new family of SELPs, S4E8Gs, with amino acid repeats of [(GVGVP)4(GGGVP)(GVGVP)3(GAGAGS)4] and tunable molecular weight. The temperature-reversible conformational switching between the hydrophilic random coils and the hydrophobic β-turns in the elastin blocks were programmed to between 50 and 60 °C by site-specific glycine mutation, as confirmed by variable-temperature proton NMR and circular dichroism (CD) spectroscopy, to trigger the nanoparticle aggregation. The dynamic self-aggregation/disaggregation of the Au-SELPs nanoparticles was regulated in size and pattern by the β-sheet-forming, thermally stable silk blocks, as revealed by transmission electron microscopy (TEM) and dynamic light scattering (DLS). The thermally reversible, shell dimension dependent, interparticle plasmon coupling was investigated by both variable-temperature UV–vis spectroscopy and finite-difference time-domain (FDTD)-based simulations. Good agreement between the calculated and measured spectra sheds light on design and synthesis of responsive plasmonic nanostructures by independently tuning the refractive index and size of the SELPs through genetic engineering. PMID:24712906

Modulation of Estrogen Response Element-Driven Gene Expressions and Cellular Proliferation with Polar Directions by Designer Transcription Regulators

PubMed Central

Muyan, Mesut; Güpür, Gizem; Yaşar, Pelin; Ayaz, Gamze; User, Sırma Damla; Kazan, Hasan Hüseyin; Huang, Yanfang

2015-01-01

Estrogen receptor α (ERα), as a ligand-dependent transcription factor, mediates 17β-estradiol (E2) effects. ERα is a modular protein containing a DNA binding domain (DBD) and transcription activation domains (AD) located at the amino- and carboxyl-termini. The interaction of the E2-activated ERα dimer with estrogen response elements (EREs) of genes constitutes the initial step in the ERE-dependent signaling pathway necessary for alterations of cellular features. We previously constructed monomeric transcription activators, or monotransactivators, assembled from an engineered ERE-binding module (EBM) using the ERα-DBD and constitutively active ADs from other transcription factors. Monotransactivators modulated cell proliferation by activating and repressing ERE-driven gene expressions that simulate responses observed with E2-ERα. We reasoned here that integration of potent heterologous repression domains (RDs) into EBM could generate monotransrepressors that alter ERE-bearing gene expressions and cellular proliferation in directions opposite to those observed with E2-ERα or monotransactivators. Consistent with this, monotransrepressors suppressed reporter gene expressions that emulate the ERE-dependent signaling pathway. Moreover, a model monotransrepressor regulated DNA synthesis, cell cycle progression and proliferation of recombinant adenovirus infected ER-negative cells through decreasing as well as increasing gene expressions with polar directions compared with E2-ERα or monotransactivator. Our results indicate that an ‘activator’ or a ‘repressor’ possesses both transcription activating/enhancing and repressing/decreasing abilities within a chromatin context. Offering a protein engineering platform to alter signal pathway-specific gene expressions and cell growth, our approach could also be used for the development of tools for epigenetic modifications and for clinical interventions wherein multigenic de-regulations are an issue. PMID:26295471

Simulating Operation of a Large Turbofan Engine

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Frederick, Dean K.; DeCastro, Jonathan

2008-01-01

The Commercial Modular Aero- Propulsion System Simulation (C-MAPSS) is a computer program for simulating transient operation of a commercial turbofan engine that can generate as much as 90,000 lb (.0.4 MN) of thrust. It includes a power-management system that enables simulation of open- or closed-loop engine operation over a wide range of thrust levels throughout the full range of flight conditions. C-MAPSS provides the user with a set of tools for performing open- and closed-loop transient simulations and comparison of linear and non-linear models throughout its operating envelope, in an easy-to-use graphical environment.

FAST Modularization Framework for Wind Turbine Simulation: Full-System Linearization

DOE PAGES

Jonkman, Jason M.; Jonkman, Bonnie J.

2016-10-03

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well-established methods and tools for analyzing linear systems. Here, this paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

FAST modularization framework for wind turbine simulation: full-system linearization

NASA Astrophysics Data System (ADS)

Jonkman, J. M.; Jonkman, B. J.

2016-09-01

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well- established methods and tools for analyzing linear systems. This paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

Broad host range vectors for expression of proteins with (Twin-) Strep-tag, His-tag and engineered, export optimized yellow fluorescent protein

PubMed Central

2013-01-01

Background In current protein research, a limitation still is the production of active recombinant proteins or native protein associations to assess their function. Especially the localization and analysis of protein-complexes or the identification of modifications and small molecule interaction partners by co-purification experiments requires a controllable expression of affinity- and/or fluorescence tagged variants of a protein of interest in its native cellular background. Advantages of periplasmic and/or homologous expressions can frequently not be realized due to a lack of suitable tools. Instead, experiments are often limited to the heterologous production in one of the few well established expression strains. Results Here, we introduce a series of new RK2 based broad host range expression plasmids for inducible production of affinity- and fluorescence tagged proteins in the cytoplasm and periplasm of a wide range of Gram negative hosts which are designed to match the recently suggested modular Standard European Vector Architecture and database. The vectors are equipped with a yellow fluorescent protein variant which is engineered to fold and brightly fluoresce in the bacterial periplasm following Sec-mediated export, as shown from fractionation and imaging studies. Expression of Strep-tag®II and Twin-Strep-tag® fusion proteins in Pseudomonas putida KT2440 is demonstrated for various ORFs. Conclusion The broad host range constructs we have produced enable good and controlled expression of affinity tagged protein variants for single-step purification and qualify for complex co-purification experiments. Periplasmic export variants enable production of affinity tagged proteins and generation of fusion proteins with a novel engineered Aequorea-based yellow fluorescent reporter protein variant with activity in the periplasm of the tested Gram-negative model bacteria Pseudomonas putida KT2440 and Escherichia coli K12 for production, localization or co-localization studies. In addition, the new tools facilitate metabolic engineering and yield assessment for cytoplasmic or periplasmic protein production in a number of different expression hosts when yields in one initially selected are insufficient. PMID:23687945

The development of a post-test diagnostic system for rocket engines

NASA Technical Reports Server (NTRS)

Zakrajsek, June F.

1991-01-01

An effort was undertaken by NASA to develop an automated post-test, post-flight diagnostic system for rocket engines. The automated system is designed to be generic and to automate the rocket engine data review process. A modular, distributed architecture with a generic software core was chosen to meet the design requirements. The diagnostic system is initially being applied to the Space Shuttle Main Engine data review process. The system modules currently under development are the session/message manager, and portions of the applications section, the component analysis section, and the intelligent knowledge server. An overview is presented of a rocket engine data review process, the design requirements and guidelines, the architecture and modules, and the projected benefits of the automated diagnostic system.

CONSTRUCTION OF MODULAR FIELD-BIOREACTOR FOR ACID MINE DRAINAGE TREATMENT

EPA Science Inventory

The paper focuses on the improvements to engineered features of a passive technology that has been used for remediation of acid rock drainage (ARD). This passive remedial technology, a sulfate-reducing bacteria (SRB) bioreactor, takes advantage of the ability of SRB that, if sup...

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT: IN-DRAIN TREATMENT DEVICE. HYDRO INTERNATIONAL UP-FLO™ FILTER

EPA Science Inventory

Verification testing of the Hydro International Up-Flo™ Filter with one filter module and CPZ Mix™ filter media was conducted at the Penn State Harrisburg Environmental Engineering Laboratory in Middletown, Pennsylvania. The Up-Flo™ Filter is designed as a passive, modular filtr...

MOUSE (MODULAR ORIENTED UNCERTAINTY SYSTEM): A COMPUTERIZED UNCERTAINTY ANALYSIS SYSTEM (FOR MICRO- COMPUTERS)

EPA Science Inventory

Environmental engineering calculations involving uncertainties; either in the model itself or in the data, are far beyond the capabilities of conventional analysis for any but the simplest of models. There exist a number of general-purpose computer simulation languages, using Mon...

Engineered outer membrane vesicle is potent to elicit HPV16E7-specific cellular immunity in a mouse model of TC-1 graft tumor.

PubMed

Wang, Shijie; Huang, Weiwei; Li, Kui; Yao, Yufeng; Yang, Xu; Bai, Hongmei; Sun, Wenjia; Liu, Cunbao; Ma, Yanbing

2017-01-01

Currently, therapeutic tumor vaccines under development generally lack significant effects in human clinical trials. Exploring a powerful antigen delivery system is a potential approach to improve vaccine efficacy. We sought to explore engineered bacterial outer membrane vesicles (OMVs) as a new vaccine carrier for efficiently delivering tumor antigens and provoking robust antitumor immune responses. First, the tumoral antigen human papillomavirus type 16 early protein E7 (HPV16E7) was presented on Escherichia coli -derived OMVs by genetic engineering methods, acquiring the recombinant OMV vaccine. Second, the ability of recombinant OMVs delivering their components and the model antigen green fluorescent protein to antigen-presenting cells was investigated in the macrophage Raw264.7 cells and in bone marrow-derived dendritic cells in vitro. Third, it was evaluated in TC-1 graft tumor model in mice that the recombinant OMVs displaying HPV16E7 stimulated specific cellular immune response and intervened the growth of established tumor. E. coli DH5α-derived OMVs could be taken up rapidly by dendritic cells, for which vesicle structure has been proven to be important. OMVs significantly stimulated the expression of dendritic cellmaturation markers CD80, CD86, CD83 and CD40. The HPV16E7 was successfully embedded in engineered OMVs through gene recombinant techniques. Subcutaneous immunization with the engineered OMVs induced E7 antigen-specific cellular immune responses, as shown by the increased numbers of interferon-gamma-expressing splenocytes by enzyme-linked immunospot assay and interferon-gamma-expressing CD4 + and CD8 + cells by flow cytometry analyses. Furthermore, the growth of grafted TC-1 tumors in mice was significantly suppressed by therapeutic vaccination. The recombinant E7 proteins presented by OMVs were more potent than those mixed with wild-type OMVs or administered alone for inducing specific cellular immunity and suppressing tumor growth. The results indicated that the nano-grade OMVs might be a useful vaccine platform for antigen delivery in cancer immunotherapy.

Expanding the scope of site-specific recombinases for genetic and metabolic engineering.

PubMed

Gaj, Thomas; Sirk, Shannon J; Barbas, Carlos F

2014-01-01

Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study. © 2013 Wiley Periodicals, Inc.

Protein glycosylation in diverse cell systems: implications for modification and analysis of recombinant proteins.

PubMed

Brooks, Susan A

2006-06-01

A major challenge for the biotechnology industry is to engineer the glycosylation pathways of expression systems to synthesize recombinant proteins with human glycosylation. Inappropriate glycosylation can result in reduced activity, limited half-life in circulation and unwanted immunogenicity. In this review, the complexities of glycosylation in human cells are explained and compared with glycosylation in bacteria, yeasts, fungi, insects, plants and nonhuman mammalian species. Key advances in the engineering of the glycosylation of expression systems are highlighted. Advances in the challenging and technically complex field of glycan analysis are also described. The emergence of a new generation of expression systems with sophisticated engineering for humanized glycosylation of glycoproteins appears to be on the horizon.

Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production.

PubMed

Roointan, Amir; Morowvat, Mohammad Hossein

The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse features of its application in biotechnology and protein production.

Development of a Turbofan Engine Simulation in a Graphical Simulation Environment

NASA Technical Reports Server (NTRS)

Parker, Khary I.; Guo, Ten-Heui

2003-01-01

This paper presents the development of a generic component level model of a turbofan engine simulation with a digital controller, in an advanced graphical simulation environment. The goal of this effort is to develop and demonstrate a flexible simulation platform for future research in propulsion system control and diagnostic technology. A previously validated FORTRAN-based model of a modern, high-performance, military-type turbofan engine is being used to validate the platform development. The implementation process required the development of various innovative procedures, which are discussed in the paper. Open-loop and closed-loop comparisons are made between the two simulations. Future enhancements that are to be made to the modular engine simulation are summarized.

NASA C-17 Usage Overview

NASA Technical Reports Server (NTRS)

Miller, Christopher R.

2008-01-01

The usage and integrated vehicle health management of the NASA C-17. Propulsion health management flight objectives for the aircraft include mapping of the High Pressure Compressor in order to calibrate a Pratt and Whitney engine model and the fusion of data collected from existing sensors and signals to develop models, analysis methods and information fusion algorithms. An additional health manage flight objective is to demonstrate that the Commercial Modular Aero-Propulsion Systems Simulation engine model can successfully execute in real time onboard the C-17 T-1 aircraft using engine and aircraft flight data as inputs. Future work will address aircraft durability and aging, airframe health management, and propulsion health management research in the areas of gas path and engine vibration.

Expansion of the gateway multisite recombination cloning toolkit.

PubMed

Shearin, Harold K; Dvarishkis, Alisa R; Kozeluh, Craig D; Stowers, R Steven

2013-01-01

Precise manipulation of transgene expression in genetic model organisms has led to advances in understanding fundamental mechanisms of development, physiology, and genetic disease. Transgene construction is, however, a precondition of transgene expression, and often limits the rate of experimental progress. Here we report an expansion of the modular Gateway MultiSite recombination-cloning platform for high efficiency transgene assembly. The expansion includes two additional destination vectors and entry clones for the LexA binary transcription system, among others. These new tools enhance the expression levels possible with Gateway MultiSite generated transgenes and make possible the generation of LexA drivers and reporters with Gateway MultiSite cloning. In vivo data from transgenic Drosophila functionally validating each novel component are presented and include neuronal LexA drivers, LexAop2 red and green fluorescent synaptic vesicle reporters, TDC2 and TRH LexA, GAL4, and QF drivers, and LexAop2, UAS, and QUAS channelrhodopsin2 T159C reporters.

Expansion of the Gateway MultiSite Recombination Cloning Toolkit

PubMed Central

Shearin, Harold K.; Dvarishkis, Alisa R.; Kozeluh, Craig D.; Stowers, R. Steven

2013-01-01

Precise manipulation of transgene expression in genetic model organisms has led to advances in understanding fundamental mechanisms of development, physiology, and genetic disease. Transgene construction is, however, a precondition of transgene expression, and often limits the rate of experimental progress. Here we report an expansion of the modular Gateway MultiSite recombination-cloning platform for high efficiency transgene assembly. The expansion includes two additional destination vectors and entry clones for the LexA binary transcription system, among others. These new tools enhance the expression levels possible with Gateway MultiSite generated transgenes and make possible the generation of LexA drivers and reporters with Gateway MultiSite cloning. In vivo data from transgenic Drosophila functionally validating each novel component are presented and include neuronal LexA drivers, LexAop2 red and green fluorescent synaptic vesicle reporters, TDC2 and TRH LexA, GAL4, and QF drivers, and LexAop2, UAS, and QUAS channelrhodopsin2 T159C reporters. PMID:24204935

Avian Paramyxovirus: A Brief Review.

PubMed

Gogoi, P; Ganar, K; Kumar, S

2017-02-01

Avian paramyxoviruses (APMVs) have been reported from a wide variety of avian species around the world. Avian paramyxoviruses are economically significant because of the huge mortality and morbidity associated with it. Twelve different serotypes of APMV have been reported till date. Avian paramyxoviruses belong to the family Paramyxoviridae under genus Avulavirus. Newcastle disease virus (APMV-1) is the most characterized members among the APMV serotypes. Complete genome sequence of all twelve APMV serotypes has been published recently. In recent years, APMV-1 has attracted the virologists for its oncolytic activity and its use as a vaccine vector for both animals and humans. The recombinant APMV-based vaccine offers a pertinent choice for the construction of live attenuated vaccine due to its minimum recombination frequency, modular nature of transcription and lack of DNA phase during its replication. Although insufficient data are available regarding other APMV serotypes, our understanding about the APMV biology is expanding rapidly because of the availability of modern molecular biology tools and high-throughput complete genome sequencing. © 2015 Blackwell Verlag GmbH.

Cell Type-Specific Manipulation with GFP-Dependent Cre Recombinase

PubMed Central

Tang, Jonathan C Y; Rudolph, Stephanie; Dhande, Onkar S; Abraira, Victoria E; Choi, Seungwon; Lapan, Sylvain; Drew, Iain R; Drokhlyansky, Eugene; Huberman, Andrew D; Regehr, Wade G; Cepko, Constance L

2016-01-01

Summary There are many transgenic GFP reporter lines that allow visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. Here we report the creation of a method that exploits GFP for gene manipulation, Cre Recombinase Dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation and AAV viral vectors, we delivered CRE-DOG to multiple GFP mouse lines, leading to effective recombination selectively in GFP-labeled cells. Further, CRE-DOG enabled optogenetic control of these neurons. Beyond providing a new set of tools for manipulation of gene expression selectively in GFP+ cells, we demonstrate that GFP can be used to reconstitute the activity of a protein not known to have a modular structure, suggesting that this strategy might be applicable to a wide range of proteins. PMID:26258682

Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae.

PubMed

Inoue, Hiroyuki; Hashimoto, Seitaro; Matsushika, Akinori; Watanabe, Seiya; Sawayama, Shigeki

2014-12-01

The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.

An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity.

PubMed

Zhang, Wenli; Fu, Jun; Liu, Jing; Wang, Hailong; Schiwon, Maren; Janz, Sebastian; Schaffarczyk, Lukas; von der Goltz, Lukas; Ehrke-Schulz, Eric; Dörner, Johannes; Solanki, Manish; Boehme, Philip; Bergmann, Thorsten; Lieber, Andre; Lauber, Chris; Dahl, Andreas; Petzold, Andreas; Zhang, Youming; Stewart, A Francis; Ehrhardt, Anja

2017-05-23

Adenoviruses (Ads) are large human-pathogenic double-stranded DNA (dsDNA) viruses presenting an enormous natural diversity associated with a broad variety of diseases. However, only a small fraction of adenoviruses has been explored in basic virology and biomedical research, highlighting the need to develop robust and adaptable methodologies and resources. We developed a method for high-throughput direct cloning and engineering of adenoviral genomes from different sources utilizing advanced linear-linear homologous recombination (LLHR) and linear-circular homologous recombination (LCHR). We describe 34 cloned adenoviral genomes originating from clinical samples, which were characterized by next-generation sequencing (NGS). We anticipate that this recombineering strategy and the engineered adenovirus library will provide an approach to study basic and clinical virology. High-throughput screening (HTS) of the reporter-tagged Ad library in a panel of cell lines including osteosarcoma disease-specific cell lines revealed alternative virus types with enhanced transduction and oncolysis efficiencies. This highlights the usefulness of this resource. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

A modular positron camera for the study of industrial processes

NASA Astrophysics Data System (ADS)

Leadbeater, T. W.; Parker, D. J.

2011-10-01

Positron imaging techniques rely on the detection of the back-to-back annihilation photons arising from positron decay within the system under study. A standard technique, called positron emitting particle tracking (PEPT) [1], uses a number of these detected events to rapidly determine the position of a positron emitting tracer particle introduced into the system under study. Typical applications of PEPT are in the study of granular and multi-phase materials in the disciplines of engineering and the physical sciences. Using components from redundant medical PET scanners a modular positron camera has been developed. This camera consists of a number of small independent detector modules, which can be arranged in custom geometries tailored towards the application in question. The flexibility of the modular camera geometry allows for high photon detection efficiency within specific regions of interest, the ability to study large and bulky systems and the application of PEPT to difficult or remote processes as the camera is inherently transportable.

BeamDyn: a high-fidelity wind turbine blade solver in the FAST modular framework

DOE PAGES

Wang, Qi; Sprague, Michael A.; Jonkman, Jason; ...

2017-03-14

Here, this paper presents a numerical implementation of the geometrically exact beam theory based on the Legendre-spectral-finite-element (LSFE) method. The displacement-based geometrically exact beam theory is presented, and the special treatment of three-dimensional rotation parameters is reviewed. An LSFE is a high-order finite element with nodes located at the Gauss-Legendre-Lobatto points. These elements can be an order of magnitude more computationally efficient than low-order finite elements for a given accuracy level. The new module, BeamDyn, is implemented in the FAST modularization framework for dynamic simulation of highly flexible composite-material wind turbine blades within the FAST aeroelastic engineering model. The frameworkmore » allows for fully interactive simulations of turbine blades in operating conditions. Numerical examples are provided to validate BeamDyn and examine the LSFE performance as well as the coupling algorithm in the FAST modularization framework. BeamDyn can also be used as a stand-alone high-fidelity beam tool.« less

BeamDyn: a high-fidelity wind turbine blade solver in the FAST modular framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qi; Sprague, Michael A.; Jonkman, Jason

Here, this paper presents a numerical implementation of the geometrically exact beam theory based on the Legendre-spectral-finite-element (LSFE) method. The displacement-based geometrically exact beam theory is presented, and the special treatment of three-dimensional rotation parameters is reviewed. An LSFE is a high-order finite element with nodes located at the Gauss-Legendre-Lobatto points. These elements can be an order of magnitude more computationally efficient than low-order finite elements for a given accuracy level. The new module, BeamDyn, is implemented in the FAST modularization framework for dynamic simulation of highly flexible composite-material wind turbine blades within the FAST aeroelastic engineering model. The frameworkmore » allows for fully interactive simulations of turbine blades in operating conditions. Numerical examples are provided to validate BeamDyn and examine the LSFE performance as well as the coupling algorithm in the FAST modularization framework. BeamDyn can also be used as a stand-alone high-fidelity beam tool.« less

Generation and development of RNA ligase ribozymes with modular architecture through "design and selection".

PubMed

Fujita, Yuki; Ishikawa, Junya; Furuta, Hiroyuki; Ikawa, Yoshiya

2010-08-26

In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed "design and selection," new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

Modular 3D-Printed Soil Gas Probes

NASA Astrophysics Data System (ADS)

Good, S. P.; Selker, J. S.; Al-Qqaili, F.; Lopez, M.; Kahel, L.

2016-12-01

ABSTRACT: Extraction of soil gas is required for a variety of applications in earth sciences and environmental engineering. However, commercially available probes can be costly and are typically limited to a single depth. Here, we present the open-source design and lab testing of a soil gas probe with modular capabilities that allow for the vertical stacking of gas extraction points at different depths in the soil column. The probe modules consist of a 3D printed spacer unit and hydrophobic gas permeable membrane made of high density Polyethylene with pore sizes 20-40 microns. Each of the modular spacer units contain both a gas extraction line and gas input line for the dilution of soil gases if needed. These 2-inch diameter probes can be installed in the field quickly with a hand auger and returned to at any frequency to extract soil gas from desired soil depths. The probes are tested through extraction of soil pore water vapors with distinct stable isotope ratios.

Modular adaptive implant based on smart materials.

PubMed

Bîzdoacă, N; Tarniţă, Daniela; Tarniţă, D N

2008-01-01

Applications of biological methods and systems found in nature to the study and design of engineering systems and modern technology are defined as Bionics. The present paper describes a bionics application of shape memory alloy in construction of orthopedic implant. The main idea of this paper is related to design modular adaptive implants for fractured bones. In order to target the efficiency of medical treatment, the implant has to protect the fractured bone, for the healing period, undertaking much as is possible from the daily usual load of the healthy bones. After a particular stage of healing period is passed, using implant modularity, the load is gradually transferred to bone, assuring in this manner a gradually recover of bone function. The adaptability of this design is related to medical possibility of the physician to made the implant to correspond to patient specifically anatomy. Using a CT realistic numerical bone models, the mechanical simulation of different types of loading of the fractured bones treated with conventional method are presented. The results are commented and conclusions are formulated.

Modern Technologies for Creating Synthetic Antibodies for Clinical application

PubMed Central

Lebedenko, E. N.

2009-01-01

The modular structure and versatility of antibodies enables one to modify natural immunoglobulins in different ways for various clinical applications. Rational design and molecular engineering make it possible to directionally modify the molecular size, affinity, specificity, and immunogenicity and effector functions of an antibody, as well as to combine them with other functional agents. This review focuses on up-to-date methods of antibody engineering for diagnosing and treating various diseases, particularly on new technologies meant to refine the effector functions of therapeutic antibodies. PMID:22649585

MT3DMS: A Modular Three-Dimensional Multispecies Transport Model for Simulation of Advection, Dispersion, and Chemical Reactions of Contaminants in Groundwater Systems; Documentation and User’s Guide

DTIC Science & Technology

1999-12-01

addition, the data files saved in the POINT format can include an optional header which is compatible with Amtec Engineering’s 2-D and 3-D visualization...34.DAT" file so that the file can be used directly by Amtec Engineering’s 2-D and 3-D visualization package Tecplot©. The ARRAY and POINT formats are

ORAC-DR: Pipelining With Other People's Code

NASA Astrophysics Data System (ADS)

Economou, Frossie; Bridger, Alan; Wright, Gillian S.; Jenness, Tim; Currie, Malcolm J.; Adamson, Andy

As part of the UKIRT ORAC project, we have developed a pipeline (orac-dr) for driving on-line data reduction using existing astronomical packages as algorithm engines and display tools. The design is modular and extensible on several levels, allowing it to be easily adapted to a wide variety of instruments. Here we briefly review the design, discuss the robustness and speed of execution issues inherent in such pipelines, and address what constitutes a desirable (in terms of ``buy-in'' effort) engine or tool.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savoie, M.J.; Schanche, G.W.; Mikucki, W.J.

This report provides technical information on modular solid-waste heat-recovery incinerators (HRIs), air-pollution regulations that apply to HRIs, air-pollutant emissions from currently marketed HRIs, and air-polution-control techniques for HRIs. The information will be useful to Army installations, Major Commands, and Corps of Engineers Districts that must plan and design HRI facilities.

Preparing to Be Wrong

DTIC Science & Technology

2016-04-30

Proceedings Magazine , 138/7/7, 313. Holtta-Otto, K., & de Weck, O. (2007). Degree of modularity in engineering systems and products with technical and...ve ls (S T A N A G ) S elect adaptable system S elect optimized system S elect adaptable system if confident in a <= X% likelihood this

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General definitions. In...) “Battery” means a modular electric power source where part or all of the fuel is contained within the unit... heat cycle engine. In this regulation there is no differentiation between a single cell and a battery...

Designing for the ISD Life Cycle.

ERIC Educational Resources Information Center

Wallace, Guy W.; Hybert, Peter R.; Smith, Kelly R.; Blecke, Brian D.

2002-01-01

Outlines the recent criticisms of traditional ISD (Instructional Systems Design) and discusses the implications that impact the life cycle costs of T&D (Training and Development) projects and their ROI (Return On Investment) potential. Describes a modified approach to ISD which mimics the modular approach of systems engineering design.…

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... STANDARDS BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General definitions. In...) “Battery” means a modular electric power source where part or all of the fuel is contained within the unit... heat cycle engine. In this regulation there is no differentiation between a single cell and a battery...

Crew appliance concepts. Volume 4, appendix C: Modular space station appliances supporting engineering data. [food management and personal hygiene

NASA Technical Reports Server (NTRS)

Proctor, B. W.; Reysa, R. P.; Russell, D. J.

1975-01-01

Data collected for the appliances considered for the space station are presented along with plotted and tabulated trade study results for each appliance. The food management, and personal hygiene data are applicable to a six-man mission of 180-days.

Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae.

PubMed

Lv, Xiaomei; Wang, Fan; Zhou, Pingping; Ye, Lidan; Xie, Wenping; Xu, Haoming; Yu, Hongwei

2016-09-21

Microbial production of isoprene from renewable feedstock is a promising alternative to traditional petroleum-based processes. Currently, efforts to improve isoprenoid production in Saccharomyces cerevisiae mainly focus on cytoplasmic engineering, whereas comprehensive engineering of multiple subcellular compartments is rarely reported. Here, we propose dual metabolic engineering of cytoplasmic and mitochondrial acetyl-CoA utilization to boost isoprene synthesis in S. cerevisiae. This strategy increases isoprene production by 2.1-fold and 1.6-fold relative to the recombinant strains with solely mitochondrial or cytoplasmic engineering, respectively. By combining a modified reiterative recombination system for rapid pathway assembly, a two-phase culture process for dynamic metabolic regulation, and aerobic fed-batch fermentation for sufficient supply of acetyl-coA and carbon, we achieve 2527, mg l(-1) of isoprene, which is the highest ever reported in engineered eukaryotes. We propose this strategy as an efficient approach to enhancing isoprene production in yeast, which might open new possibilities for bioproduction of other value-added chemicals.

Protein nanoparticles are nontoxic, tuneable cell stressors.

PubMed

de Pinho Favaro, Marianna Teixeira; Sánchez-García, Laura; Sánchez-Chardi, Alejandro; Roldán, Mónica; Unzueta, Ugutz; Serna, Naroa; Cano-Garrido, Olivia; Azzoni, Adriano Rodrigues; Ferrer-Miralles, Neus; Villaverde, Antonio; Vázquez, Esther

2018-02-01

Nanoparticle-cell interactions can promote cell toxicity and stimulate particular behavioral patterns, but cell responses to protein nanomaterials have been poorly studied. By repositioning oligomerization domains in a simple, modular self-assembling protein platform, we have generated closely related but distinguishable homomeric nanoparticles. Composed by building blocks with modular domains arranged in different order, they share amino acid composition. These materials, once exposed to cultured cells, are differentially internalized in absence of toxicity and trigger distinctive cell adaptive responses, monitored by the emission of tubular filopodia and enhanced drug sensitivity. The capability to rapidly modulate such cell responses by conventional protein engineering reveals protein nanoparticles as tuneable, versatile and potent cell stressors for cell-targeted conditioning.

Servicer system demonstration plan and capability development

NASA Technical Reports Server (NTRS)

1987-01-01

An orbital maneuvering vehicle (OMV) front end kit is defined which is capable of performing in-situ fluid resupply and modular maintenance of free flying spacecraft based on the integrated orbital servicing system (IOSS) concept. The compatibility of the IOSS to perform gas and fluid umbilical connect and disconnect functions utilizing connect systems currently available or in development is addressed. A series of tasks involving on-orbit servicing and the engineering test unit (ETU) of the on-orbit service were studied. The objective is the advancement of orbital servicing by expanding the Spacecraft Servicing Demonstration Plan (SSDP) to include detail demonstration planning using the Multimission Modular Spacecraft (MMS) and upgrading the ETU control.

Progress toward Modular UAS for Geoscience Applications

NASA Astrophysics Data System (ADS)

Dahlgren, R. P.; Clark, M. A.; Comstock, R. J.; Fladeland, M.; Gascot, H., III; Haig, T. H.; Lam, S. J.; Mazhari, A. A.; Palomares, R. R.; Pinsker, E. A.; Prathipati, R. T.; Sagaga, J.; Thurling, J. S.; Travers, S. V.

2017-12-01

Small Unmanned Aerial Systems (UAS) have become accepted tools for geoscience, ecology, agriculture, disaster response, land management, and industry. A variety of consumer UAS options exist as science and engineering payload platforms, but their incompatibilities with one another contribute to high operational costs compared with those of piloted aircraft. This research explores the concept of modular UAS, demonstrating airframes that can be reconfigured in the field for experimental optimization, to enable multi-mission support, facilitate rapid repair, or respond to changing field conditions. Modular UAS is revolutionary in allowing aircraft to be optimized around the payload, reversing the conventional wisdom of designing the payload to accommodate an unmodifiable aircraft. UAS that are reconfigurable like Legos™ are ideal for airborne science service providers, system integrators, instrument designers and end users to fulfill a wide range of geoscience experiments. Modular UAS facilitate the adoption of open-source software and rapid prototyping technology where design reuse is important in the context of a highly regulated industry like aerospace. The industry is now at a stage where consolidation, acquisition, and attrition will reduce the number of small manufacturers, with a reduction of innovation and motivation to reduce costs. Modularity leads to interface specifications, which can evolve into de facto or formal standards which contain minimum (but sufficient) details such that multiple vendors can then design to those standards and demonstrate interoperability. At that stage, vendor coopetition leads to robust interface standards, interoperability standards and multi-source agreements which in turn drive costs down significantly.

A versatile modular bioreactor platform for Tissue Engineering

PubMed Central

Schuerlein, Sebastian; Schwarz, Thomas; Krziminski, Steffan; Gätzner, Sabine; Hoppensack, Anke; Schwedhelm, Ivo; Schweinlin, Matthias; Walles, Heike

2016-01-01

Abstract Tissue Engineering (TE) bears potential to overcome the persistent shortage of donor organs in transplantation medicine. Additionally, TE products are applied as human test systems in pharmaceutical research to close the gap between animal testing and the administration of drugs to human subjects in clinical trials. However, generating a tissue requires complex culture conditions provided by bioreactors. Currently, the translation of TE technologies into clinical and industrial applications is limited due to a wide range of different tissue‐specific, non‐disposable bioreactor systems. To ensure a high level of standardization, a suitable cost‐effectiveness, and a safe graft production, a generic modular bioreactor platform was developed. Functional modules provide robust control of culture processes, e.g. medium transport, gas exchange, heating, or trapping of floating air bubbles. Characterization revealed improved performance of the modules in comparison to traditional cell culture equipment such as incubators, or peristaltic pumps. By combining the modules, a broad range of culture conditions can be achieved. The novel bioreactor platform allows using disposable components and facilitates tissue culture in closed fluidic systems. By sustaining native carotid arteries, engineering a blood vessel, and generating intestinal tissue models according to a previously published protocol the feasibility and performance of the bioreactor platform was demonstrated. PMID:27492568

A Low-Cost Modular Platform for Heterogeneous Data Acquisition with Accurate Interchannel Synchronization

PubMed Central

Blanco-Claraco, José Luis; López-Martínez, Javier; Torres-Moreno, José Luis; Giménez-Fernández, Antonio

2015-01-01

Most experimental fields of science and engineering require the use of data acquisition systems (DAQ), devices in charge of sampling and converting electrical signals into digital data and, typically, performing all of the required signal preconditioning. Since commercial DAQ systems are normally focused on specific types of sensors and actuators, systems engineers may need to employ mutually-incompatible hardware from different manufacturers in applications demanding heterogeneous inputs and outputs, such as small-signal analog inputs, differential quadrature rotatory encoders or variable current outputs. A common undesirable side effect of heterogeneous DAQ hardware is the lack of an accurate synchronization between samples captured by each device. To solve such a problem with low-cost hardware, we present a novel modular DAQ architecture comprising a base board and a set of interchangeable modules. Our main design goal is the ability to sample all sources at predictable, fixed sampling frequencies, with a reduced synchronization mismatch (<1 μs) between heterogeneous signal sources. We present experiments in the field of mechanical engineering, illustrating vibration spectrum analyses from piezoelectric accelerometers and, as a novelty in these kinds of experiments, the spectrum of quadrature encoder signals. Part of the design and software will be publicly released online. PMID:26516865

Assembly of tissue engineered blood vessels with spatially-controlled heterogeneities.

PubMed

Strobel, Hannah A; Hookway, Tracy; Piola, Marco; Fiore, Gianfranco Beniamino; Soncini, Monica; Alsberg, Eben; Rolle, Marsha

2018-05-04

Tissue-engineered human blood vessels may enable in vitro disease modeling and drug screening to accelerate advances in vascular medicine. Existing methods for tissue engineered blood vessel (TEBV) fabrication create homogenous tubes not conducive to modeling the focal pathologies characteristic of vascular disease. We developed a system for generating self-assembled human smooth muscle cell ring-units, which were fused together into TEBVs. The goal of this study was to assess the feasibility of modular assembly and fusion of ring building units to fabricate spatially-controlled, heterogeneous tissue tubes. We first aimed to enhance fusion and reduce total culture time, and determined that reducing ring pre-culture duration improved tube fusion. Next, we incorporated electrospun polymer ring units onto tube ends as reinforced extensions, which allowed us to cannulate tubes after only 7 days of fusion, and culture tubes with luminal flow in a custom bioreactor. To create focal heterogeneities, we incorporated gelatin microspheres into select ring units during self-assembly, and fused these rings between ring units without microspheres. Cells within rings maintained their spatial position within tissue tubes after fusion. This work describes a platform approach for creating modular TEBVs with spatially-defined structural heterogeneities, which may ultimately be applied to mimic focal diseases such as intimal hyperplasia or aneurysm.

NRC Reviewer Aid for Evaluating the Human Factors Engineering Aspects of Small Modular Reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

OHara J. M.; Higgins, J.C.

Small modular reactors (SMRs) are a promising approach to meeting future energy needs. Although the electrical output of an individual SMR is relatively small compared to that of typical commercial nuclear plants, they can be grouped to produce as much energy as a utility demands. Furthermore, SMRs can be used for other purposes, such as producing hydrogen and generating process heat. The design characteristics of many SMRs differ from those of current conventional plants and may require a distinct concept of operations (ConOps). The U.S. Nuclear Regulatory Commission (NRC) conducted research to examine the human factors engineering (HFE) and themore » operational aspects of SMRs. The research identified thirty potential human-performance issues that should be considered in the NRC's reviews of SMR designs and in future research activities. The purpose of this report is to support NRC HFE reviewers of SMR applications by identifying some of the questions that can be asked of applicants whose designs have characteristics identified in the issues. The questions for each issue were identified and organized based on the review elements and guidance contained in Chapter 18 of the Standard Review Plan (NUREG-0800), and the Human Factors Engineering Program Review Model (NUREG-0711).« less

Genetic Engineering of Bee Gut Microbiome Bacteria with a Toolkit for Modular Assembly of Broad-Host-Range Plasmids.

PubMed

Leonard, Sean P; Perutka, Jiri; Powell, J Elijah; Geng, Peng; Richhart, Darby D; Byrom, Michelle; Kar, Shaunak; Davies, Bryan W; Ellington, Andrew D; Moran, Nancy A; Barrick, Jeffrey E

2018-05-18

Engineering the bacteria present in animal microbiomes promises to lead to breakthroughs in medicine and agriculture, but progress is hampered by a dearth of tools for genetically modifying the diverse species that comprise these communities. Here we present a toolkit of genetic parts for the modular construction of broad-host-range plasmids built around the RSF1010 replicon. Golden Gate assembly of parts in this toolkit can be used to rapidly test various antibiotic resistance markers, promoters, fluorescent reporters, and other coding sequences in newly isolated bacteria. We demonstrate the utility of this toolkit in multiple species of Proteobacteria that are native to the gut microbiomes of honey bees ( Apis mellifera) and bumble bees (B ombus sp.). Expressing fluorescent proteins in Snodgrassella alvi, Gilliamella apicola, Bartonella apis, and Serratia strains enables us to visualize how these bacteria colonize the bee gut. We also demonstrate CRISPRi repression in B. apis and use Cas9-facilitated knockout of an S. alvi adhesion gene to show that it is important for colonization of the gut. Beyond characterizing how the gut microbiome influences the health of these prominent pollinators, this bee microbiome toolkit (BTK) will be useful for engineering bacteria found in other natural microbial communities.

A versatile modular bioreactor platform for Tissue Engineering.

PubMed

Schuerlein, Sebastian; Schwarz, Thomas; Krziminski, Steffan; Gätzner, Sabine; Hoppensack, Anke; Schwedhelm, Ivo; Schweinlin, Matthias; Walles, Heike; Hansmann, Jan

2017-02-01

Tissue Engineering (TE) bears potential to overcome the persistent shortage of donor organs in transplantation medicine. Additionally, TE products are applied as human test systems in pharmaceutical research to close the gap between animal testing and the administration of drugs to human subjects in clinical trials. However, generating a tissue requires complex culture conditions provided by bioreactors. Currently, the translation of TE technologies into clinical and industrial applications is limited due to a wide range of different tissue-specific, non-disposable bioreactor systems. To ensure a high level of standardization, a suitable cost-effectiveness, and a safe graft production, a generic modular bioreactor platform was developed. Functional modules provide robust control of culture processes, e.g. medium transport, gas exchange, heating, or trapping of floating air bubbles. Characterization revealed improved performance of the modules in comparison to traditional cell culture equipment such as incubators, or peristaltic pumps. By combining the modules, a broad range of culture conditions can be achieved. The novel bioreactor platform allows using disposable components and facilitates tissue culture in closed fluidic systems. By sustaining native carotid arteries, engineering a blood vessel, and generating intestinal tissue models according to a previously published protocol the feasibility and performance of the bioreactor platform was demonstrated. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modular and selective biosynthesis of gasoline-range alkanes.

PubMed

Sheppard, Micah J; Kunjapur, Aditya M; Prather, Kristala L J

2016-01-01

Typical renewable liquid fuel alternatives to gasoline are not entirely compatible with current infrastructure. We have engineered Escherichia coli to selectively produce alkanes found in gasoline (propane, butane, pentane, heptane, and nonane) from renewable substrates such as glucose or glycerol. Our modular pathway framework achieves carbon-chain extension by two different mechanisms. A fatty acid synthesis route is used to generate longer chains heptane and nonane, while a more energy efficient alternative, reverse-β-oxidation, is used for synthesis of propane, butane, and pentane. We demonstrate that both upstream (thiolase) and intermediate (thioesterase) reactions can act as control points for chain-length specificity. Specific free fatty acids are subsequently converted to alkanes using a broad-specificity carboxylic acid reductase and a cyanobacterial aldehyde decarbonylase (AD). The selectivity obtained by different module pairings provides a foundation for tuning alkane product distribution for desired fuel properties. Alternate ADs that have greater activity on shorter substrates improve observed alkane titer. However, even in an engineered host strain that significantly reduces endogenous conversion of aldehyde intermediates to alcohol byproducts, AD activity is observed to be limiting for all chain lengths. Given these insights, we discuss guiding principles for pathway selection and potential opportunities for pathway improvement. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Talin determines the nanoscale architecture of focal adhesions.

PubMed

Liu, Jaron; Wang, Yilin; Goh, Wah Ing; Goh, Honzhen; Baird, Michelle A; Ruehland, Svenja; Teo, Shijia; Bate, Neil; Critchley, David R; Davidson, Michael W; Kanchanawong, Pakorn

2015-09-01

Insight into how molecular machines perform their biological functions depends on knowledge of the spatial organization of the components, their connectivity, geometry, and organizational hierarchy. However, these parameters are difficult to determine in multicomponent assemblies such as integrin-based focal adhesions (FAs). We have previously applied 3D superresolution fluorescence microscopy to probe the spatial organization of major FA components, observing a nanoscale stratification of proteins between integrins and the actin cytoskeleton. Here we combine superresolution imaging techniques with a protein engineering approach to investigate how such nanoscale architecture arises. We demonstrate that talin plays a key structural role in regulating the nanoscale architecture of FAs, akin to a molecular ruler. Talin diagonally spans the FA core, with its N terminus at the membrane and C terminus demarcating the FA/stress fiber interface. In contrast, vinculin is found to be dispensable for specification of FA nanoscale architecture. Recombinant analogs of talin with modified lengths recapitulated its polarized orientation but altered the FA/stress fiber interface in a linear manner, consistent with its modular structure, and implicating the integrin-talin-actin complex as the primary mechanical linkage in FAs. Talin was found to be ∼97 nm in length and oriented at ∼15° relative to the plasma membrane. Our results identify talin as the primary determinant of FA nanoscale organization and suggest how multiple cellular forces may be integrated at adhesion sites.

Economic feasibility and environmental impact of synthetic spider silk production from escherichia coli.

PubMed

Edlund, Alan M; Jones, Justin; Lewis, Randolph; Quinn, Jason C

2018-05-25

Major ampullate spider silk represents a promising protein-based biomaterial with diverse commercial potential ranging from textiles to medical devices due to its excellent physical and thermal properties. Recent advancements in synthetic biology have facilitated the development of recombinant spider silk proteins from Escherichia coli (E. coli). This study specifically investigates the economic feasibility and environmental impact of synthetic spider silk manufacturing. Pilot scale data was used to validate an engineering process model that includes all of the required sub-processing steps for synthetic fiber manufacture: production, harvesting, purification, drying, and spinning. Modeling was constructed modularly to support assessment of alternative downstream processing technologies. The techno-economic analysis indicates a minimum sale price from pioneer and optimized E. coli plants of $761 kg -1 and $23 kg -1 with greenhouse gas emissions of 572 kg CO 2-eq. kg -1 and 55 kg CO 2-eq. kg -1 , respectively. Elevated costs and emissions from the pioneer plant can be directly tied to the high material consumption and low protein yield. Decreased production costs associated with the optimized plant includes improved protein yield, process optimization, and an N th plant assumption. Discussion focuses on the commercial potential of spider silk, the production performance requirements for commercialization, and the impact of alternative technologies on the system. Copyright © 2018 Elsevier B.V. All rights reserved.

Designing protein-based biomaterials for medical applications.

PubMed

Gagner, Jennifer E; Kim, Wookhyun; Chaikof, Elliot L

2014-04-01

Biomaterials produced by nature have been honed through billions of years, evolving exquisitely precise structure-function relationships that scientists strive to emulate. Advances in genetic engineering have facilitated extensive investigations to determine how changes in even a single peptide within a protein sequence can produce biomaterials with unique thermal, mechanical and biological properties. Elastin, a naturally occurring protein polymer, serves as a model protein to determine the relationship between specific structural elements and desirable material characteristics. The modular, repetitive nature of the protein facilitates the formation of well-defined secondary structures with the ability to self-assemble into complex three-dimensional architectures on a variety of length scales. Furthermore, many opportunities exist to incorporate other protein-based motifs and inorganic materials into recombinant protein-based materials, extending the range and usefulness of these materials in potential biomedical applications. Elastin-like polypeptides (ELPs) can be assembled into 3-D architectures with precise control over payload encapsulation, mechanical and thermal properties, as well as unique functionalization opportunities through both genetic and enzymatic means. An overview of current protein-based materials, their properties and uses in biomedicine will be provided, with a focus on the advantages of ELPs. Applications of these biomaterials as imaging and therapeutic delivery agents will be discussed. Finally, broader implications and future directions of these materials as diagnostic and therapeutic systems will be explored. Copyright © 2013 Elsevier Ltd. All rights reserved.

Designing Protein-Based Biomaterials for Medical Applications

PubMed Central

Gagner, Jennifer E.; Kim, Wookhyun; Chaikof, Elliot L.

2013-01-01

Biomaterials produced by nature have been honed through billions of years, evolving exquisitely precise structure-function relationships that scientists strive to emulate. Advances in genetic engineering have facilitated extensive investigations to determine how changes in even a single peptide within a protein sequence can produce biomaterials with unique thermal, mechanical and biological properties. Elastin, a naturally occurring protein polymer, serves as a model protein to determine the relationship between specific structural elements and desirable material characteristics. The modular, repetitive nature of the protein facilitates the formation of well-defined secondary structures with the ability to self-assemble into complex three-dimensional architectures on a variety of length scales. Furthermore, many opportunities exist to incorporate other protein-based motifs and inorganic materials into recombinant protein-based materials, extending the range and usefulness of these materials in potential biomedical applications. Elastin-like polypeptides can be assembled into 3D architectures with precise control over payload encapsulation, mechanical and thermal properties, as well as unique functionalization opportunities through both genetic and enzymatic means. An overview of current protein-based materials, their properties and uses in biomedicine will be provided, with a focus on the advantages of elastin-like polypeptides. Applications of these biomaterials as imaging and therapeutic delivery agents will be discussed. Finally, broader implications and future directions of these materials as diagnostic and therapeutic systems will be explored. PMID:24121196

A polyvalent hybrid protein elicits antibodies against the diverse allelic types of block 2 in Plasmodium falciparum merozoite surface protein 1.

PubMed

Tetteh, Kevin K A; Conway, David J

2011-10-13

Merozoite surface protein 1 (MSP1) of Plasmodium falciparum has been implicated as an important target of acquired immunity, and candidate components for a vaccine include polymorphic epitopes in the N-terminal polymorphic block 2 region. We designed a polyvalent hybrid recombinant protein incorporating sequences of the three major allelic types of block 2 together with a composite repeat sequence of one of the types and N-terminal flanking T cell epitopes, and compared this with a series of recombinant proteins containing modular sub-components and similarly expressed in Escherichia coli. Immunogenicity of the full polyvalent hybrid protein was tested in both mice and rabbits, and comparative immunogenicity studies of the sub-component modules were performed in mice. The full hybrid protein induced high titre antibodies against each of the major block 2 allelic types expressed as separate recombinant proteins and against a wide range of allelic types naturally expressed by a panel of diverse P. falciparum isolates, while the sub-component modules had partial antigenic coverage as expected. This encourages further development and evaluation of the full MSP1 block 2 polyvalent hybrid protein as a candidate blood-stage component of a malaria vaccine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Effects of unique biomedical education programs for engineers: REDEEM and ESTEEM projects.

PubMed

Matsuki, Noriaki; Takeda, Motohiro; Yamano, Masahiro; Imai, Yohsuke; Ishikawa, Takuji; Yamaguchi, Takami

2009-06-01

Current engineering applications in the medical arena are extremely progressive. However, it is rather difficult for medical doctors and engineers to discuss issues because they do not always understand one another's jargon or ways of thinking. Ideally, medical engineers should become acquainted with medicine, and engineers should be able to understand how medical doctors think. Tohoku University in Japan has managed a number of unique reeducation programs for working engineers. Recurrent Education for the Development of Engineering Enhanced Medicine has been offered as a basic learning course since 2004, and Education through Synergetic Training for Engineering Enhanced Medicine has been offered as an advanced learning course since 2006. These programs, which were developed especially for engineers, consist of interactive, modular, and disease-based lectures (case studies) and substantial laboratory work. As a result of taking these courses, all students obtained better objective outcomes, on tests, and subjective outcomes, through student satisfaction. In this article, we report on our unique biomedical education programs for engineers and their effects on working engineers.

Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

USDA-ARS?s Scientific Manuscript database

Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...

Engineering of living cells for the expression of holo-phycobiliprotein-based constructs

DOEpatents

Glazer, Alexander N.; Tooley, Aaron J.; Cai, Yuping

2004-05-25

Recombinant cells which express a fluorescent holo-phycobiliprotein fusion protein and methods of use are described. The cells comprises a bilin, a recombinant bilin reductase, an apo-phycobiliprotein fusion protein precursor of the fusion protein comprising a corresponding apo-phycobiliprotein domain, and a recombinant phycobiliprotein domain-bilin lyase, which components react to form the holo-phycobiliprotein fusion protein. Also described are holo-phycobiliprotein based transcription reporter cells and assays, which cells conditionally express a heterologous-to-the-cell, fluorescent, first holo-phycobiliprotein domain.

Selection of recombinant MVA by rescue of the essential D4R gene.

PubMed

Ricci, Patricia S; Schäfer, Birgit; Kreil, Thomas R; Falkner, Falko G; Holzer, Georg W

2011-12-12

Modified vaccinia virus Ankara (MVA) has become a promising vaccine vector due to its immunogenicity and its proven safety in humans. As a general approach for stringent and rapid selection of recombinant MVA, we assessed marker rescue of the essential viral D4R gene in an engineered deletion mutant that is fully replication defective in wild-type cells. Recombinant, replicating virus was obtained by re-introduction of the deleted viral gene as a dominant selection marker into the deletion mutant.

Development of CFD model for augmented core tripropellant rocket engine

NASA Astrophysics Data System (ADS)

Jones, Kenneth M.

1994-10-01

The Space Shuttle era has made major advances in technology and vehicle design to the point that the concept of a single-stage-to-orbit (SSTO) vehicle appears more feasible. NASA presently is conducting studies into the feasibility of certain advanced concept rocket engines that could be utilized in a SSTO vehicle. One such concept is a tripropellant system which burns kerosene and hydrogen initially and at altitude switches to hydrogen. This system will attain a larger mass fraction because LOX-kerosene engines have a greater average propellant density and greater thrust-to-weight ratio. This report describes the investigation to model the tripropellant augmented core engine. The physical aspects of the engine, the CFD code employed, and results of the numerical model for a single modular thruster are discussed.

Automated multiplex genome-scale engineering in yeast

PubMed Central

Si, Tong; Chao, Ran; Min, Yuhao; Wu, Yuying; Ren, Wen; Zhao, Huimin

2017-01-01

Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and widely used microbial cell factory. Standardized genetic parts encoding overexpression and knockdown mutations of >90% yeast genes are created in a single step from a full-length cDNA library. With the aid of CRISPR-Cas, these genetic parts are iteratively integrated into the repetitive genomic sequences in a modular manner using robotic automation. This system allows functional mapping and multiplex optimization on a genome scale for diverse phenotypes including cellulase expression, isobutanol production, glycerol utilization and acetic acid tolerance, and may greatly accelerate future genome-scale engineering endeavours in yeast. PMID:28469255

Modular magazine for suitable handling of microparts in industry

NASA Astrophysics Data System (ADS)

Grimme, Ralf; Schmutz, Wolfgang; Schlenker, Dirk; Schuenemann, Matthias; Stock, Achim; Schaefer, Wolfgang

1998-01-01

Microassembly and microadjustment techniques are key technologies in the industrial production of hybrid microelectromechanical systems. One focal point in current microproduction research and engineering is the design and development of high-precision microassembly and microadjustment equipment capable of operating within the framework of flexible automated industrial production. As well as these developments, suitable microassembly tools for industrial use also need to be equipped with interfaces for the supply and delivery of microcomponents. The microassembly process necessitates the supply of microparts in a geometrically defined manner. In order to reduce processing steps and production costs, there is a demand for magazines capable of providing free accessibility to the fixed microcomponents. Commonly used at present are feeding techniques, which originate from the field of semiconductor production. However none of these techniques fully meets the requirements of industrial microassembly technology. A novel modular magazine set, developed and tested in a joint project, is presented here. The magazines are able to hold microcomponents during cleaning, inspection and assembly without nay additional handling steps. The modularity of their design allows for maximum technical flexibility. The modular magazine fits into currently practiced SEMI standards. The design and concept of the magazine enables industrial manufacturers to promote a cost-efficient and flexible precision assembly of microelectromechanical systems.

Modular Closed-Loop Control of Diabetes

PubMed Central

Magni, L.; Dassau, E.; Hughes-Karvetski, C.; Toffanin, C.; De Nicolao, G.; Del Favero, S.; Breton, M.; Man, C. Dalla; Renard, E.; Zisser, H.; Doyle, F. J.; Cobelli, C.; Kovatchev, B. P.

2015-01-01

Modularity plays a key role in many engineering systems, allowing for plug-and-play integration of components, enhancing flexibility and adaptability, and facilitating standardization. In the control of diabetes, i.e., the so-called “artificial pancreas,” modularity allows for the step-wise introduction of (and regulatory approval for) algorithmic components, starting with subsystems for assured patient safety and followed by higher layer components that serve to modify the patient’s basal rate in real time. In this paper, we introduce a three-layer modular architecture for the control of diabetes, consisting in a sensor/pump interface module (IM), a continuous safety module (CSM), and a real-time control module (RTCM), which separates the functions of insulin recommendation (postmeal insulin for mitigating hyperglycemia) and safety (prevention of hypoglycemia). In addition, we provide details of instances of all three layers of the architecture: the APS© serving as the IM, the safety supervision module (SSM) serving as the CSM, and the range correction module (RCM) serving as the RTCM. We evaluate the performance of the integrated system via in silico preclinical trials, demonstrating 1) the ability of the SSM to reduce the incidence of hypoglycemia under nonideal operating conditions and 2) the ability of the RCM to reduce glycemic variability. PMID:22481809

One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy

PubMed Central

Casini, Arturo; MacDonald, James T.; Jonghe, Joachim De; Christodoulou, Georgia; Freemont, Paul S.; Baldwin, Geoff S.; Ellis, Tom

2014-01-01

Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications. PMID:24153110

The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

PubMed

Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

2016-10-05

Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.

Split green fluorescent protein as a modular binding partner for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.

2013-12-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was testedmore » by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.« less

MACOP modular architecture with control primitives

PubMed Central

Waegeman, Tim; Hermans, Michiel; Schrauwen, Benjamin

2013-01-01

Walking, catching a ball and reaching are all tasks in which humans and animals exhibit advanced motor skills. Findings in biological research concerning motor control suggest a modular control hierarchy which combines movement/motor primitives into complex and natural movements. Engineers inspire their research on these findings in the quest for adaptive and skillful control for robots. In this work we propose a modular architecture with control primitives (MACOP) which uses a set of controllers, where each controller becomes specialized in a subregion of its joint and task-space. Instead of having a single controller being used in this subregion [such as MOSAIC (modular selection and identification for control) on which MACOP is inspired], MACOP relates more to the idea of continuously mixing a limited set of primitive controllers. By enforcing a set of desired properties on the mixing mechanism, a mixture of primitives emerges unsupervised which successfully solves the control task. We evaluate MACOP on a numerical model of a robot arm by training it to generate desired trajectories. We investigate how the tracking performance is affected by the number of controllers in MACOP and examine how the individual controllers and their generated control primitives contribute to solving the task. Furthermore, we show how MACOP compensates for the dynamic effects caused by a fixed control rate and the inertia of the robot. PMID:23888140

Enhanced Functional Recombinant Factor VII Production by HEK 293 Cells Stably Transfected with VKORC1 where the Gamma-Carboxylase Inhibitor Calumenin is Stably Suppressed by shRNA Transfection

PubMed Central

Wajih, Nadeem; Owen, John; Wallin, Reidar

2008-01-01

Introduction Recombinant members of the vitamin K-dependent protein family (factors IX and VII and protein C) have become important pharmaceuticals in treatment of bleeding disorders and sepsis. However, because the in vivo γ-carboxylation system in stable cell lines used for transfection has a limited capacity of post translational γ carboxylation, the recovery of fully γ-carboxylated and functional proteins is low. Materials and Methods In this work we have engineered recombinant factor VII producing HEK 293 cells to stably overexpress VKORC1, the reduced vitamin K γ-carboxylase cofactor and in addition stably silenced the γ-carboxylase inhibitory protein calumenin. Results and Conclusions Stable cell lines transfected with only a factor VII cDNA had a 9% production of functional recombinant factor VII. On the other hand, these recombinant factor VII producing cells when engineered to overexpress VKORC1 and having calumenin stably suppressed more than 80% by shRNA expression, produced 68% functional factor VII. The technology presented should be applicable to all vertebrae members of the vitamin K-dependent protein family and should lower the production cost of the clinically used factors VII, IX and protein C. PMID:18177690

Toward solar biodiesel production from CO2 using engineered cyanobacteria.

PubMed

Woo, Han Min; Lee, Hyun Jeong

2017-05-01

Metabolic engineering of cyanobacteria has received attention as a sustainable strategy to convert carbon dioxide to various biochemicals including fatty acid-derived biodiesel. Recently, Synechococcus elongatus PCC 7942, a model cyanobacterium, has been engineered to convert CO2 to fatty acid ethyl esters (FAEEs) as biodiesel. Modular pathway has been constructed for FAEE production. Several metabolic engineering strategies were discussed to improve the production levels of FAEEs, including host engineering by improving CO2 fixation rate and photosynthetic efficiency. In addition, protein engineering of key enzyme in S. elongatus PCC 7942 was implemented to address issues on FAEE secretions toward sustainable FAEE production from CO2. Finally, advanced metabolic engineering will promote developing biosolar cell factories to convert CO2 to feasible amount of FAEEs toward solar biodiesel. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Transition in Gas Turbine Control System Architecture: Modular, Distributed, and Embedded

NASA Technical Reports Server (NTRS)

Culley, Dennis

2010-01-01

Controls systems are an increasingly important component of turbine-engine system technology. However, as engines become more capable, the control system itself becomes ever more constrained by the inherent environmental conditions of the engine; a relationship forced by the continued reliance on commercial electronics technology. A revolutionary change in the architecture of turbine-engine control systems will change this paradigm and result in fully distributed engine control systems. Initially, the revolution will begin with the physical decoupling of the control law processor from the hostile engine environment using a digital communications network and engine-mounted high temperature electronics requiring little or no thermal control. The vision for the evolution of distributed control capability from this initial implementation to fully distributed and embedded control is described in a roadmap and implementation plan. The development of this plan is the result of discussions with government and industry stakeholders

An Accelerated Development, Reduced Cost Approach to Lunar/Mars Exploration Using a Modular NTR-Based Space Transportation System

NASA Technical Reports Server (NTRS)

Borowski, S.; Clark, J.; Sefcik, R.; Corban, R.; Alexander, S.

1995-01-01

The results of integrated systems and mission studies are presented which quantify the benefits and rationale for developing a common, modular lunar/Mars space transportation system (STS) based on nuclear thermal rocket (NTR) technology. At present NASA's Exploration Program Office (ExPO) is considering chemical propulsion for an 'early return to the Moon' and NTR propulsion for the more demanding Mars missions to follow. The time and cost to develop these multiple systems are expected to be significant. The Nuclear Propulsion Office (NPO) has examined a variety of lunar and Mars missions and heavy lift launch vehicle (HLLV) options in an effort to determine a 'standardized' set of engine and stage components capable of satisfying a wide range of Space Exploration Initiative (SEI) missions. By using these components in a 'building block' fashion, a variety of single and multi-engine lunar and Mars vehicles can be configured. For NASA's 'First Lunar Outpost' (FLO) mission, an expendable NTR stage powered by two 50 klbf engines can deliver approximately 96 metric tons (t) to translunar injection (TLI) conditions for an initial mass in low earth orbit (IMLEO) of approximately 198 t compared to 250 t for a cryogenic chemical TLI stage. The NTR stage liquid hydrogen (LH2) tank has a 10 m diameter, 14.5 m length, and 66 t LH2 capacity. The NTR utilizes a UC-ZrC-graphite 'composite' fuel with a specific impulse (Isp) capability of approximately 900 s and an engine thrust-to-weight ratio of approximately 4.3. By extending the size and LH2 capacity of the lunar NTR stage to approximately 20 m and 96 t, respectively, a single launch Mars cargo vehicle capable of delivering approximately 50 t of surface payload is possible. Three 50 klbf NTR engines and the two standardized LH2 tank sizes developed for lunar and Mars cargo vehicle applications would be used to configure the Mars piloted vehicle for a mission as early as 2010. The paper describes the features of the 'common' NTR-based moon/Mars STS, examines performance sensitivities resulting from different 'mission mode' assumptions, and quantifies potential schedule and cost benefits resulting from this modular moon/Mars NTR vehicle approach.

Computational System For Rapid CFD Analysis In Engineering

NASA Technical Reports Server (NTRS)

Barson, Steven L.; Ascoli, Edward P.; Decroix, Michelle E.; Sindir, Munir M.

1995-01-01

Computational system comprising modular hardware and software sub-systems developed to accelerate and facilitate use of techniques of computational fluid dynamics (CFD) in engineering environment. Addresses integration of all aspects of CFD analysis process, including definition of hardware surfaces, generation of computational grids, CFD flow solution, and postprocessing. Incorporates interfaces for integration of all hardware and software tools needed to perform complete CFD analysis. Includes tools for efficient definition of flow geometry, generation of computational grids, computation of flows on grids, and postprocessing of flow data. System accepts geometric input from any of three basic sources: computer-aided design (CAD), computer-aided engineering (CAE), or definition by user.

Enhanced Engine Performance During Emergency Operation Using a Model-Based Engine Control Architecture

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Connolly, Joseph W.

2016-01-01

This paper discusses the design and application of model-based engine control (MBEC) for use during emergency operation of the aircraft. The MBEC methodology is applied to the Commercial Modular Aero-Propulsion System Simulation 40k (CMAPSS40k) and features an optimal tuner Kalman Filter (OTKF) to estimate unmeasured engine parameters, which can then be used for control. During an emergency scenario, normally-conservative engine operating limits may be relaxed to increase the performance of the engine and overall survivability of the aircraft; this comes at the cost of additional risk of an engine failure. The MBEC architecture offers the advantage of estimating key engine parameters that are not directly measureable. Estimating the unknown parameters allows for tighter control over these parameters, and on the level of risk the engine will operate at. This will allow the engine to achieve better performance than possible when operating to more conservative limits on a related, measurable parameter.

Enhanced Engine Performance During Emergency Operation Using a Model-Based Engine Control Architecture

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Connolly, Joseph W.

2015-01-01

This paper discusses the design and application of model-based engine control (MBEC) for use during emergency operation of the aircraft. The MBEC methodology is applied to the Commercial Modular Aero-Propulsion System Simulation 40,000 (CMAPSS40,000) and features an optimal tuner Kalman Filter (OTKF) to estimate unmeasured engine parameters, which can then be used for control. During an emergency scenario, normally-conservative engine operating limits may be relaxed to increase the performance of the engine and overall survivability of the aircraft; this comes at the cost of additional risk of an engine failure. The MBEC architecture offers the advantage of estimating key engine parameters that are not directly measureable. Estimating the unknown parameters allows for tighter control over these parameters, and on the level of risk the engine will operate at. This will allow the engine to achieve better performance than possible when operating to more conservative limits on a related, measurable parameter.

Photocharge accumulation and recombination in perovskite solar cells regarding device performance and stability

NASA Astrophysics Data System (ADS)

Li, Yusheng; Li, Yiming; Shi, Jiangjian; Li, Hongshi; Zhang, Huiyin; Wu, Jionghua; Li, Dongmei; Luo, Yanhong; Wu, Huijue; Meng, Qingbo

2018-01-01

Photocharge accumulation and recombination in perovskite solar cells have been systematically investigated in this paper by electrochemical spectroscopy and transient photocurrent/photovoltage methods. It is found that the non-equilibrium photocharges stored in the selective charge transport layers follow a backward recombination mechanism. That is, the photocharges are first captured by the interface defects corresponding to the fast photovoltage decay, while the bulk charge recombination instead of the diffusion process dominates the slow photovoltage decay process. Further investigation reveals that the device degradation preferentially takes place at the interface under working conditions, which thus can confirm the importance of interface engineering to enhance the device stability.

[Advances of consolidated bioprocessing based on recombinant strategy].

PubMed

Zheng, Zongbao; Zhao, Meina; Chen, Tao; Zhao, Xueming

2013-10-01

Lignocellulosic biomass represents an abundant, low-cost and renewable source of potentially fermentable sugars. It is acandidate besides petroleum as feedstock for fuel and chemical production. Recent researches on utilizing lignocellulosicsas feedstock boost development of numerous-promising processes for a variety of fuels and chemicals, such as biodiesel, biohydrogen and ethanol. However, high cost in depolymerization is a primary obstacle preventing the use of lignocellulosic biomass as feedstock. Consolidated bioprocessing (CBP), refers to the bioprocess without any exogenous cellulolyotic enzymes added, converting the lignocellulosic material into biochemicals directly, which could potentially avoid the cost of the dedicated enzyme generation step by incorporating enzyme-generating, biomass-degrading and bioproduct-producing capabilities into a single organism through genetic engineering. There are two CBP strategies, native strategy and recombinant strategy. We mainly introduce the recombinant strategy, including its principle, the two responding styles, the contributions of synthetic biology and metabolic engineering and the future challenges.

Genetically engineering adenoviral vectors for gene therapy.

PubMed

Coughlan, Lynda

2014-01-01

Adenoviral (Ad) vectors are commonly used for various gene therapy applications. Significant advances in the genetic engineering of Ad vectors in recent years has highlighted their potential for the treatment of metastatic disease. There are several methods to genetically modify the Ad genome to incorporate retargeting peptides which will redirect the natural tropism of the viruses, including homologous recombination in bacteria or yeast. However, homologous recombination in yeast is highly efficient and can be achieved without the need for extensive cloning strategies. In addition, the method does not rely on the presence of unique restriction sites within the Ad genome and the reagents required for this method are widely available and inexpensive. Large plasmids containing the entire adenoviral genome (~36 kbp) can be modified within Saccharomyces cerevisiae yeast and genomes easily rescued in Escherichia coli hosts for analysis or amplification. A method for two-step homologous recombination in yeast is described in this chapter.

Architectural mutation and leaf form, for the palmate series.

PubMed

White, D A

2005-07-21

Palmate leaf form occurs in both the ferns and angiosperms. The palmate leaf form, and its variants, is present in distantly separated clades within both ferns and angiosperms. There tend not to be intermediate forms which link these palmate leaves to other leaf forms within the taxonomic groups in question. The recurrence of homoplasious leaf forms in separate taxonomic groups could be a consequence of the algorithmic like mode of leaf growth. Leaves develop through the reiteration of modular units. It is probable that the homoplasious leaf forms in different taxa are derived independently through re-combinations of the parameters in the basic leaf form development algorithm.

Steam engine research for solar parabolic dish

NASA Technical Reports Server (NTRS)

Demler, R. L.

1981-01-01

The parabolic dish solar concentrator provides an opportunity to generate high grade energy in a modular system. Most of the capital is projected to be in the dish and its installation. Assurance of a high production demand of a standard dish could lead to dramatic cost reductions. High production volume in turn depends upon maximum application flexibility by providing energy output options, e.g., heat, electricity, chemicals and combinations thereof. Subsets of these options include energy storage and combustion assist. A steam engine design and experimental program is described which investigate the efficiency potential of a small 25 kW compound reheat cycle piston engine. An engine efficiency of 35 percent is estimated for a 700 C steam temperature from the solar receiver.

Implications of multiplane-multispeed balancing for future turbine engine design and cost

NASA Technical Reports Server (NTRS)

Badgley, R. H.

1974-01-01

This paper describes several alternative approaches, provided by multiplane-multispeed balancing, to traditional gas turbine engine manufacture and assembly procedures. These alternatives, which range from addition of trim-balancing at the end of the traditional assembly process to modular design of the rotating system for assembly and balancing external to the engine, require attention by the engine designer as an integral part of the design process. Since multiplane-multispeed balancing may be incorporated at one or more of several points during manufacture-assembly, its deliberate use is expected to provide significant cost and performance (reduced vibration) benefits. Moreover, its availability provides the designer with a firm base from which he may advance, with reasonable assurance of success, into the flexible rotor dynamic regime.

Instructor's Guide for Fluid Mechanics: A Modular Approach.

ERIC Educational Resources Information Center

Cox, John S.

This guide is designed to assist engineering teachers in developing an understanding of fluid mechanics in their students. The course is designed around a set of nine self-paced learning modules, each of which contains a discussion of the subject matter; incremental objectives; problem index, set and answers; resource materials; and a quiz with…

Monitoring and Stimulating Development of Integrated Professional Skills in University Study Programmes

ERIC Educational Resources Information Center

Wahlgren, Marie; Ahlberg, Anders

2013-01-01

In Swedish higher education, quality assurance mainly focuses on course module outcomes. With this in mind we developed a qualitative method to monitor and stimulate progression of learning in two modularized engineering study programmes. A set of core professional values and skills were triangulated through interviews with students, teachers,…

A Comparative Evaluation of Computer-Managed and Instructor-Managed Instruction.

ERIC Educational Resources Information Center

Ellis, John A.

This study compares an instructor-managed (IMI) and a computer-managed (CMI) version of a modularized, individualized Navy Training course; the main difference between groups was in testing and remediation. Subjects were 240 students enrolled in the Propulsion Engineering School at Great Lakes, Illinois, who were divided into three groups: CMI…

Modular Biopower System Providing Combined Heat and Power for DoD Installations

DTIC Science & Technology

2013-12-01

Cycle Cost evaluation using the experimental results of the 6-month field demonstration and the system’s projected cost and performance for the...34 5.6 SAMPLING RESULTS ...premises, which resulted in a significant program delay. After a short period of operation, the custom-designed engine developed mechanical

Performance of the NEXT Engineering Model Power Processing Unit

NASA Technical Reports Server (NTRS)

Pinero, Luis R.; Hopson, Mark; Todd, Philip C.; Wong, Brian

2007-01-01

The NASA s Evolutionary Xenon Thruster (NEXT) project is developing an advanced ion propulsion system for future NASA missions for solar system exploration. An engineering model (EM) power processing unit (PPU) for the NEXT project was designed and fabricated by L-3 Communications under contract with NASA Glenn Research Center (GRC). This modular PPU is capable of processing up from 0.5 to 7.0 kW of output power for the NEXT ion thruster. Its design includes many significant improvements for better performance over the state-of-the-art PPU. The most significant difference is the beam supply which is comprised of six modules and capable of very efficient operation through a wide voltage range because of innovative features like dual controls, module addressing, and a high current mode. The low voltage power supplies are based on elements of the previously validated NASA Solar Electric Propulsion Technology Application Readiness (NSTAR) PPU. The highly modular construction of the PPU resulted in improved manufacturability, simpler scalability, and lower cost. This paper describes the design of the EM PPU and the results of the bench-top performance tests.

Distributed Engine Control Empirical/Analytical Verification Tools

NASA Technical Reports Server (NTRS)

DeCastro, Jonathan; Hettler, Eric; Yedavalli, Rama; Mitra, Sayan

2013-01-01

NASA's vision for an intelligent engine will be realized with the development of a truly distributed control system featuring highly reliable, modular, and dependable components capable of both surviving the harsh engine operating environment and decentralized functionality. A set of control system verification tools was developed and applied to a C-MAPSS40K engine model, and metrics were established to assess the stability and performance of these control systems on the same platform. A software tool was developed that allows designers to assemble easily a distributed control system in software and immediately assess the overall impacts of the system on the target (simulated) platform, allowing control system designers to converge rapidly on acceptable architectures with consideration to all required hardware elements. The software developed in this program will be installed on a distributed hardware-in-the-loop (DHIL) simulation tool to assist NASA and the Distributed Engine Control Working Group (DECWG) in integrating DCS (distributed engine control systems) components onto existing and next-generation engines.The distributed engine control simulator blockset for MATLAB/Simulink and hardware simulator provides the capability to simulate virtual subcomponents, as well as swap actual subcomponents for hardware-in-the-loop (HIL) analysis. Subcomponents can be the communication network, smart sensor or actuator nodes, or a centralized control system. The distributed engine control blockset for MATLAB/Simulink is a software development tool. The software includes an engine simulation, a communication network simulation, control algorithms, and analysis algorithms set up in a modular environment for rapid simulation of different network architectures; the hardware consists of an embedded device running parts of the CMAPSS engine simulator and controlled through Simulink. The distributed engine control simulation, evaluation, and analysis technology provides unique capabilities to study the effects of a given change to the control system in the context of the distributed paradigm. The simulation tool can support treatment of all components within the control system, both virtual and real; these include communication data network, smart sensor and actuator nodes, centralized control system (FADEC full authority digital engine control), and the aircraft engine itself. The DECsim tool can allow simulation-based prototyping of control laws, control architectures, and decentralization strategies before hardware is integrated into the system. With the configuration specified, the simulator allows a variety of key factors to be systematically assessed. Such factors include control system performance, reliability, weight, and bandwidth utilization.

Infection and transmission of live recombinant Newcastle disease virus vaccines in Rock Pigeons, European House Sparrows, and Japanese Quail

USDA-ARS?s Scientific Manuscript database

In China and Mexico, engineered recombinant Newcastle disease virus (rNDV) strains are used as live vaccines for the control of Newcastle disease and as vectors to express the avian influenza virus hemagglutinin (HA) gene to control avian influenza in poultry. In this study, non-target species wer...

Ion-ion Recombination and Chemiion Concentrations In Aircraft Exhaust

NASA Astrophysics Data System (ADS)

Turco, R. P.; Yu, F.

Jet aircraft emit large quantities of ultrafine volatile aerosols, as well as soot parti- cles, into the environment. To determine the long-term effects of these emissions, a better understanding of the mechanisms that control particle formation and evolution is needed, including the number and size dispersion. A recent explanation for aerosol nucleation in a jet wake involves the condensation of sulfuric acid vapor, and cer- tain organic compounds, onto charged molecular clusters (chemiions) generated in the engine combustors (Yu and Turco, 1997). Massive charged aggregates, along with sulfuric acid and organic precursor vapors, have been detected in jet plumes under cruise conditions. In developing the chemiion nucleation theory, Yu and Turco noted that ion-ion recombination in the engine train and jet core should limit the chemiion emission index to 1017/kg-fuel. This value is consistent with ion-ion recombination coefficients of 1×10-7 cm3/s over time scales of 10-2 s. However, the evolution of the ions through the engine has not been adequately studied. The conditions at the combustor exit are extreme-temperatures approach 1500 K, and pressures can reach 30 atmospheres. In this presentation, we show that as the combustion gases expand and cool, two- and three-body ion-ion recombination processes control the chemiion concentration. The concepts of mutual neutralization and Thomson recombination are first summarized, and appropriate temperature and pressure dependent recombination rate coefficients are derived for the aircraft problem. A model for ion losses in jet exhaust is then formulated using an "invariance" principle discussed by Turco and Yu (1997) in the context of a coagulating aerosol in an expanding plume. This recombina- tion model is applied to estimate chemiion emission indices for a range of operational engine conditions. The predicted ion emission rates are found to be consistent with observations. We discuss the sources of variance in chemiion exhaust concentrations based on the physical processes occurring in the exhaust stream. References: Turco, R. P., and F. Yu, Aerosol invariance in expanding, coagulating plumes, Geo- phys. Res. Lett., 24, 1223-1226, 1997. Yu, F., and R. P. Turco, The role of ions in the formation and evolution of particles in aircraft plumes, Geophys. Res. Lett., 24, 1927-1930, 1997.

Distributed utility technology cost, performance, and environmental characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wan, Y; Adelman, S

1995-06-01

Distributed Utility (DU) is an emerging concept in which modular generation and storage technologies sited near customer loads in distribution systems and specifically targeted demand-side management programs are used to supplement conventional central station generation plants to meet customer energy service needs. Research has shown that implementation of the DU concept could provide substantial benefits to utilities. This report summarizes the cost, performance, and environmental and siting characteristics of existing and emerging modular generation and storage technologies that are applicable under the DU concept. It is intended to be a practical reference guide for utility planners and engineers seeking informationmore » on DU technology options. This work was funded by the Office of Utility Technologies of the US Department of Energy.« less

Optimizing Aspect-Oriented Mechanisms for Embedded Applications

NASA Astrophysics Data System (ADS)

Hundt, Christine; Stöhr, Daniel; Glesner, Sabine

As applications for small embedded mobile devices are getting larger and more complex, it becomes inevitable to adopt more advanced software engineering methods from the field of desktop application development. Aspect-oriented programming (AOP) is a promising approach due to its advanced modularization capabilities. However, existing AOP languages tend to add a substantial overhead in both execution time and code size which restricts their practicality for small devices with limited resources. In this paper, we present optimizations for aspect-oriented mechanisms at the level of the virtual machine. Our experiments show that these optimizations yield a considerable performance gain along with a reduction of the code size. Thus, our optimizations establish the base for using advanced aspect-oriented modularization techniques for developing Java applications on small embedded devices.

BeamDyn: A High-Fidelity Wind Turbine Blade Solver in the FAST Modular Framework: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Q.; Sprague, M.; Jonkman, J.

2015-01-01

BeamDyn, a Legendre-spectral-finite-element implementation of geometrically exact beam theory (GEBT), was developed to meet the design challenges associated with highly flexible composite wind turbine blades. In this paper, the governing equations of GEBT are reformulated into a nonlinear state-space form to support its coupling within the modular framework of the FAST wind turbine computer-aided engineering (CAE) tool. Different time integration schemes (implicit and explicit) were implemented and examined for wind turbine analysis. Numerical examples are presented to demonstrate the capability of this new beam solver. An example analysis of a realistic wind turbine blade, the CX-100, is also presented asmore » validation.« less

Analysis of In-Space Assembly of Modular Systems

NASA Technical Reports Server (NTRS)

Moses, Robert W.; VanLaak, James; Johnson, Spencer L.; Chytka, Trina M.; Reeves, John D.; Todd, B. Keith; Moe, Rud V.; Stambolian, Damon B.

2005-01-01

Early system-level life cycle assessments facilitate cost effective optimization of system architectures to enable implementation of both modularity and in-space assembly, two key Exploration Systems Research & Technology (ESR&T) Strategic Challenges. Experiences with the International Space Station (ISS) demonstrate that the absence of this rigorous analysis can result in increased cost and operational risk. An effort is underway, called Analysis of In-Space Assembly of Modular Systems, to produce an innovative analytical methodology, including an evolved analysis toolset and proven processes in a collaborative engineering environment, to support the design and evaluation of proposed concepts. The unique aspect of this work is that it will produce the toolset, techniques and initial products to analyze and compare the detailed, life cycle costs and performance of different implementations of modularity for in-space assembly. A multi-Center team consisting of experienced personnel from the Langley Research Center, Johnson Space Center, Kennedy Space Center, and the Goddard Space Flight Center has been formed to bring their resources and experience to this development. At the end of this 30-month effort, the toolset will be ready to support the Exploration Program with an integrated assessment strategy that embodies all life-cycle aspects of the mission from design and manufacturing through operations to enable early and timely selection of an optimum solution among many competing alternatives. Already there are many different designs for crewed missions to the Moon that present competing views of modularity requiring some in-space assembly. The purpose of this paper is to highlight the approach for scoring competing designs.

Sensor Data Qualification Technique Applied to Gas Turbine Engines

NASA Technical Reports Server (NTRS)

Csank, Jeffrey T.; Simon, Donald L.

2013-01-01

This paper applies a previously developed sensor data qualification technique to a commercial aircraft engine simulation known as the Commercial Modular Aero-Propulsion System Simulation 40,000 (C-MAPSS40k). The sensor data qualification technique is designed to detect, isolate, and accommodate faulty sensor measurements. It features sensor networks, which group various sensors together and relies on an empirically derived analytical model to relate the sensor measurements. Relationships between all member sensors of the network are analyzed to detect and isolate any faulty sensor within the network.

Reprogramming cellular functions with engineered membrane proteins.

PubMed

Arber, Caroline; Young, Melvin; Barth, Patrick

2017-10-01

Taking inspiration from Nature, synthetic biology utilizes and modifies biological components to expand the range of biological functions for engineering new practical devices and therapeutics. While early breakthroughs mainly concerned the design of gene circuits, recent efforts have focused on engineering signaling pathways to reprogram cellular functions. Since signal transduction across cell membranes initiates and controls intracellular signaling, membrane receptors have been targeted by diverse protein engineering approaches despite limited mechanistic understanding of their function. The modular architecture of several receptor families has enabled the empirical construction of chimeric receptors combining domains from distinct native receptors which have found successful immunotherapeutic applications. Meanwhile, progress in membrane protein structure determination, computational modeling and rational design promise to foster the engineering of a broader range of membrane receptor functions. Marrying empirical and rational membrane protein engineering approaches should enable the reprogramming of cells with widely diverse fine-tuned functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

An Overview and History of Glyco-Engineering in Insect Expression Systems.

PubMed

Geisler, Christoph; Mabashi-Asazuma, Hideaki; Jarvis, Donald L

2015-01-01

Insect systems, including the baculovirus-insect cell and Drosophila S2 cell systems are widely used as recombinant protein production platforms. Historically, however, no insect-based system has been able to produce glycoproteins with human-type glycans, which often influence the clinical efficacy of therapeutic glycoproteins and the overall structures and functions of other recombinant glycoprotein products. In addition, some insect cell systems produce N-glycans with immunogenic epitopes. Over the past 20 years, these problems have been addressed by efforts to glyco-engineer insect-based expression systems. These efforts have focused on introducing the capacity to produce complex-type, terminally sialylated N-glycans and eliminating the capacity to produce immunogenic N-glycans. Various glyco-engineering approaches have included genetically engineering insect cells, baculoviral vectors, and/or insects with heterologous genes encoding the enzymes required to produce various glycosyltransferases, sugars, nucleotide sugars, and nucleotide sugar transporters, as well as an enzyme that can deplete GDP-fucose. In this chapter, we present an overview and history of glyco-engineering in insect expression systems as a prelude to subsequent chapters, which will highlight various methods used for this purpose.

Tissue engineering for lateral ridge augmentation with recombinant human bone morphogenetic protein 2 combination therapy: a case report.

PubMed

Mandelaris, George A; Spagnoli, Daniel B; Rosenfeld, Alan L; McKee, James; Lu, Mei

2015-01-01

This case report describes a tissue-engineered reconstruction with recombinant human bone morphogenetic protein 2/acellular collagen sponge (rhBMP-2/ ACS) + cancellous allograft and space maintenance via Medpor Contain mesh in the treatment of a patient requiring maxillary and mandibular horizontal ridge augmentation to enable implant placement. The patient underwent a previously unsuccessful corticocancellous bone graft at these sites. Multiple and contiguous sites in the maxilla and in the mandibular anterior, demonstrating advanced lateral ridge deficiencies, were managed using a tissue engineering approach as an alternative to autogenous bone harvesting. Four maxillary and three mandibular implants were placed 9 and 10 months, respectively, after tissue engineering reconstruction, and all were functioning successfully after 24 months of follow-up. Histomorphometric analysis of a bone core obtained at the time of the maxillary implant placement demonstrated a mean of 76.1% new vital bone formation, 22.2% marrow/cells, and 1.7% residual graft tissue. Tissue engineering for lateral ridge augmentation with combination therapy requires further research to determine predictability and limitations.

Bacterial Genome Engineering and Synthetic Biology: Combating Pathogens

DTIC Science & Technology

2016-11-04

engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats ( CRISPR ), and bacterial cell-cell...Cholera# Yersinia pseudotuberculosis# Staphylococcus aureus* Phage Engineering CRISPR /Cas9 Delivery of CRISPR genes and RNA guides for sequence...bear very close sequence alignment to the harmless strains via the use of the CRISPR /Cas9 system. The CRISPR system specifically targets a DNA sequence

Space Station redesign option A: Modular buildup concept

NASA Technical Reports Server (NTRS)

1993-01-01

In early 1993, President Clinton mandated that NASA look at lower cost alternatives to Space Station Freedom. He also established an independent advisory committee - the Blue Ribbon Panel - to review the redesign work and evaluate alternatives. Daniel Goldin, NASA Administrator, established a Station Redesign Team that began operating in late March from Crystal City, Virginia. NASA intercenter teams - one each at Marshall Space Flight Center, Johnson Space Center, and Langley Research Center provided engineering and other support. The results of the Option A study done at Marshall Space Flight Center are summarized. Two configurations (A-1 and A-2) are covered. Additional data is provided in the briefing package MSFC SRT-001, Final System Review to SRT-002, Space Station Option A Modular Buildup Concept, Volumes 1-5, Revision B, June 10, 1993. In June 1993, President Clinton decided to proceed with a modular concept consistent with Option A, and asked NASA to provide an Implementation Plan by September. All data from the Option A redesign activity was provided to NASA's Transition Team for use in developing the Implementation Plan.

Modular open RF architecture: extending VICTORY to RF systems

NASA Astrophysics Data System (ADS)

Melber, Adam; Dirner, Jason; Johnson, Michael

2015-05-01

Radio frequency products spanning multiple functions have become increasingly critical to the warfighter. Military use of the electromagnetic spectrum now includes communications, electronic warfare (EW), intelligence, and mission command systems. Due to the urgent needs of counterinsurgency operations, various quick reaction capabilities (QRCs) have been fielded to enhance warfighter capability. Although these QRCs were highly successfully in their respective missions, they were designed independently resulting in significant challenges when integrated on a common platform. This paper discusses how the Modular Open RF Architecture (MORA) addresses these challenges by defining an open architecture for multifunction missions that decomposes monolithic radio systems into high-level components with welldefined functions and interfaces. The functional decomposition maximizes hardware sharing while minimizing added complexity and cost due to modularization. MORA achieves significant size, weight and power (SWaP) savings by allowing hardware such as power amplifiers and antennas to be shared across systems. By separating signal conditioning from the processing that implements the actual radio application, MORA exposes previously inaccessible architecture points, providing system integrators with the flexibility to insert third-party capabilities to address technical challenges and emerging requirements. MORA leverages the Vehicular Integration for Command, Control, Communication, Computers, Intelligence, Surveillance, and Reconnaissance (C4ISR)/EW Interoperability (VICTORY) framework. This paper concludes by discussing how MORA, VICTORY and other standards such as OpenVPX are being leveraged by the U.S. Army Research, Development, and Engineering Command (RDECOM) Communications Electronics Research, Development, and Engineering Center (CERDEC) to define a converged architecture enabling rapid technology insertion, interoperability and reduced SWaP.

Bioelectrochemical conversion of CO2 to value added product formate using engineered Methylobacterium extorquens.

PubMed

Jang, Jungho; Jeon, Byoung Wook; Kim, Yong Hwan

2018-05-08

The conversion of carbon dioxide to formate is a fundamental step for building C1 chemical platforms. Methylobacterium extorquens AM1 was reported to show remarkable activity converting carbon dioxide into formate. Formate dehydrogenase 1 from M. extorquens AM1 (MeFDH1) was verified as the key responsible enzyme for the conversion of carbon dioxide to formate in this study. Using a 2% methanol concentration for induction, microbial harboring the recombinant MeFDH1 expressing plasmid produced the highest concentration of formate (26.6 mM within 21 hours) in electrochemical reactor. 60 μM of sodium tungstate in the culture medium was optimal for the expression of recombinant MeFDH1 and production of formate (25.7 mM within 21 hours). The recombinant MeFDH1 expressing cells showed maximum formate productivity of 2.53 mM/g-wet cell/hr, which was 2.5 times greater than that of wild type. Thus, M. extorquens AM1 was successfully engineered by expressing MeFDH1 as recombinant enzyme to elevate the production of formate from CO 2 after elucidating key responsible enzyme for the conversion of CO 2 to formate.

Production of recombinant protein G through high-density fermentation of engineered bacteria as well as purification.

PubMed

Zhang, Hu-Cheng; Yang, Jun; Yang, Guo-Wei; Wang, Xiao-Jie; Fan, Hai-Tao

2015-08-01

Recombinant Streptococcus Protein G (PG) is a cell wall protein, which, when combined with mammal immunoglobulin, is used in separating antibody technology. High-density fermentation technologies using an engineered recombinant PG-producing bacteria as well as PG separation and purification technologies have a direct impact on the availability and application of PG. Through primary and secondary seed cultivation, a recombinant E. coli strain was subjected to high-density fermentation with controlled feed supplement concentration under stimulation with isopropyl β-D-1-thiogalactopyranoside. The present study investigated the effect of factors including inoculum size, oxygen levels, pH and the cultivating method on the fermentation process, as well as the effect of the separation and purification technologies, including ultrasonication, nickel column affinity chromatography, Sephadex G-25 gel filtration chromatography and diethylaminoethanol-sepharose fast flow ion exchange chromatography on the yield and purity of PG. The efficiency of extraction was detected using SDS-PAGE. High-density fermentation yielded 80-150 g/l of bacteria and 1 g PG was obtained from one liter broth. The present study delivered a highly efficient novel method via which PG can be obtained at a high concentration and a purity >95%.

Preparation of umami octopeptide with recombined Escherichia coli: Feasibility and challenges.

PubMed

Zhao, Liming; Zhang, Yin; Venkitasamy, Chandrasekar; Pan, Zhongli; Zhang, Longyi; Guo, Siya; Xiong, Wei; Xia, Hu; Wenlong, Liu; Xinhua, Gou

2018-01-01

The taste of umami peptide H-Lys-Gly-Asp-Glu-Glu-Ser-Leu-Ala-OH (LGAGGSLA) is controversial. One possible reason for this controversy is the use of chemically synthesized LGAGGSLA to confirm its taste. To explore other ways to further confirm the flavor of LGAGGSLA, we developed a new strategy to prepare a bio-source peptide by adopting a gene engineering method to express LGAGGSLA in recombinant Escherichia coli. In our previous work, we structured the LGAGGSLA recombinant expression system and optimized the culturing conditions for preparing a fusion protein. However, the fusion protein was not cleaved by enterokinase to obtain LGAGGSLA. Because the cleavage conditions of commercial enterokinase were not specific and recombinant engineered bacteria had the potential to be used in industrial processes, in this addendum, we calculated the mass and volume yields of key processing steps in the preparation of LGAGGSLA, and established a model of cleavage conditions with the cleavage ratio of LGAGGSLA. When the LGAGGSLA was confirmed to show umami taste, it is considered as a new umami or umami enhancer. The gene information of LGAGGSLA should have a great potential in the development of new flavor product and food product containing high umami flavor.

Impact of IgG Fc-Oligosaccharides on Recombinant Monoclonal Antibody Structure, Stability, Safety, and Efficacy.

PubMed

Liu, Hongcheng; Nowak, Christine; Andrien, Bruce; Shao, Mei; Ponniah, Gomathinayagam; Neill, Alyssa

2017-09-01

Glycosylation of the conserved asparagine residue in the CH2 domain is the most common posttranslational modification of recombinant monoclonal antibodies. Ideally, a consistent oligosaccharide profile should be maintained from early clinical material to commercial material for the development of recombinant monoclonal therapeutics, though variation in the profile is a typical result of process changes. The risk of oligosaccharide variation posed to further development is required to be thoroughly evaluated based on its impact on antibody structure, stability, efficacy and safety. The variation should be controlled within a range so that there is no detrimental impact on safety and efficacy and thus allowing the use of early phase safety and efficacy data to support project advancement to later phase. This review article focuses on the current scientific understanding of the commonly observed oligosaccharides found in recombinant monoclonal antibodies and their impact on structure, stability and biological functions, which are the basis to evaluate safety and efficacy. It also provides a brief discussion on critical quality attribute (CQA) assessment with regard to oligosaccharides based on the mechanism of action (MOA). © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1173-1181, 2017. © 2017 American Institute of Chemical Engineers.

Development of a novel engineered E. coli host cell line platform with improved column capacity performance for ion-exchange chromatography.

PubMed

Mukherjee, Rudra Palash; Fruchtl, McKinzie S; Beitle, Robert R; Brune, Ellen M

2018-02-01

This article reports on the analysis of an engineered Escherichia coli designed to reduce the host cell protein (HCP) burden on recombinant protein purification by column chromatography. Since downstream purification accounts for a major portion of production costs when using a recombinant platform, minimization of HCPs that are initially captured or otherwise interfere during chromatography will positively impact the entire purification process. Such a strategy, of course, would also require the cell line to grow, and express recombinant proteins, at levels comparable to, or better than, its parent strain. An E. coli strain with a small number of strategic deletions (LTSF06) was transformed to produce three different recombinant biologics to examine growth and expression, and with another model protein to assess growth and the effect of selectively reduced HCPs on target product capture on DEAE ion exchange medium. Cell growth levels were maintained or increased for all constructs, and a significant reduction in HCP adsorption was realized. Indeed, a breakthrough analysis indicated that as a result of reducing adsorption of particular HCPs, a 37% increase in target protein capture was observed. This increase in product capture efficiency was achieved by focusing not on HCPs that co-elute with the recombinant target, but rather on those possessing particular column adsorption and elution characteristics. Copyright © 2017 Elsevier Inc. All rights reserved.

Concept Development Modular Hybrid Pier (MHP)

DTIC Science & Technology

2000-02-01

rated FRP composite bridge or bridge deck is commercially available from Creative Pultrusions, Kansas Structural Systems, Martin - Marietta , Hardcore...NAVAL FACILITIES ENGINEERING SERVICE CENTER Port Hueneme, California 93043-4370 Contract Report CR 00-001-SHR FINAL REPORT PHASE 1 - CONCEPT...20000301 043 Approved for public release; distribution is unlimited. DTIC QUALITY IMWSOfBD 4 ^^ Printed on recycled paper REPORT DOCUMENTATION PAGE

A Training Tool and Methodology to Allow Concurrent Multidisciplinary Experimental Projects in Engineering Education

ERIC Educational Resources Information Center

Maseda, F. J.; Martija, I.; Martija, I.

2012-01-01

This paper describes a novel Electrical Machine and Power Electronic Training Tool (EM&PE[subscript TT]), a methodology for using it, and associated experimental educational activities. The training tool is implemented by recreating a whole power electronics system, divided into modular blocks. This process is similar to that applied when…

Physics Based Modeling in Design and Development for U.S. Defense Held in Denver, Colorado on November 14-17, 2011. Volume 2: Audio and Movie Files

DTIC Science & Technology

2011-11-17

Mr. Frank Salvatore, High Performance Technologies FIXED AND ROTARY WING AIRCRAFT 13274 - “CREATE-AV DaVinci : Model-Based Engineering for Systems... Tools for Reliability Improvement and Addressing Modularity Issues in Evaluation and Physical Testing”, Dr. Richard Heine, Army Materiel Systems

Modularity and Perspectives of Command and Control of Contingent Army of the Czech Republic during the Operation in Afghanistan

DTIC Science & Technology

2011-06-01

are provided as needed: − RCP requesting – in favour of mobile patrols, due to engineer reconnaissance in areas with higher risk of IED occurrence... hospitals , EOD and other military specialists gradually operated. PRT established by the Czech Republic within the ISAF operation in the province of Logar

On-Line Analysis of Southern FIA Data

Treesearch

Michael P. Spinney; Paul C. Van Deusen; Francis A. Roesch

2006-01-01

The Southern On-Line Estimator (SOLE) is a web-based FIA database analysis tool designed with an emphasis on modularity. The Java-based user interface is simple and intuitive to use and the R-based analysis engine is fast and stable. Each component of the program (data retrieval, statistical analysis and output) can be individually modified to accommodate major...

Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research.

PubMed

Kim, Moon-Soo; Kini, Anu Ganesh

2017-08-01

Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.

The Rolls Royce Allison RB580 turbofan - Matching the market requirement for regional transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadler, J.H.R.; Peacock, N.J.; Snyder, L.

1989-01-01

The RB580 high bypass turbofan engine has a thrust growth capability to 10,000 lb and has been optimized for efficient operation in regional markets involving 50-70 seat airliners with higher-than-turboprop cruise speeds. The two-spool engine configuration achieves an overall pressure ratio of 24 and features a single-stage wide-chord fan for high efficiency/low noise operation. The highly modular design of the configuration facilitates maintenance and repair; a dual-redundant full-authority digital electronic control system is incorporated. An SFC reduction of the order of 10 percent at cruise thrust is achieved, relative to current engines of comparable thrust class.

Survey of supersonic combustion ramjet research at Langley

NASA Technical Reports Server (NTRS)

Northam, G. B.; Anderson, G. Y.

1986-01-01

The Hypersonic Propulsion Branch at NASA Langley Research Center has maintained an active research program in supersonic combustion ramjet (scramjet) and high speed ramjet propulsion since the 1960s. The focus for this research has centered on propulsion for manned reuseable vehicles with cryogenic hydrogen fuel. This paper presents some highlights of this research. The design philosophy of the Langley fixed-geometry airframe-integrated modular scramjet is discussed. The component development and research programs that have supported the successful demonstration of the engine concept using subscale engine module hardware is reviewed and a brief summary of the engine tests presented. An extensive bibliography of research supported by the Langley program is also included.

The Application of Hardware in the Loop Testing for Distributed Engine Control

NASA Technical Reports Server (NTRS)

Thomas, George L.; Culley, Dennis E.; Brand, Alex

2016-01-01

The essence of a distributed control system is the modular partitioning of control function across a hardware implementation. This type of control architecture requires embedding electronics in a multitude of control element nodes for the execution of those functions, and their integration as a unified system. As the field of distributed aeropropulsion control moves toward reality, questions about building and validating these systems remain. This paper focuses on the development of hardware-in-the-loop (HIL) test techniques for distributed aero engine control, and the application of HIL testing as it pertains to potential advanced engine control applications that may now be possible due to the intelligent capability embedded in the nodes.

What is the role of curvature on the properties of nanomaterials for biomedical applications?

PubMed Central

Solveyra, Estefania Gonzalez

2015-01-01

The use of nanomaterials for drug delivery and theranostics applications is a promising paradigm in nanomedicine, as it brings together the best features of nanotechnolgy, molecular biology and medicine. To fully exploit the synergistic potential of such interdisciplinary strategy, a comprehensive description of the interactions at the interface between nanomaterials and biological systems is not only crucial, but also mandatory. Routine strategies to engineer nanomaterial-based drugs comprise modifying their surface with biocompatible and targeting ligands, in many cases resorting to modular approaches that assume additive behavior. However, emergent behavior can be observed when combining confinement and curvature. The final properties of functionalized nanomaterials become dependent not only on the properties of their constituents but also on the geometry of the nano-bio interface, and on the local molecular environment. Modularity no longer holds, and the coupling between interactions, chemical equilibrium and molecular organization has to be directly addressed in order to design smart nanomaterials with controlled spatial functionalization envisioning optimized biomedical applications. Nanoparticle’s curvature becomes an integral part of the design strategy, enabling to control and engineer the chemical and surface properties with molecular precision. Understanding how NP size, morphology, and surface chemistry are interrelated will put us one step closer to engineering nanobiomaterials capable of mimicking biological structures and their behaviors, paving the way into applications and the possibility to elucidate the use of curvature by biological systems. PMID:26310432

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

PubMed

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.

Dual Cross-Linked Biofunctional and Self-Healing Networks to Generate User-Defined Modular Gradient Hydrogel Constructs.

PubMed

Wei, Zhao; Lewis, Daniel M; Xu, Yu; Gerecht, Sharon

2017-08-01

Gradient hydrogels have been developed to mimic the spatiotemporal differences of multiple gradient cues in tissues. Current approaches used to generate such hydrogels are restricted to a single gradient shape and distribution. Here, a hydrogel is designed that includes two chemical cross-linking networks, biofunctional, and self-healing networks, enabling the customizable formation of modular gradient hydrogel construct with various gradient distributions and flexible shapes. The biofunctional networks are formed via Michael addition between the acrylates of oxidized acrylated hyaluronic acid (OAHA) and the dithiol of matrix metalloproteinase (MMP)-sensitive cross-linker and RGD peptides. The self-healing networks are formed via dynamic Schiff base reaction between N-carboxyethyl chitosan (CEC) and OAHA, which drives the modular gradient units to self-heal into an integral modular gradient hydrogel. The CEC-OAHA-MMP hydrogel exhibits excellent flowability at 37 °C under shear stress, enabling its injection to generate gradient distributions and shapes. Furthermore, encapsulated sarcoma cells respond to the gradient cues of RGD peptides and MMP-sensitive cross-linkers in the hydrogel. With these superior properties, the dual cross-linked CEC-OAHA-MMP hydrogel holds significant potential for generating customizable gradient hydrogel constructs, to study and guide cellular responses to their microenvironment such as in tumor mimicking, tissue engineering, and stem cell differentiation and morphogenesis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phase separation and mechanical properties of an elastomeric biomaterial from spider wrapping silk and elastin block copolymers.

PubMed

Muiznieks, Lisa D; Keeley, Fred W

2016-10-01

Elastin and silk spidroins are fibrous, structural proteins with elastomeric properties of extension and recoil. While elastin is highly extensible and has excellent recovery of elastic energy, silks are particularly strong and tough. This study describes the biophysical characterization of recombinant polypeptides designed by combining spider wrapping silk and elastin-like sequences as a strategy to rationally increase the strength of elastin-based materials while maintaining extensibility. We demonstrate a thermo-responsive phase separation and spontaneous colloid-like droplet formation from silk-elastin block copolymers, and from a 34 residue disordered region of Argiope trifasciata wrapping silk alone, and measure a comprehensive suite of tensile mechanical properties from cross-linked materials. Silk-elastin materials exhibited significantly increased strength, toughness, and stiffness compared to an elastin-only material, while retaining high failure strains and low energy loss upon recoil. These data demonstrate the mechanical tunability of protein polymer biomaterials through modular, chimeric recombination, and provide structural insights into mechanical design. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 693-703, 2016. © 2016 Wiley Periodicals, Inc.

n-CoDeR concept: unique types of antibodies for diagnostic use and therapy.

PubMed

Carlsson, R; Söderlind, E

2001-05-01

The n-CoDeR recombinant antibody gene libraries are built on a single master framework, into which diverse in vivo-formed complementarity determining regions (CDRs) are allowed to recombine. These CDRs are sampled from in vivo-processed and proof-read gene sequences, thus ensuring an optimal level of correctly folded and functional molecules. By the modularized assembly process, up to six CDRs can be varied at the same time, providing a possibility for the creation of a hitherto undescribed genetic and functional variation. The n-CoDeR antibody gene libraries can be used to select highly specific, human antibody fragments with specificities to virtually any antigen, including carbohydrates and human self-proteins and with affinities down into the subnanomolar range. Furthermore, combining CDRs sampled from in vivo-processed sequences into a single framework result in molecules exhibiting a lower immunogenicity compared to normal human immunoglobulins, as determined by computer analyses. The distinguished features of the n-CoDeR libraries in the therapeutic and diagnostic areas are discussed.

Recombinant antibodies and their use in biosensors.

PubMed

Zeng, Xiangqun; Shen, Zhihong; Mernaugh, Ray

2012-04-01

Inexpensive, noninvasive immunoassays can be used to quickly detect disease in humans. Immunoassay sensitivity and specificity are decidedly dependent upon high-affinity, antigen-specific antibodies. Antibodies are produced biologically. As such, antibody quality and suitability for use in immunoassays cannot be readily determined or controlled by human intervention. However, the process through which high-quality antibodies can be obtained has been shortened and streamlined by use of genetic engineering and recombinant antibody techniques. Antibodies that traditionally take several months or more to produce when animals are used can now be developed in a few weeks as recombinant antibodies produced in bacteria, yeast, or other cell types. Typically most immunoassays use two or more antibodies or antibody fragments to detect antigens that are indicators of disease. However, a label-free biosensor, for example, a quartz-crystal microbalance (QCM) needs one antibody only. As such, the cost and time needed to design and develop an immunoassay can be substantially reduced if recombinant antibodies and biosensors are used rather than traditional antibody and assay (e.g. enzyme-linked immunosorbant assay, ELISA) methods. Unlike traditional antibodies, recombinant antibodies can be genetically engineered to self-assemble on biosensor surfaces, at high density, and correctly oriented to enhance antigen-binding activity and to increase assay sensitivity, specificity, and stability. Additionally, biosensor surface chemistry and physical and electronic properties can be modified to further increase immunoassay performance above and beyond that obtained by use of traditional methods. This review describes some of the techniques investigators have used to develop highly specific and sensitive, recombinant antibody-based biosensors for detection of antigens in simple or complex biological samples.

Controlled Release from Recombinant Polymers

PubMed Central

Price, Robert; Poursaid, Azadeh; Ghandehari, Hamidreza

2014-01-01

Recombinant polymers provide a high degree of molecular definition for correlating structure with function in controlled release. The wide array of amino acids available as building blocks for these materials lend many advantages including biorecognition, biodegradability, potential biocompatibility, and control over mechanical properties among other attributes. Genetic engineering and DNA manipulation techniques enable the optimization of structure for precise control over spatial and temporal release. Unlike the majority of chemical synthetic strategies used, recombinant DNA technology has allowed for the production of monodisperse polymers with specifically defined sequences. Several classes of recombinant polymers have been used for controlled drug delivery. These include, but are not limited to, elastin-like, silk-like, and silk-elastinlike proteins, as well as emerging cationic polymers for gene delivery. In this article, progress and prospects of recombinant polymers used in controlled release will be reviewed. PMID:24956486

Getting the big beast to work--systems biotechnology of Bacillus megaterium for novel high-value proteins.

PubMed

Korneli, Claudia; David, Florian; Biedendieck, Rebekka; Jahn, Dieter; Wittmann, Christoph

2013-01-20

The high industrial relevance of the soil bacterium Bacillus megaterium as host for recombinant proteins is driving systems-wide analyses of its metabolic and regulatory networks. The present review highlights novel systems biology tools available to unravel the various cellular components on the level of metabolic and regulatory networks. These provide a rational platform for systems metabolic engineering of B. megaterium. In line, a number of interesting studies have particularly focused on studying recombinant B. megaterium in its industrial bioprocess environment thus integrating systems metabolic engineering with systems biotechnology and providing the full picture toward optimal processes. Copyright © 2012 Elsevier B.V. All rights reserved.

Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates.

PubMed

Aldor, Ilana S; Keasling, Jay D

2003-10-01

Implementing several metabolic engineering strategies, either individually or in combination, it is possible to construct microbial plastic factories to produce a variety of polyhydroxyalkanoate (PHA) biopolymers with desirable structures and material properties. Approaches include external substrate manipulation, inhibitor addition, recombinant gene expression, host cell genome manipulation and, most recently, protein engineering of PHA biosynthetic enzymes. In addition, mathematical models and molecular methods can be used to elucidate metabolically engineered systems and to identify targets for performance improvement.

A 5′ Noncoding Exon Containing Engineered Intron Enhances Transgene Expression from Recombinant AAV Vectors in vivo

PubMed Central

Lu, Jiamiao; Williams, James A.; Luke, Jeremy; Zhang, Feijie; Chu, Kirk; Kay, Mark A.

2017-01-01

We previously developed a mini-intronic plasmid (MIP) expression system in which the essential bacterial elements for plasmid replication and selection are placed within an engineered intron contained within a universal 5′ UTR noncoding exon. Like minicircle DNA plasmids (devoid of bacterial backbone sequences), MIP plasmids overcome transcriptional silencing of the transgene. However, in addition MIP plasmids increase transgene expression by 2 and often >10 times higher than minicircle vectors in vivo and in vitro. Based on these findings, we examined the effects of the MIP intronic sequences in a recombinant adeno-associated virus (AAV) vector system. Recombinant AAV vectors containing an intron with a bacterial replication origin and bacterial selectable marker increased transgene expression by 40 to 100 times in vivo when compared with conventional AAV vectors. Therefore, inclusion of this noncoding exon/intron sequence upstream of the coding region can substantially enhance AAV-mediated gene expression in vivo. PMID:27903072

Tailoring recombinant protein quality by rational media design.

PubMed

Brühlmann, David; Jordan, Martin; Hemberger, Jürgen; Sauer, Markus; Stettler, Matthieu; Broly, Hervé

2015-01-01

Clinical efficacy and safety of recombinant proteins are closely associated with their structural characteristics. The major quality attributes comprise glycosylation, charge variants (oxidation, deamidation, and C- & N-terminal modifications), aggregates, low-molecular-weight species (LMW), and misincorporation of amino acids in the protein backbone. Cell culture media design has a great potential to modulate these quality attributes due to the vital role of medium in mammalian cell culture. The purpose of this review is to provide an overview of the way both classical cell culture medium components and novel supplements affect the quality attributes of recombinant therapeutic proteins expressed in mammalian hosts, allowing rational and high-throughput optimization of mammalian cell culture media. A selection of specific and/or potent inhibitors and activators of oligosaccharide processing as well as components affecting multiple quality attributes are presented. Extensive research efforts in this field show the feasibility of quality engineering through media design, allowing to significantly modulate the protein function. © 2015 American Institute of Chemical Engineers.

Over production of lignocellulosic enzymes of Coriolus versicolor by genetic engineering methodology. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, A.L.

1998-07-01

The project seeks to understand the biological and chemical processes involved in the secretion of the enzyme polyphenol oxidase (PPO) by the hyphae, the basic unit of the filamentous fungus Coriolus versicolor. These studies are made to determine rational strategies for enhanced secretion of PPO, both with the use of recombinant DNA techniques and without. This effort focuses on recombinant DNA techniques to enhance enzyme production. The major thrust of this project was two-fold: to mass produce C. versicolor tyrosinase (polyphenol oxidase) by genetic engineering as well as cultural manipulations; and to utilize PPO as a biocatalyst in the processingmore » of lignocellulose as a renewable energy resource. In this study, the assessment of genomic and cDNA recombinant clones with regards to the overproduction of PPO continued. Further, immunocytochemical techniques were employed to assess the mechanism(s) involved in the secretion of PPO by the hyphae. Also, factors influencing PPO secretion were examined.« less

Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae

Treesearch

Yong-Su Jin; Thomas W. Jeffries

2004-01-01

Metabolic pathway engineering is constrained by the thermodynamic and stoichiometric feasibility of enzymatic activities of introduced genes. Engineering of xylose metabolism in Saccharomyces cerevisiae has focused on introducing genes for the initial xylose assimilation steps from Pichia stipitis, a xylose-fermenting yeast, into S. cerevisiae, a yeast raditionally...

CRBRP modular steam generator tube-to-tubesheet and shell-closure welding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Viri, D.P.

1982-01-01

The original Modular Steam Generator (MSG), whiand inh was designed, built, and tested by the Energy Systems Group (ESG) of Rockwell International, was a departure from conventional boilers or heat exchangers. The design was a hockeystick concept - the upper section of the generator is curved 90/sup 0/. Factors affecting operating parameters were considered and incorporated in the original MSG design. The MSG was fully instrumented and functionally tested at the Energy Technology Engineering Center at Rockwell. The MSG steamed continuously for over 4000 h, and at the conclusion of the 9000-h test cycle, it was systematically dismantled and examinedmore » for wear to critical components. This paper explains the solutions to several manufacturing challenges presented by the unique design of the MSG.« less

KSC-03pd0578

NASA Image and Video Library

2003-03-04

KENNEDY SPACE CENTER, FLA. -- -- Lifting their shovels for the groundbreaking of the Operations Support Building II are (left to right) Bill Pickavance, Vice President & Deputy Program Manager Florida Operations, United Space Alliance; Mike Wetmore, director of Shuttle Processing; Miguel Morales, chief, Facilities Division, Spaceport Services; Mike Sumner, chief of operations, Spaceport Services; David Wolfberg, designer of the facility, with Architect and Engineers Wolfberg, Alvarez and Partners of Coral Gables; Roy Bridges, KSC director; and Don Minderman, OSB II project manager, Spaceport Services. Not shown: David Boland, David Boland Inc.(construction company). The new building will replace modular housing constructed more than 20 years ago and house NASA and contractor support staff for shuttle operations. The demolition of the modular buildings has begun and construction will immediately follow. The new structure is projected to be ready in April 2005.

KSC-03PD-0578

NASA Technical Reports Server (NTRS)

2003-01-01

KENNEDY SPACE CENTER, FLA. -- -- Lifting their shovels for the groundbreaking of the Operations Support Building II are (left to right) Bill Pickavance, Vice President & Deputy Program Manager Florida Operations, United Space Alliance; Mike Wetmore, director of Shuttle Processing; Miguel Morales, chief, Facilities Division, Spaceport Services; Mike Sumner, chief of operations, Spaceport Services; David Wolfberg, designer of the facility, with Architect and Engineers Wolfberg, Alvarez and Partners of Coral Gables; Roy Bridges, KSC director; and Don Minderman, OSB II project manager, Spaceport Services. Not shown: David Boland, David Boland Inc.(construction company). The new building will replace modular housing constructed more than 20 years ago and house NASA and contractor support staff for shuttle operations. The demolition of the modular buildings has begun and construction will immediately follow. The new structure is projected to be ready in April 2005.

Evaluation of a focused virtual library of heterobifunctional ligands for Clostridium difficile toxins.

PubMed

Sanhueza, Carlos A; Cartmell, Jonathan; El-Hawiet, Amr; Szpacenko, Adam; Kitova, Elena N; Daneshfar, Rambod; Klassen, John S; Lang, Dean E; Eugenio, Luiz; Ng, Kenneth K-S; Kitov, Pavel I; Bundle, David R

2015-01-07

A focused library of virtual heterobifunctional ligands was generated in silico and a set of ligands with recombined fragments was synthesized and evaluated for binding to Clostridium difficile toxins. The position of the trisaccharide fragment was used as a reference for filtering docked poses during virtual screening to match the trisaccharide ligand in a crystal structure. The peptoid, a diversity fragment probing the protein surface area adjacent to a known binding site, was generated by a multi-component Ugi reaction. Our approach combines modular fragment-based design with in silico screening of synthetically feasible compounds and lays the groundwork for future efforts in development of composite bifunctional ligands for large clostridial toxins.

Rocket engine system reliability analyses using probabilistic and fuzzy logic techniques

NASA Technical Reports Server (NTRS)

Hardy, Terry L.; Rapp, Douglas C.

1994-01-01

The reliability of rocket engine systems was analyzed by using probabilistic and fuzzy logic techniques. Fault trees were developed for integrated modular engine (IME) and discrete engine systems, and then were used with the two techniques to quantify reliability. The IRRAS (Integrated Reliability and Risk Analysis System) computer code, developed for the U.S. Nuclear Regulatory Commission, was used for the probabilistic analyses, and FUZZYFTA (Fuzzy Fault Tree Analysis), a code developed at NASA Lewis Research Center, was used for the fuzzy logic analyses. Although both techniques provided estimates of the reliability of the IME and discrete systems, probabilistic techniques emphasized uncertainty resulting from randomness in the system whereas fuzzy logic techniques emphasized uncertainty resulting from vagueness in the system. Because uncertainty can have both random and vague components, both techniques were found to be useful tools in the analysis of rocket engine system reliability.

Recombinant protein expression in Escherichia coli: advances and challenges

PubMed Central

Rosano, Germán L.; Ceccarelli, Eduardo A.

2014-01-01

Escherichia coli is one of the organisms of choice for the production of recombinant proteins. Its use as a cell factory is well-established and it has become the most popular expression platform. For this reason, there are many molecular tools and protocols at hand for the high-level production of heterologous proteins, such as a vast catalog of expression plasmids, a great number of engineered strains and many cultivation strategies. We review the different approaches for the synthesis of recombinant proteins in E. coli and discuss recent progress in this ever-growing field. PMID:24860555

Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology

PubMed Central

Kouprina, Natalay; Larionov, Vladimir

2016-01-01

Transformation-associated recombination (TAR) cloning represents a unique tool for isolation and manipulation of large DNA molecules. The technique exploits a high level of homologous recombination in the yeast Sacharomyces cerevisiae. So far, TAR cloning is the only method available to selectively recover chromosomal segments up to 300 kb in length from complex and simple genomes. In addition, TAR cloning allows the assembly and cloning of entire microbe genomes up to several Mb as well as engineering of large metabolic pathways. In this review, we summarize applications of TAR cloning for functional/structural genomics and synthetic biology. PMID:27116033

A multi-landing pad DNA integration platform for mammalian cell engineering

PubMed Central

Gaidukov, Leonid; Wroblewska, Liliana; Teague, Brian; Nelson, Tom; Zhang, Xin; Liu, Yan; Jagtap, Kalpana; Mamo, Selamawit; Tseng, Wen Allen; Lowe, Alexis; Das, Jishnu; Bandara, Kalpanie; Baijuraj, Swetha; Summers, Nevin M; Zhang, Lin; Weiss, Ron

2018-01-01

Abstract Engineering mammalian cell lines that stably express many transgenes requires the precise insertion of large amounts of heterologous DNA into well-characterized genomic loci, but current methods are limited. To facilitate reliable large-scale engineering of CHO cells, we identified 21 novel genomic sites that supported stable long-term expression of transgenes, and then constructed cell lines containing one, two or three ‘landing pad’ recombination sites at selected loci. By using a highly efficient BxB1 recombinase along with different selection markers at each site, we directed recombinase-mediated insertion of heterologous DNA to selected sites, including targeting all three with a single transfection. We used this method to controllably integrate up to nine copies of a monoclonal antibody, representing about 100 kb of heterologous DNA in 21 transcriptional units. Because the integration was targeted to pre-validated loci, recombinant protein expression remained stable for weeks and additional copies of the antibody cassette in the integrated payload resulted in a linear increase in antibody expression. Overall, this multi-copy site-specific integration platform allows for controllable and reproducible insertion of large amounts of DNA into stable genomic sites, which has broad applications for mammalian synthetic biology, recombinant protein production and biomanufacturing. PMID:29617873

Accumulation and processing of a recombinant protein designed as a cleavable fusion to the endogenous Rubisco LSU protein in Chlamydomonas chloroplast

PubMed Central

Muto, Machiko; Henry, Ryan E; Mayfield, Stephen P

2009-01-01

Background Expression of recombinant proteins in green algal chloroplast holds substantial promise as a platform for the production of human therapeutic proteins. A number of proteins have been expressed in the chloroplast of Chlamydomonas reinhardtii, including complex mammalian proteins, but many of these proteins accumulate to significantly lower levels than do endogenous chloroplast proteins. We examined if recombinant protein accumulation could be enhanced by genetically fusing the recombinant reporter protein, luciferase, to the carboxy-terminal end of an abundant endogenous protein, the large subunit of ribulose bisphosphate carboxylase (Rubisco LSU). Additionally, as recombinant proteins fused to endogenous proteins are of little clinical or commercial value, we explored the possibility of engineering our recombinant protein to be cleavable from the endogenous protein in vivo. This strategy would obviate the need for further in vitro processing steps in order to produce the desired recombinant protein. To achieve this, a native protein-processing site from preferredoxin (preFd) was placed between the Rubisco LSU and luciferase coding regions in the fusion protein construct. Results The luciferase from the fusion protein accumulated to significantly higher levels than luciferase expressed alone. By eliminating the endogenous Rubisco large subunit gene (rbcL), we achieved a further increase in luciferase accumulation with respect to luciferase expression in the WT background. Importantly, near-wild type levels of functional Rubisco holoenzyme were generated following the proteolytic removal of the fused luciferase, while luciferase activity for the fusion protein was almost ~33 times greater than luciferase expressed alone. These data demonstrate the utility of using fusion proteins to enhance recombinant protein accumulation in algal chloroplasts, and also show that engineered proteolytic processing sites can be used to liberate the exogenous protein from the endogenous fusion partner, allowing for the purification of the intended mature protein. Conclusion These results demonstrate the utility of fusion proteins in algal chloroplast as a method to increase accumulation of recombinant proteins that are difficult to express. Since Rubisco is ubiquitous to land plants and green algae, this strategy may also be applied to higher plant transgenic expression systems. PMID:19323825

Metabolic engineering of the Stevia rebaudiana ent-kaurene biosynthetic pathway in recombinant Escherichia coli.

PubMed

Kong, Min Kyung; Kang, Hyun-Jun; Kim, Jin Ho; Oh, Soon Hwan; Lee, Pyung Cheon

2015-11-20

The ent-kaurene is a dedicated precursor pool and is responsible for synthesizing natural sweeteners such as steviol glycosides. In this study, to produce ent-kaurene in Escherichia coli, we modularly constructed and expressed two ent-kaurene genes encoding ent-copalyl diphosphate synthase (CPPS) and ent-kaurene synthase (KS) from Stevia rebaudiana known as a typical plant producing steviol glycoside. The CPPS and KS from S. rebaudiana were functionally expressed in a heterologous host E. coli. Furthermore, in order to enhance ent-kaurene production in E. coli, six geranylgeranyl diphosphate synthases (GGPPS) from various microorganisms and eight strains of E. coli as host were compared by measuring ent-kaurene production. The highest ent-kaurene production of approximately 41.1mg/L was demonstrated in E. coli strain MG1655 co-expressing synthetic CPPS-KS module and GGPPS from Rhodobacter sphaeroides. The ent-kaurene production was further increased up to 179.6 mg/L by overexpression of the three key enzymes for isoprenoid precursor, 1-deoxyxylulose-5-phosphate synthase (DXS), farnesyl diphosphate synthase (IspA) and isopentenyl diphosphate isomerase (IDI) from E. coli. Finally, the highest titer of ent-kaurene (578 mg/L) with a specific yield of ent-kaurene of 143.5mg/g dry cell weight was obtained by culturing E. coli strain MG1655 co-expressing the ent-kaurene module, DXS, IDI and IspA in 1L bioreactor containing 20 g/L glycerol. Copyright © 2015 Elsevier B.V. All rights reserved.

A recombinant pseudorabies virus co-expressing capsid proteins precursor P1-2A of FMDV and VP2 protein of porcine parvovirus: a trivalent vaccine candidate.

PubMed

Hong, Qi; Qian, Ping; Li, Xiang-Min; Yu, Xiao-Lan; Chen, Huan-Chun

2007-11-01

Pseudorabies (PR), foot-and-mouth disease (FMD), and porcine parvovirus disease are three important infectious diseases in swine worldwide. The gene-deleted pseudorabies virus (PRV) has been used as a live-viral vector to develop multivalent genetic engineering vaccine. In this study, a recombinant PRV, which could co-express protein precursor P1-2A of FMDV and VP2 protein of PPV, was constructed using PRV TK(-)/gE(-)/LacZ(+) mutant as the vector. After homologous recombination and plaque purification, recombinant virus PRV TK(-)/gE(-)/P1-2A-VP2 was acquired and identified. Immunogenicity, safety of the recombinant PRV and its protection against PRV were confirmed in a mouse model by indirect ELISA and serum neutralization test. The results show that the recombinant PRV is a candidate vaccine strain to develop a novel trivalent vaccine against PRV, FMDV and PPV in swine.

Engine Icing Modeling and Simulation (Part 2): Performance Simulation of Engine Rollback Phenomena

NASA Technical Reports Server (NTRS)

May, Ryan D.; Guo, Ten-Huei; Veres, Joseph P.; Jorgenson, Philip C. E.

2011-01-01

Ice buildup in the compressor section of a commercial aircraft gas turbine engine can cause a number of engine failures. One of these failure modes is known as engine rollback: an uncommanded decrease in thrust accompanied by a decrease in fan speed and an increase in turbine temperature. This paper describes the development of a model which simulates the system level impact of engine icing using the Commercial Modular Aero-Propulsion System Simulation 40k (C-MAPSS40k). When an ice blockage is added to C-MAPSS40k, the control system responds in a manner similar to that of an actual engine, and, in cases with severe blockage, an engine rollback is observed. Using this capability to simulate engine rollback, a proof-of-concept detection scheme is developed and tested using only typical engine sensors. This paper concludes that the engine control system s limit protection is the proximate cause of iced engine rollback and that the controller can detect the buildup of ice particles in the compressor section. This work serves as a feasibility study for continued research into the detection and mitigation of engine rollback using the propulsion control system.

Advanced Energy Storage and Conversion Devices

DTIC Science & Technology

2008-12-01

determined lithium-ion insertion mechanisms. 3.1 Background and Objectives Polymer electrolyte membrane fuel cells ( PEMFCs ) function by permitting...is one of the most critical components in the polymer electrolyte fuel cells. In recent years, PEMFCs have been identified as promising power...and residual hydrocarbons that are commonly produced by internal combustion engines. PEMFCs , due to their high efficiency and modularity of design

Modular architecture of protein binding units for designing properties of cellulose nanomaterials.

PubMed

Malho, Jani-Markus; Arola, Suvi; Laaksonen, Päivi; Szilvay, Géza R; Ikkala, Olli; Linder, Markus B

2015-10-05

Molecular biomimetic models suggest that proteins in the soft matrix of nanocomposites have a multimodular architecture. Engineered proteins were used together with nanofibrillated cellulose (NFC) to show how this type of architecture leads to function. The proteins consist of two cellulose-binding modules (CBM) separated by 12-, 24-, or 48-mer linkers. Engineering the linkers has a considerable effects on the interaction between protein and NFC in both wet colloidal state and a dry film. The protein optionally incorporates a multimerizing hydrophobin (HFB) domain connected by another linker. The modular structure explains effects in the hydrated gel state, as well as the deformation of composite materials through stress distribution and crosslinking. Based on this work, strategies can be suggested for tuning the mechanical properties of materials through the coupling of protein modules and their interlinking architectures. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution Non-Commercial NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Construction, expression, purification and biotin labeling of a single recombinant multi-epitope antigen for double-antigen sandwich ELISA to detect hepatitis C virus antibody.

PubMed

He, Jing; Xiu, Bingshui; Wang, Guohua; Chen, Kun; Feng, Xiaoyan; Song, Xiaoguo; Zhu, Cuixia; Yang, Xiqin; Bai, Guanzhong; Ling, Shigan; Zhang, Heqiu

2011-08-01

Based on B cell epitope predictions, a recombinant antigen with multiple epitopes from four Hepatitis C Virus fragments (C, NS3, NS4 and NS5) were engineered. The recombinant gene was then highly expressed in E. coli. The non-modified and C-terminal-modified recombinant proteins were used for coating and biotin labeling, respectively, to establish the double-antigen sandwich ELISA. Ten positive reference samples confirmed by the CHIRON RIBA HCV 3.0 SIA kit were detected positive, Forty one plasma samples were positive among samples from 441 volunteers, which indicated that the recombinant antigen could readily react well with plasma HCV antibody. As critical reagents of double-antigen sandwich ELISA, the recombinant multi-epitope antigen and the C-terminal-modified and biotin-conjugated antigen show good antigenicity. In this study, we provide a simple approach to produce multiple epitopes within one recombinant protein in order to avoid the costly expression of less-effective pools of multiple proteins, which is the conventional strategy of diagnostic antigen production for HCV antibody detection.

Integrated Evaluation of Closed Loop Air Revitalization System Components

NASA Technical Reports Server (NTRS)

Murdock, K.

2010-01-01

NASA s vision and mission statements include an emphasis on human exploration of space, which requires environmental control and life support technologies. This Contractor Report (CR) describes the development and evaluation of an Air Revitalization System, modeling and simulation of the components, and integrated hardware testing with the goal of better understanding the inherent capabilities and limitations of this closed loop system. Major components integrated and tested included a 4-Bed Modular Sieve, Mechanical Compressor Engineering Development Unit, Temperature Swing Adsorption Compressor, and a Sabatier Engineering and Development Unit. The requisite methodolgy and technical results are contained in this CR.

Sustainable, Reliable Mission-Systems Architecture

NASA Technical Reports Server (NTRS)

O'Neil, Graham; Orr, James K.; Watson, Steve

2005-01-01

A mission-systems architecture, based on a highly modular infrastructure utilizing open-standards hardware and software interfaces as the enabling technology is essential for affordable md sustainable space exploration programs. This mission-systems architecture requires (8) robust communication between heterogeneous systems, (b) high reliability, (c) minimal mission-to-mission reconfiguration, (d) affordable development, system integration, end verification of systems, and (e) minimal sustaining engineering. This paper proposes such an architecture. Lessons learned from the Space Shuttle program and Earthbound complex engineered systems are applied to define the model. Technology projections reaching out 5 years are made to refine model details.

Diagnostic and Condition Monitoring System Assessment for Army Helicopter Modular Turboshaft Engines.

DTIC Science & Technology

1980-10-01

from the sun. The longer bell mouth will also require that the water brake be located further from the engine, which mod- ifies the forward mount...unless there are over- riding considerations which are not readily quantifiable such as aircraft availabilit \\ and flight safety considerations...T M 1’ M Std (C) Moid. ’S-td C) M jSt- (C) 1I6’ 7 8 Prep and Install T700 4 4 5 4 5 4 5 4 Facility Check-Out and Water -Wash 1 1 /2 2 1 1-1 1!-󈧙 1

Sustainable, Reliable Mission-Systems Architecture

NASA Technical Reports Server (NTRS)

O'Neil, Graham; Orr, James K.; Watson, Steve

2007-01-01

A mission-systems architecture, based on a highly modular infrastructure utilizing: open-standards hardware and software interfaces as the enabling technology is essential for affordable and sustainable space exploration programs. This mission-systems architecture requires (a) robust communication between heterogeneous system, (b) high reliability, (c) minimal mission-to-mission reconfiguration, (d) affordable development, system integration, and verification of systems, and (e) minimal sustaining engineering. This paper proposes such an architecture. Lessons learned from the Space Shuttle program and Earthbound complex engineered system are applied to define the model. Technology projections reaching out 5 years are mde to refine model details.

Production of Japanese encephalitis virus-like particles in insect cells.

PubMed

Yamaji, Hideki; Konishi, Eiji

2013-01-01

Virus-like particles (VLPs) are composed of one or several recombinant viral surface proteins that spontaneously assemble into particulate structures without the incorporation of virus DNA or RNA. The baculovirus-insect cell system has been used extensively for the production of recombinant virus proteins including VLPs. While the baculovirus-insect cell system directs the transient expression of recombinant proteins in a batch culture, stably transformed insect cells allow constitutive production. In our recent study, a secretory form of Japanese encephalitis (JE) VLPs was successfully produced by Trichoplusia ni BTI-TN-5B1-4 (High Five) cells engineered to coexpress the JE virus (JEV) premembrane (prM) and envelope (E) proteins. A higher yield of E protein was attained with recombinant High Five cells than with the baculovirus-insect cell system. This study demonstrated that recombinant insect cells offer a promising approach to the high-level production of VLPs for use as vaccines and diagnostic antigens.

A Protein Chimera Strategy Supports Production of a Model "Difficult-to-Express" Recombinant Target.

PubMed

Hussain, Hirra; Fisher, David I; Roth, Robert G; Abbott, W Mark; Carballo-Amador, Manuel Alejandro; Warwicker, Jim; Dickson, Alan J

2018-06-22

Due in part to the needs of the biopharmaceutical industry, there has been an increased drive to generate high quality recombinant proteins in large amounts. However, achieving high yields can be a challenge as the novelty and increased complexity of new targets often makes them 'difficult-to-express'. This study aimed to define the molecular features that restrict the production of a model 'difficult-to-express' recombinant protein, Tissue Inhibitor Metalloproteinase-3 (TIMP-3). Building from experimental data, computational approaches were used to rationalise the re-design of this recombinant target to generate a chimera with enhanced secretion. The results highlight the importance of early identification of unfavourable sequence attributes, enabling the generation of engineered protein forms that bypass 'secretory' bottlenecks and result in efficient recombinant protein production. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The Development of Novel Recombinant Human Gelatins as Replacements for Animal-Derived Gelatin in Pharmaceutical Applications

NASA Astrophysics Data System (ADS)

Olsen, David; Chang, Robert; Williams, Kim E.; Polarek, James W.

We have developed a recombinant expression system to produce a series of novel recombinant human gelatins that can substitute for animal sourced gelatin preparations currently used in pharmaceutical and nutraceutical applications. This system allows the production of human sequence gelatins, or, if desired, gelatins from any other species depending on the availability of the cloned gene. The gelatins produced with this recombinant system are of defined molecular weight, unlike the animal-sourced gelatins, which consist of numerous polypeptides of varying size. The fermentation and purification process used to prepare these recombinant gelatins does not use any human- or animal-derived components and thus this recombinant material should be free from viruses and agents that cause transmissible spongiform encephalopathies. The recombinant gelatins exhibit lot-to-lot reproducibility and we have performed extensive analytical testing on them. We have demonstrated the utility of these novel gelatins as biological stabilizers and plasma expanders, and we have shown they possess qualities that are important in applications where gel formation is critical. Finally, we provide examples of how our system allows the engineering of these recombinant gelatins to optimize the production process.

Aircraft turbofans: new economic and environmental benefits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sampl, F.R.; Shank, M.E.

1985-09-01

This article describes turbofan and turboprop engines. Advanced turbofans and turboprop engines, by continuing to reduce the velocities of the jet exhaust and fan tip speed, can provide significant noise reductions. New combustors incorporated into these engines have reduced smoke, hydrocarbons and carbon monoxide to levels below the current requirements. The third generation of turbofans will continue to increase fuel efficiency and reduce aircraft operating costs. They are more modular in design and consist of half as many parts as the earlier engines, reducing maintenance time by half. Some of the key features of the new turbofan concept include: amore » very high bypass ratio/compression ratio cycle; swept fan blades; a thin, low-loss nacelle; low-loss reduction gearing; new materials; advanced compressor/turbine airfoils; and high-speed rotors with improved clearance control.« less

Reusable Rocket Engine Turbopump Health Management System

NASA Technical Reports Server (NTRS)

Surko, Pamela

1994-01-01

A health monitoring expert system software architecture has been developed to support condition-based health monitoring of rocket engines. Its first application is in the diagnosis decisions relating to the health of the high pressure oxidizer turbopump (HPOTP) of Space Shuttle Main Engine (SSME). The post test diagnostic system runs off-line, using as input the data recorded from hundreds of sensors, each running typically at rates of 25, 50, or .1 Hz. The system is invoked after a test has been completed, and produces an analysis and an organized graphical presentation of the data with important effects highlighted. The overall expert system architecture has been developed and documented so that expert modules analyzing other line replaceable units may easily be added. The architecture emphasizes modularity, reusability, and open system interfaces so that it may be used to analyze other engines as well.

Artificially Engineered Protein Polymers.

PubMed

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.

Use of bacterial co-cultures for the efficient production of chemicals.

PubMed

Jones, J Andrew; Wang, Xin

2017-12-02

The microbial production of chemicals has traditionally relied on a single engineered microbe to enable the complete bioconversion of substrate to final product. Recently, a growing fraction of research has transitioned towards employing a modular co-culture engineering strategy using multiple microbes growing together to facilitate a divide-and-conquer approach for chemical biosynthesis. Here, we review key success stories that leverage the unique advantages of co-culture engineering, while also addressing the critical concerns that will limit the wide-spread implementation of this technology. Future studies that address the need to monitor and control the population dynamics of each strain module, while maintaining robust flux routes towards a wide range of desired products will lead the efforts to realize the true potential of co-culture engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering the smart factory

NASA Astrophysics Data System (ADS)

Harrison, Robert; Vera, Daniel; Ahmad, Bilal

2016-10-01

The fourth industrial revolution promises to create what has been called the smart factory. The vision is that within such modular structured smart factories, cyber-physical systems monitor physical processes, create a virtual copy of the physical world and make decentralised decisions. This paper provides a view of this initiative from an automation systems perspective. In this context it considers how future automation systems might be effectively configured and supported through their lifecycles and how integration, application modelling, visualisation and reuse of such systems might be best achieved. The paper briefly describes limitations in current engineering methods, and new emerging approaches including the cyber physical systems (CPS) engineering tools being developed by the automation systems group (ASG) at Warwick Manufacturing Group, University of Warwick, UK.

Regulatory RNA-assisted genome engineering in microorganisms.

PubMed

Si, Tong; HamediRad, Mohammad; Zhao, Huimin

2015-12-01

Regulatory RNAs are increasingly recognized and utilized as key modulators of gene expression in diverse organisms. Thanks to their modular and programmable nature, trans-acting regulatory RNAs are especially attractive in genome-scale applications. Here we discuss the recent examples in microbial genome engineering implementing various trans-acting RNA platforms, including sRNA, RNAi, asRNA and CRISRP-Cas. In particular, we focus on how the scalable and multiplex nature of trans-acting RNAs has been used to tackle the challenges in creating genome-wide and combinatorial diversity for functional genomics and metabolic engineering applications. Advances in computational design and context-dependent regulation are also discussed for their contribution in improving fine-tuning capabilities of trans-acting RNAs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Achieving Energy Savings in Municipal Construction in Long Beach, CA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parrish, Kristen; Regnier, Cindy

Long Beach Gas and Oil (LBGO), the public gas utility in Long Beach, California, partnered with the U.S. Department of Energy (DOE) to develop and implement solutions to build a new, low-energy modular office building that is at least 50% below requirements set by Energy Standard 90.1-2007 of the American Society of Heating, Refrigerating, and Air-conditioning Engineers (ASHRAE), the American National Standards Institute (ANSI), and the Illuminating Engineering Society of America (IESNA) as part of DOE’s Commercial Building Partnerships (CBP) program.3 The LBGO building, which demonstrates that modular construction can be very energy efficient, is expected to exceed the ASHRAEmore » baseline by about 45%. The new 15,000-square foot (ft2) LBGO office building has two stories and houses private offices, open-plan cubicle offices, and a conference room and call center on the second floor. The building’s modular nature allowed LBGO to realize the cost benefits of fasttracked construction while saving substantial energy and reducing operational costs. The project was funded by the utility’s ratepayer revenue, which imposed a tight budget limit. The design process was a collaborative effort involving LBGO and its design-build team, Lawrence Berkeley National Laboratory (Berkeley Lab), and subcontractors Stantec (formerly Burt Hill) and LHB Inc. The team proposed efficiency measures based on computer modeling of the building in full compliance with ASHRAE 90.1-2007; in the modeled building, the lighting and cooling systems were the largest energy users, so increasing the efficiency of these systems was a top priority. Promising measures were modeled to estimate their energy performance, and each measure was evaluated for its feasibility within the budget.« less

Use of linalool synthase in genetic engineering of scent production

DOEpatents

Pichersky, E.

1998-12-15

A purified S-linalool synthase polypeptide from Clarkia breweri is disclosed as is the recombinant polypeptide and nucleic acid sequences encoding the polypeptide. Also disclosed are antibodies immunoreactive with the purified peptide and with recombinant versions of the polypeptide. Methods of using the nucleic acid sequences, as well as methods of enhancing the smell and the flavor of plants expressing the nucleic acid sequences are also disclosed. 5 figs.

Use of linalool synthase in genetic engineering of scent production

DOEpatents

Pichersky, Eran

1998-01-01

A purified S-linalool synthase polypeptide from Clarkia breweri is disclosed as is the recombinant polypeptide and nucleic acid sequences encoding the polypeptide. Also disclosed are antibodies immunoreactive with the purified peptide and with recombinant versions of the polypeptide. Methods of using the nucleic acid sequences, as well as methods of enhancing the smell and the flavor of plants expressing the nucleic acid sequences are also disclosed.

Re-engineering adenovirus vector systems to enable high-throughput analyses of gene function.

PubMed

Stanton, Richard J; McSharry, Brian P; Armstrong, Melanie; Tomasec, Peter; Wilkinson, Gavin W G

2008-12-01

With the enhanced capacity of bioinformatics to interrogate extensive banks of sequence data, more efficient technologies are needed to test gene function predictions. Replication-deficient recombinant adenovirus (Ad) vectors are widely used in expression analysis since they provide for extremely efficient expression of transgenes in a wide range of cell types. To facilitate rapid, high-throughput generation of recombinant viruses, we have re-engineered an adenovirus vector (designated AdZ) to allow single-step, directional gene insertion using recombineering technology. Recombineering allows for direct insertion into the Ad vector of PCR products, synthesized sequences, or oligonucleotides encoding shRNAs without requirement for a transfer vector Vectors were optimized for high-throughput applications by making them "self-excising" through incorporating the I-SceI homing endonuclease into the vector removing the need to linearize vectors prior to transfection into packaging cells. AdZ vectors allow genes to be expressed in their native form or with strep, V5, or GFP tags. Insertion of tetracycline operators downstream of the human cytomegalovirus major immediate early (HCMV MIE) promoter permits silencing of transgenes in helper cells expressing the tet repressor thus making the vector compatible with the cloning of toxic gene products. The AdZ vector system is robust, straightforward, and suited to both sporadic and high-throughput applications.

Advanced technologies for improved expression of recombinant proteins in bacteria: perspectives and applications.

PubMed

Gupta, Sanjeev K; Shukla, Pratyoosh

2016-12-01

Prokaryotic expression systems are superior in producing valuable recombinant proteins, enzymes and therapeutic products. Conventional microbial technology is evolving gradually and amalgamated with advanced technologies in order to give rise to improved processes for the production of metabolites, recombinant biopharmaceuticals and industrial enzymes. Recently, several novel approaches have been employed in a bacterial expression platform to improve recombinant protein expression. These approaches involve metabolic engineering, use of strong promoters, novel vector elements such as inducers and enhancers, protein tags, secretion signals, high-throughput devices for cloning and process screening as well as fermentation technologies. Advancement of the novel technologies in E. coli systems led to the production of "difficult to express" complex products including small peptides, antibody fragments, few proteins and full-length aglycosylated monoclonal antibodies in considerable large quantity. Wacker's secretion technologies, Pfenex system, inducers, cell-free systems, strain engineering for post-translational modification, such as disulfide bridging and bacterial N-glycosylation, are still under evaluation for the production of complex proteins and peptides in E. coli in an efficient manner. This appraisal provides an impression of expression technologies developed in recent times for enhanced production of heterologous proteins in E. coli which are of foremost importance for diverse applications in microbiology and biopharmaceutical production.

Computationally mapping sequence space to understand evolutionary protein engineering.

PubMed

Armstrong, Kathryn A; Tidor, Bruce

2008-01-01

Evolutionary protein engineering has been dramatically successful, producing a wide variety of new proteins with altered stability, binding affinity, and enzymatic activity. However, the success of such procedures is often unreliable, and the impact of the choice of protein, engineering goal, and evolutionary procedure is not well understood. We have created a framework for understanding aspects of the protein engineering process by computationally mapping regions of feasible sequence space for three small proteins using structure-based design protocols. We then tested the ability of different evolutionary search strategies to explore these sequence spaces. The results point to a non-intuitive relationship between the error-prone PCR mutation rate and the number of rounds of replication. The evolutionary relationships among feasible sequences reveal hub-like sequences that serve as particularly fruitful starting sequences for evolutionary search. Moreover, genetic recombination procedures were examined, and tradeoffs relating sequence diversity and search efficiency were identified. This framework allows us to consider the impact of protein structure on the allowed sequence space and therefore on the challenges that each protein presents to error-prone PCR and genetic recombination procedures.

Ligand-targeted theranostic nanomedicines against cancer

DOE PAGES

Yao, Virginia J.; D'Angelo, Sara; Butler, Kimberly S.; ...

2016-01-06

Nanomedicines have significant potential for cancer treatment. Although the majority of nanomedicines currently tested in clinical trials utilize simple, biocompatible liposome-based nanocarriers, their widespread use is limited by non-specificity and low target site concentration and thus, do not provide a substantial clinical advantage over conventional, systemic chemotherapy. In the past 20 years, we have identified specific receptors expressed on the surfaces of tumor endothelial and perivascular cells, tumor cells, the extracellular matrix and stromal cells using combinatorial peptide libraries displayed on bacteriophage. These studies corroborate the notion that unique receptor proteins such as IL-11Rα, GRP78, EphA5, among others, are differentiallymore » overexpressed in tumors and present opportunities to deliver tumor-specific therapeutic drugs. By using peptides that bind to tumor-specific cell-surface receptors, therapeutic agents such as apoptotic peptides, suicide genes, imaging dyes or chemotherapeutics can be precisely and systemically delivered to reduce tumor growth in vivo, without harming healthy cells. Given the clinical applicability of peptide-based therapeutics, targeted delivery of nanocarriers loaded with therapeutic cargos seems plausible. We propose a modular design of a functionalized protocell in which a tumor-targeting moiety, such as a peptide or recombinant human antibody single chain variable fragment (scFv), is conjugated to a lipid bilayer surrounding a silica-based nanocarrier core containing a protected therapeutic cargo. The functionalized protocell can be tailored to a specific cancer subtype and treatment regimen by exchanging the tumor-targeting moiety and/or therapeutic cargo or used in combination to create unique, theranostic agents. In this review, we summarize the identification of tumor-specific receptors through combinatorial phage display technology and the use of antibody display selection to identify recombinant human scFvs against these tumor-specific receptors. We compare the characteristics of different types of simple and complex nanocarriers, and discuss potential types of therapeutic cargos and conjugation strategies. As a result, the modular design of functionalized protocells may improve the efficacy and safety of nanomedicines for future cancer therapy.« less

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks

PubMed Central

2011-01-01

Background Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. Results A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Conclusions Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced. PMID:21849086

Evolutionary versatility of eukaryotic protein domains revealed by their bigram networks.

PubMed

Xie, Xueying; Jin, Jing; Mao, Yongyi

2011-08-18

Protein domains are globular structures of independently folded polypeptides that exert catalytic or binding activities. Their sequences are recognized as evolutionary units that, through genome recombination, constitute protein repertoires of linkage patterns. Via mutations, domains acquire modified functions that contribute to the fitness of cells and organisms. Recent studies have addressed the evolutionary selection that may have shaped the functions of individual domains and the emergence of particular domain combinations, which led to new cellular functions in multi-cellular animals. This study focuses on modeling domain linkage globally and investigates evolutionary implications that may be revealed by novel computational analysis. A survey of 77 completely sequenced eukaryotic genomes implies a potential hierarchical and modular organization of biological functions in most living organisms. Domains in a genome or multiple genomes are modeled as a network of hetero-duplex covalent linkages, termed bigrams. A novel computational technique is introduced to decompose such networks, whereby the notion of domain "networking versatility" is derived and measured. The most and least "versatile" domains (termed "core domains" and "peripheral domains" respectively) are examined both computationally via sequence conservation measures and experimentally using selected domains. Our study suggests that such a versatility measure extracted from the bigram networks correlates with the adaptivity of domains during evolution, where the network core domains are highly adaptive, significantly contrasting the network peripheral domains. Domain recombination has played a major part in the evolution of eukaryotes attributing to genome complexity. From a system point of view, as the results of selection and constant refinement, networks of domain linkage are structured in a hierarchical modular fashion. Domains with high degree of networking versatility appear to be evolutionary adaptive, potentially through functional innovations. Domain bigram networks are informative as a model of biological functions. The networking versatility indices extracted from such networks for individual domains reflect the strength of evolutionary selection that the domains have experienced.

Ligand-targeted theranostic nanomedicines against cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yao, Virginia J.; D'Angelo, Sara; Butler, Kimberly S.

Nanomedicines have significant potential for cancer treatment. Although the majority of nanomedicines currently tested in clinical trials utilize simple, biocompatible liposome-based nanocarriers, their widespread use is limited by non-specificity and low target site concentration and thus, do not provide a substantial clinical advantage over conventional, systemic chemotherapy. In the past 20 years, we have identified specific receptors expressed on the surfaces of tumor endothelial and perivascular cells, tumor cells, the extracellular matrix and stromal cells using combinatorial peptide libraries displayed on bacteriophage. These studies corroborate the notion that unique receptor proteins such as IL-11Rα, GRP78, EphA5, among others, are differentiallymore » overexpressed in tumors and present opportunities to deliver tumor-specific therapeutic drugs. By using peptides that bind to tumor-specific cell-surface receptors, therapeutic agents such as apoptotic peptides, suicide genes, imaging dyes or chemotherapeutics can be precisely and systemically delivered to reduce tumor growth in vivo, without harming healthy cells. Given the clinical applicability of peptide-based therapeutics, targeted delivery of nanocarriers loaded with therapeutic cargos seems plausible. We propose a modular design of a functionalized protocell in which a tumor-targeting moiety, such as a peptide or recombinant human antibody single chain variable fragment (scFv), is conjugated to a lipid bilayer surrounding a silica-based nanocarrier core containing a protected therapeutic cargo. The functionalized protocell can be tailored to a specific cancer subtype and treatment regimen by exchanging the tumor-targeting moiety and/or therapeutic cargo or used in combination to create unique, theranostic agents. In this review, we summarize the identification of tumor-specific receptors through combinatorial phage display technology and the use of antibody display selection to identify recombinant human scFvs against these tumor-specific receptors. We compare the characteristics of different types of simple and complex nanocarriers, and discuss potential types of therapeutic cargos and conjugation strategies. As a result, the modular design of functionalized protocells may improve the efficacy and safety of nanomedicines for future cancer therapy.« less

A controlled double-duration inducible gene expression system for cartilage tissue engineering.

PubMed

Ma, Ying; Li, Junxiang; Yao, Yi; Wei, Daixu; Wang, Rui; Wu, Qiong

2016-05-25

Cartilage engineering that combines competent seeding cells and a compatible scaffold is increasingly gaining popularity and is potentially useful for the treatment of various bone and cartilage diseases. Intensive efforts have been made by researchers to improve the viability and functionality of seeding cells of engineered constructs that are implanted into damaged cartilage. Here, we designed an integrative system combining gene engineering and the controlled-release concept to solve the problems of both seeding cell viability and functionality through precisely regulating the anti-apoptotic gene bcl-2 in the short-term and the chondrogenic master regulator Sox9 in the long-term. Both in vitro and in vivo experiments demonstrated that our system enhances the cell viability and chondrogenic effects of the engineered scaffold after introduction of the system while restricting anti-apoptotic gene expression to only the early stage, thereby preventing potential oncogenic and overdose effects. Our system was designed to be modular and can also be readily adapted to other tissue engineering applications with minor modification.

[PERSPECTIVES OF DEVELOPMENT OF LIVE RECOMBINANT ANTHRAX VACCINES BASED ON OPPORTUNISTIC AND APATHOGENIC MICROORGANISMS].

PubMed

Popova, P Yu; Mikshis, N I

2016-01-01

Live genetic engineering anthrax vaccines on the platform of avirulent and probiotic micro-organisms are a safe and adequate alternative to preparations based on attenuated Bacillus anthracis strains. Mucosal application results in a direct contact of the vaccine preparations with mucous membranes in those organs arid tissues of the macro-organisms, that are exposed to the pathogen in the first place, resulting in a development of local and systemic immune response. Live recombinant anthrax vaccines could be used both separately as well as in a prime-boost immunization scheme. The review focuses on immunogenic and protective properties of experimental live genetic engineering prearations, created based on members of geni of Salmonella, Lactobacillus and adenoviruses.

Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code.

PubMed

Hauf, Matthias; Richter, Florian; Schneider, Tobias; Faidt, Thomas; Martins, Berta M; Baumann, Tobias; Durkin, Patrick; Dobbek, Holger; Jacobs, Karin; Möglich, Andreas; Budisa, Nediljko

2017-09-19

Marine mussels exhibit potent underwater adhesion abilities under hostile conditions by employing 3,4-dihydroxyphenylalanine (DOPA)-rich mussel adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Herein, a novel strategy based on genetic code expansion has been developed by engineering efficient aminoacyl-transfer RNA synthetases (aaRSs) for the photocaged noncanonical amino acid ortho-nitrobenzyl DOPA (ONB-DOPA). The engineered ONB-DOPARS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-DOPA to yield photocaged, spatiotemporally controlled underwater adhesives. Upon exposure to UV light, these proteins feature elevated wet adhesion properties. This concept offers new perspectives for the production of recombinant bioadhesives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rewiring the Glucose Transportation and Central Metabolic Pathways for Overproduction of N-Acetylglucosamine in Bacillus subtilis.

PubMed

Gu, Yang; Deng, Jieying; Liu, Yanfeng; Li, Jianghua; Shin, Hyun-Dong; Du, Guocheng; Chen, Jian; Liu, Long

2017-10-01

N-acetylglucosamine (GlcNAc) is an important amino sugar extensively used in the healthcare field. In a previous study, the recombinant Bacillus subtilis strain BSGN6-P xylA -glmS-pP43NMK-GNA1 (BN0-GNA1) had been constructed for microbial production of GlcNAc by pathway design and modular optimization. Here, the production of GlcNAc is further improved by rewiring both the glucose transportation and central metabolic pathways. First, the phosphotransferase system (PTS) is blocked by deletion of three genes, yyzE (encoding the PTS system transporter subunit IIA YyzE), ypqE (encoding the PTS system transporter subunit IIA YpqE), and ptsG (encoding the PTS system glucose-specific EIICBA component), resulting in 47.6% increase in the GlcNAc titer (from 6.5 ± 0.25 to 9.6 ± 0.16 g L -1 ) in shake flasks. Then, reinforcement of the expression of the glcP and glcK genes and optimization of glucose facilitator proteins are performed to promote glucose import and phosphorylation. Next, the competitive pathways for GlcNAc synthesis, namely glycolysis, peptidoglycan synthesis pathway, pentose phosphate pathway, and tricarboxylic acid cycle, are repressed by initiation codon-optimization strategies, and the GlcNAc titer in shake flasks is improved from 10.8 ± 0.25 to 13.2 ± 0.31 g L -1 . Finally, the GlcNAc titer is further increased to 42.1 ± 1.1 g L -1 in a 3-L fed-batch bioreactor, which is 1.72-fold that of the original strain, BN0-GNA1. This study shows considerably enhanced GlcNAc production, and the metabolic engineering strategy described here will be useful for engineering other prokaryotic microorganisms for the production of GlcNAc and related molecules. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modular and Orthogonal Synthesis of Hybrid Polymers and Networks

PubMed Central

Liu, Shuang; Dicker, Kevin T.; Jia, Xinqiao

2015-01-01

Biomaterials scientists strive to develop polymeric materials with distinct chemical make-up, complex molecular architectures, robust mechanical properties and defined biological functions by drawing inspirations from biological systems. Salient features of biological designs include (1) repetitive presentation of basic motifs; and (2) efficient integration of diverse building blocks. Thus, an appealing approach to biomaterials synthesis is to combine synthetic and natural building blocks in a modular fashion employing novel chemical methods. Over the past decade, orthogonal chemistries have become powerful enabling tools for the modular synthesis of advanced biomaterials. These reactions require building blocks with complementary functionalities, occur under mild conditions in the presence of biological molecules and living cells and proceed with high yield and exceptional selectivity. These chemistries have facilitated the construction of complex polymers and networks in a step-growth fashion, allowing facile modulation of materials properties by simple variations of the building blocks. In this review, we first summarize features of several types of orthogonal chemistries. We then discuss recent progress in the synthesis of step growth linear polymers, dendrimers and networks that find application in drug delivery, 3D cell culture and tissue engineering. Overall, orthogonal reactions and modulular synthesis have not only minimized the steps needed for the desired chemical transformations but also maximized the diversity and functionality of the final products. The modular nature of the design, combined with the potential synergistic effect of the hybrid system, will likely result in novel hydrogel matrices with robust structures and defined functions. PMID:25572255

Automatic Identification System modular receiver for academic purposes

NASA Astrophysics Data System (ADS)

Cabrera, F.; Molina, N.; Tichavska, M.; Araña, V.

2016-07-01

The Automatic Identification System (AIS) standard is encompassed within the Global Maritime Distress and Safety System (GMDSS), in force since 1999. The GMDSS is a set of procedures, equipment, and communication protocols designed with the aim of increasing the safety of sea crossings, facilitating navigation, and the rescue of vessels in danger. The use of this system not only is increasingly attractive to security issues but also potentially creates intelligence products throughout the added-value information that this network can transmit from ships on real time (identification, position, course, speed, dimensions, flag, among others). Within the marine electronics market, commercial receivers implement this standard and allow users to access vessel-broadcasted information if in the range of coverage. In addition to satellite services, users may request actionable information from private or public AIS terrestrial networks where real-time feed or historical data can be accessed from its nodes. This paper describes the configuration of an AIS receiver based on a modular design. This modular design facilitates the evaluation of specific modules and also a better understanding of the standard and the possibility of changing hardware modules to improve the performance of the prototype. Thus, the aim of this paper is to describe the system's specifications, its main hardware components, and to present educational didactics on the setup and use of a modular and terrestrial AIS receiver. The latter is for academic purposes and in undergraduate studies such as electrical engineering, telecommunications, and maritime studies.

Adenovirus Particles that Display the Plasmodium falciparum Circumsporozoite Protein NANP Repeat Induce Sporozoite-Neutralizing Antibodies in Mice

PubMed Central

Palma, Christopher; Overstreet, Michael G.; Guedon, Jean-Marc; Hoiczyk, Egbert; Ward, Cameron; Karen, Kasey A.; Zavala, Fidel; Ketner, Gary

2011-01-01

Adenovirus particles can be engineered to display exogenous peptides on their surfaces by modification of viral capsid proteins, and particles that display pathogen-derived peptides can induce protective immunity. We constructed viable recombinant adenoviruses that display B-cell epitopes from the Plasmodium falciparum circumsporozoite protein (PfCSP) in the major adenovirus capsid protein, hexon. Recombinants induced high-titer antibodies against CSP when injected intraperitoneally into mice. Serum obtained from immunized mice recognized both recombinant PfCSP protein and P. falciparum sporozoites, and neutralized P. falciparum sporozoites in vitro. Replicating adenovirus vaccines have provided economical protection against adenovirus disease for over three decades. The recombinants described here may provide a path to an affordable malaria vaccine in the developing world. PMID:21199707

A versatile modular vector system for rapid combinatorial mammalian genetics.

PubMed

Albers, Joachim; Danzer, Claudia; Rechsteiner, Markus; Lehmann, Holger; Brandt, Laura P; Hejhal, Tomas; Catalano, Antonella; Busenhart, Philipp; Gonçalves, Ana Filipa; Brandt, Simone; Bode, Peter K; Bode-Lesniewska, Beata; Wild, Peter J; Frew, Ian J

2015-04-01

Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases.

Modular and scalable RESTful API to sustain STAR collaboration's record keeping

NASA Astrophysics Data System (ADS)

Arkhipkin, D.; Lauret, J.; Shanmuganathan, P. V.

2015-12-01

STAR collaboration's record system is a collection of heterogeneous and sparse information associated to each members and institutions. In its original incarnation, only flat information was stored revealing many restrictions such as the lack of historical change information, the inability to keep track of members leaving and re-joining STAR, or the ability to easily extend the saved information as new requirements appeared. In mid-2013, a new project was launched covering an extensive set of revisited requirements. The requirements led us to a design based on a RESTful API, back-end storage engine relying on key/value pair data representation model coupled with a tiered architecture design. This design was motivated by the fact that unifying many STAR tools, relying on the same business logic and storage engine, was a key and central feature for the maintainability and presentation of records. This central service API would leave no ambiguities and provide easy service integration between STAR tools. The new design stores the changes in records dynamically and allows tracking the changes chronologically. The storage engine is extensible as new field of information emerges (member specific or general) without affecting the presentation or the business logic layers. The new record system features a convenient administrative interface, fuzzy algorithms for data entry and search, and provides basic statistics and graphs. Finally, this modular approach is supplemented with access control, allowing private information and administrative operations to be hidden away from public eyes.

Influenza type A virus: an outstandingly protean pathogen and a potent modular weapon.

PubMed

Shoham, Dany

2013-05-01

A remarkable debate recently arose on a global scale, about bioethics, biohazard, bioweaponry and bioterrorism issues related to scientific research concerning the induced transition of the highly lethal H5N1 avian flu virus from a non-pandemic to a tentatively pandemic strain, which might fall into malevolent hands. Appreciable ecogenetic complexity marks the main attributes of influenza type A viruses, namely infectivity, virulence, antigenicity, transmissibility, host range, endemicity, and epidemicity. They all shape, conjunctively, the outstanding protean nature of this pathogen, hence the modularity of the latter as a potent weapon. The present analysis inquires into those attributes, so as to profile and gauge threat, usability, impact and coping, particularly that the dimension of genetic engineering of this virus largely amplifies its potential. Within that context, various human interventions and misuses, including human experimental infections, undesirable vaccinations, as well as unauthorized and unskillful operations, led to bad corollaries and are also discussed in the present study. Altogether, a variety of interrelated properties underlying the complicatedness of and menaces posed by influenza A virus as a grave medical challenge, a dually explorable pathogen, and a modular biological warfare agent, are thereby illuminated, alongside with their scientific, strategic and practical implications.

Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis

DOE PAGES

Winter, Jaclyn M.; Cascio, Duilio; Dietrich, David; ...

2015-07-14

Modular collaboration between iterative fungal polyketide synthases (IPKSs) is an important mechanism for generating structural diversity of polyketide natural products. Inter-PKS communication and substrate channeling are controlled in large by the starter unit acyl carrier protein transacylase (SAT) domain found in the accepting IPKS module. Here in this study, we reconstituted the modular biosynthesis of the benzaldehyde core of the chaetoviridin and chaetomugilin azaphilone natural products using the IPKSs CazF and CazM. Our studies revealed a critical role of CazM’s SAT domain in selectively transferring a highly reduced triketide product from CazF. In contrast, a more oxidized triketide that ismore » also produced by CazF and required in later stages of biosynthesis of the final product is not recognized by the SAT domain. The structural basis for the acyl unit selectivity was uncovered by the first X-ray structure of a fungal SAT domain, highlighted by a covalent hexanoyl thioester intermediate in the SAT active site. Finally, the crystal structure of SAT domain will enable protein engineering efforts aimed at mixing and matching different IPKS modules for the biosynthesis of new compounds.« less

Engineering modular ‘ON’ RNA switches using biological components

PubMed Central

Ceres, Pablo; Trausch, Jeremiah J.; Batey, Robert T.

2013-01-01

Riboswitches are cis-acting regulatory elements broadly distributed in bacterial mRNAs that control a wide range of critical metabolic activities. Expression is governed by two distinct domains within the mRNA leader: a sensory ‘aptamer domain’ and a regulatory ‘expression platform’. Riboswitches have also received considerable attention as important tools in synthetic biology because of their conceptually simple structure and the ability to obtain aptamers that bind almost any conceivable small molecule using in vitro selection (referred to as SELEX). In the design of artificial riboswitches, a significant hurdle has been to couple the two domains enabling their efficient communication. We previously demonstrated that biological transcriptional ‘OFF’ expression platforms are easily coupled to diverse aptamers, both biological and SELEX-derived, using simple design rules. Here, we present two modular transcriptional ‘ON’ riboswitch expression platforms that are also capable of hosting foreign aptamers. We demonstrate that these biological parts can be used to facilely generate artificial chimeric riboswitches capable of robustly regulating transcription both in vitro and in vivo. We expect that these modular expression platforms will be of great utility for various synthetic biological applications that use RNA-based biosensors. PMID:23999097

Coating graphene paper with 2D-assembly of electrocatalytic nanoparticles: a modular approach toward high-performance flexible electrodes.

PubMed

Xiao, Fei; Song, Jibin; Gao, Hongcai; Zan, Xiaoli; Xu, Rong; Duan, Hongwei

2012-01-24

The development of flexible electrodes is of considerable current interest because of the increasing demand for modern electronics, portable medical products, and compact energy devices. We report a modular approach to fabricating high-performance flexible electrodes by structurally integrating 2D-assemblies of nanoparticles with freestanding graphene paper. We have shown that the 2D array of gold nanoparticles at oil-water interfaces can be transferred on freestanding graphene oxide paper, leading to a monolayer of densely packed gold nanoparticles of uniform sizes loaded on graphene oxide paper. One major finding is that the postassembly electrochemical reduction of graphene oxide paper restores the ordered structure and electron-transport properties of graphene, and gives rise to robust and biocompatible freestanding electrodes with outstanding electrocatalytic activities, which have been manifested by the sensitive and selective detection of two model analytes: glucose and hydrogen peroxide (H(2)O(2)) secreted by live cells. The modular nature of this approach coupled with recent progress in nanocrystal synthesis and surface engineering opens new possibilities to systematically study the dependence of catalytic performance on the structural parameters and chemical compositions of the nanocrystals. © 2011 American Chemical Society

The modular architecture of protein-protein binding interfaces.

PubMed

Reichmann, D; Rahat, O; Albeck, S; Meged, R; Dym, O; Schreiber, G

2005-01-04

Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is comprised of a number of closely interacting residues, with few interactions between the modules. The boundaries between modules are defined by clustering the contact map of the interface. We show that mutations in one module do not affect residues located in a neighboring module. As a result, the structural and energetic consequences of the deletion of entire modules are surprisingly small. To the contrary, within their module, mutations cause complex energetic and structural consequences. Experimentally, this phenomenon is shown on the interaction between TEM1-beta-lactamase and beta-lactamase inhibitor protein (BLIP) by using multiple-mutant analysis and x-ray crystallography. Replacing an entire module of five interface residues with Ala created a large cavity in the interface, with no effect on the detailed structure of the remaining interface. The modular architecture of binding sites, which resembles human engineering design, greatly simplifies the design of new protein interactions and provides a feasible view of how these interactions evolved.

Functional Requirements for DjlA- and RraA-Mediated Enhancement of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR.

PubMed

Gialama, Dimitra; Delivoria, Dafni Chrysanthi; Michou, Myrsini; Giannakopoulou, Artemis; Skretas, Georgios

2017-06-16

In previous work, we have generated the engineered Escherichia coli strains SuptoxD and SuptoxR, which upon co-expression of the effector genes djlA or rraA, respectively, are capable of suppressing the cytotoxicity caused by membrane protein (MP) overexpression and of producing dramatically enhanced yields for a variety of recombinant MPs of both prokaryotic and eukaryotic origin. Here, we investigated the functional requirements for DnaJ-like protein A (DjlA)- and regulator of ribonuclease activity A (RraA)-mediated enhancement of recombinant MP production in these strains and show that: (i) DjlA and RraA act independently, that is, the beneficial effects of each protein on recombinant MP production occur through a mechanism that does not involve the other, and in a non-additive manner; (ii) full-length and membrane-bound DjlA is required for exerting its beneficial effects on recombinant MP production in E. coli SuptoxD; (iii) the MP production-promoting properties of DjlA in SuptoxD involve the action of the molecular chaperone DnaK but do not rely on the activation of the regulation of capsular synthesis response, a well-established consequence of djlA overexpression; (iv) the observed RraA-mediated effects in E. coli SuptoxR involve the ribonucleolytic activity of RNase E, but not that of its paralogous ribonuclease RNase G; and (v) DjlA and RraA are unique among similar E. coli proteins in their ability to promote bacterial recombinant MP production. These observations provide important clues about the molecular requirements for suppressed toxicity and enhanced MP accumulation in SuptoxD/SuptoxR and will guide future studies aiming to decipher the exact mechanism of DjlA- and RraA-mediated enhancement of recombinant MP production in these strains. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modular Gravitational Reference Sensor (MGRS) For Astrophysics and Astronomy

NASA Astrophysics Data System (ADS)

Sun, Ke-Xun; Buchman, S.; Byer, R. L.; DeBra, D.; Goebel, J.; Allen, G.; Conklin, J.; Gerardi, D.; Higuchi, S.; Leindecker, N.; Lu, P.; Swank, A.; Torres, E.; Trillter, M.; Zoellner, A.

2009-01-01

The study of space-time for gravitational wave detection and cosmology beyond Einstein will be an important theme for astrophysics and astronomy in decades to come. Laser Interferometric Space Antenna (LISA) is designed for detecting gravitational wave in space. The Modular Gravitational Reference Sensor (MGRS) is developed as the next generation core instrument for space-time research, including gravitational wave detection beyond LISA, and an array of precision experiments in space. The MGRS provide a stable gravitational cardinal point in space-time by using a test sphere, which eliminates the need for orientation control, minimizing disturbances. The MGRS measures the space-time variation via a two step process: measurement between test mass and housing, and between housings of two spacecraft. Our Stanford group is conducting systematic research and development on the MGRS. Our initial objectives are to gain a system perspective of the MGRS, to develop component technologies, and to establish test platforms. We will review our recent progress in system technologies, optical displacement and angle sensing, diffractive optics, proof mass characterization, UV LED charge management system and space qualification, thermal control and sensor development. Some highlights of our recent results are: Demonstration of the extreme radiation hardness of UV LED which sustained 2 trillion protons per square centimeter; measurement of mass center offset down to 300 nm, and measurement of small angle 0.2 nrad per root hertz using a compact grating angular sensor. The Stanford MGRS program has made exceptional contribution to education of next generation scientists and engineers. We have undergraduate and graduate students in aeronautical and astronautic engineering, applied physics, cybernetics, electrical engineering, mechanical engineering, and physics. We have also housed a number of high school students in our labs for education and public outreach.

Modular Hydropower Engineering and Pilot Scale Manufacturing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chesser, Phillip C.

Emrgy has developed, prototyped and tested a modular hydropower system for renewable energy generation. ORNL worked with Emrgy to demonstrate the use of additive manufacturing in the production of the hydrofoils and spokes for the hydrokinetic system. Specifically, during Phase 1 of this effort, ORNL printed and finished machined patterns for both the hydrofoils and spokes that were subsequently used in a sand casting manufacturing process. Emrgy utilized the sand castings for a pilot installation in Denver, CO, where the parts represented an 80% cost savings from the previous prototype build that was manufactured using subtractive manufacturing. In addition, themore » castings were completed with ORNL’s newly developed AlCeMg alloy that will be tested for performance improvements including higher corrosion resistance in a water application than the 6160 alloy used previously« less

The enzymology of polyether biosynthesis.

PubMed

Liu, Tiangang; Cane, David E; Deng, Zixin

2009-01-01

Polyether ionophore antibiotics are a special class of polyketides widely used in veterinary medicine, and as food additives in animal husbandry. In this article, we review current knowledge about the mechanism of polyether biosynthesis, and the genetic and biochemical strategies used for its study. Several clear differences distinguish it from traditional type I modular polyketide biosynthesis: polyether backbones are assembled by modular polyketide synthases but are modified by two key enzymes, epoxidase and epoxide hydrolase, to generate the product. All double bonds involved in the oxidative cyclization in the polyketide backbone are of E geometry. Chain release in the polyether biosynthetic pathway requires a special type II thioesterase which specifically hydrolyzes the polyether thioester. All these discoveries should be very helpful for a deep understanding of the biosynthetic mechanism of this class of important natural compounds, and for the targeted engineering of polyether derivatives.

A modular assembly method of a feed and thruster system for Cubesats

NASA Astrophysics Data System (ADS)

Louwerse, Marcus; Jansen, Henri; Elwenspoek, Miko

2010-11-01

A modular assembly method for devices based on micro system technology is presented. The assembly method forms the foundation for a miniaturized feed and thruster system as part of a micro propulsion unit working as a simple blow-down system of a rocket engine. The micro rocket is designed to be used for constellation maintenance of Cubesats, which measure 10 × 10 × 10 cm and have a mass less than 1 kg. The feed and thruster system contains an active valve, control electronics, a particle filter and an axisymmetric converging-diverging nozzle, all fabricated as separate modules. A novel method is used to integrate these modules by placing them on or in a glass tube package. The assembly method is shown to be a valid method but the valve module needs to be improved considerably.

The regulatory software of cellular metabolism.

PubMed

Segrè, Daniel

2004-06-01

Understanding the regulation of metabolic pathways in the cell is like unraveling the 'software' that is running on the 'hardware' of the metabolic network. Transcriptional regulation of enzymes is an important component of this software. A recent systematic analysis of metabolic gene-expression data in Saccharomyces cerevisiae reveals a complex modular organization of co-expressed genes, which could increase our ability to understand and engineer cellular metabolic functions.

Engineering Supply Management System: The Next Generation

DTIC Science & Technology

1991-09-01

010 Partia! receipts 0018 Automatic inventory update 0 048 Discrepant material 0 004 Order processing requirements Transaction reversal capability 0 012...August 1991. 2-5 sys.em’s modules that support the DEH’s needs are the Sales Order Processing , Register Sales, Purchase Order Processing , Inventory...modular system developed by PIC Business Systems, Incorporated. This system possesses Order Processing , Inventory Management, Purchase Orders, and

Preliminary candidate advanced avionics system for general aviation

NASA Technical Reports Server (NTRS)

Mccalla, T. M.; Grismore, F. L.; Greatline, S. E.; Birkhead, L. M.

1977-01-01

An integrated avionics system design was carried out to the level which indicates subsystem function, and the methods of overall system integration. Sufficient detail was included to allow identification of possible system component technologies, and to perform reliability, modularity, maintainability, cost, and risk analysis upon the system design. Retrofit to older aircraft, availability of this system to the single engine two place aircraft, was considered.

Generalized Operations Simulation Environment for Aircraft Maintenance Training

DTIC Science & Technology

2004-04-01

Operations Simulation Environment ( GOSE ) project is a collaborative effort between AETC and AFRL to develop common, cost-effective, generalized VR training...maintenance training domain since it provided an opportunity to build on the VEST architecture. Development of GOSE involves re-engineering VEST as a scalable...modular, immersive VR training system comprised of PC-based hardware and software. GOSE initiatives include: (a) formalize training needs across

T-vector and in vivo recombination as tools to construct a large antibody library of breast cancer.

PubMed

Lv, Yong-Gang; Wang, Ting; Yuan, Shi-Fang; Li, Nan-Lin; Chen, Jiang-Hao; Zhao, Ai-Zhi; Ling, Rui; Wang, Ling

2010-06-01

The emergence of phage antibody libraries is an important advance in the field of antibody engineering. It provides a useful methodology to produce human antibodies and has the potential to replace traditional hybridoma technology. In our research, we used T-vector and in vivo recombination to construct a large antibody library from breast cancer patients. The use of T-vector considerably increased the cloning efficiency, and the diversity of the library could be increased easily using in vivo recombination. Taken together, a combination of these two techniques might be valuable in constructing a large antibody library.

Sexual recombination as a tool for engineering industrial Penicillium chrysogenum strains.

PubMed

Dahlmann, Tim A; Böhm, Julia; Becker, Kordula; Kück, Ulrich

2015-11-01

The recent discovery and functional characterization of opposite mating-type loci in the industrial penicillin producer Penicillium chrysogenum demonstrated their regulatory role in sexual as well as asexual development. Subsequent experiments further showed that a sexual life cycle can be induced in P. chrysogenum that was for long believed to reproduce exclusively by asexual propagation. Finally, crossing of wild type and production strains resulted in the generation of recombinant ascospore isolates. We predict from these recent findings that recombinant progeny for industrial applications can be obtained by sexual crossings and discuss experimental difficulties that occur when parental strains with karyotype heterogeneity are used for mating.

New trends and affinity tag designs for recombinant protein purification.

PubMed

Wood, David W

2014-06-01

Engineered purification tags can facilitate very efficient purification of recombinant proteins, resulting in high yields and purities in a few standard steps. Over the years, many different purification tags have been developed, including short peptides, epitopes, folded protein domains, non-chromatographic tags and more recently, compound multifunctional tags with optimized capabilities. Although classic proteases are still primarily used to remove the tags from target proteins, new self-cleaving methods are gaining traction as a highly convenient alternative. In this review, we discuss some of these emerging trends, and examine their potential impacts and remaining challenges in recombinant protein research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Advances in yeast genome engineering.

PubMed

David, Florian; Siewers, Verena

2015-02-01

Genome engineering based on homologous recombination has been applied to yeast for many years. However, the growing importance of yeast as a cell factory in metabolic engineering and chassis in synthetic biology demands methods for fast and efficient introduction of multiple targeted changes such as gene knockouts and introduction of multistep metabolic pathways. In this review, we summarize recent improvements of existing genome engineering methods, the development of novel techniques, for example for advanced genome redesign and evolution, and the importance of endonucleases as genome engineering tools. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response

Treesearch

Yong-Su Jin; Jose M. Laplaza; Thomas W. Jeffries

2004-01-01

Native strains of Saccharomyces cerevisiae do not assimilate xylose. S. cerevisiae engineered for D-xylose utilization through the heterologous expression of genes for aldose reductase ( XYL1), xylitol dehydrogenase (XYL2), and D-xylulokinase ( XYL3 or XKS1) produce only limited amounts of ethanol in xylose medium. In recombinant S. cerevisiae expressing XYL1, XYL2,...

The Language Grid: supporting intercultural collaboration

NASA Astrophysics Data System (ADS)

Ishida, T.

2018-03-01

A variety of language resources already exist online. Unfortunately, since many language resources have usage restrictions, it is virtually impossible for each user to negotiate with every language resource provider when combining several resources to achieve the intended purpose. To increase the accessibility and usability of language resources (dictionaries, parallel texts, part-of-speech taggers, machine translators, etc.), we proposed the Language Grid [1]; it wraps existing language resources as atomic services and enables users to create new services by combining the atomic services, and reduces the negotiation costs related to intellectual property rights [4]. Our slogan is “language services from language resources.” We believe that modularization with recombination is the key to creating a full range of customized language environments for various user communities.

Biodistribution of modular nanotransporter carrying Auger electron emitter and targeted at melanoma cells in murine tumor model

NASA Astrophysics Data System (ADS)

Vorontsova, M. S.; Morozova, N. B.; Karmakova, T. A.; Rosenkranz, A. A.; Slastnikova, T. A.; Petriev, V. M.; Smoryzanova, O. A.; Tischenko, V. K.; Yakubovskaya, R. I.; Kaprin, A. D.; Sobolev, A. S.

2017-09-01

Recombinant modular nanotransporter containing α-melanocyte-stimulating hormone peptide sequence (MNT-MSH) as a ligand module was designed for nucleus-targeted delivery of cytotoxic agents into melanoma cells. MNT-MSH radiolabeled with Auger electron emitter (111In-NOTA-MNT-MSH) showed a high antitumor efficacy in mice bearing syngeneic melanoma after intratumoral (i.t.) injection. This study is aimed at evaluating the biodistribution of the radioconjugate in melanoma tumor model in vivo. 111In-NOTA-MNT-MSH was administered i.t. in C57Bl/6j mice bearing subcutaneously implanted B16-F1 murine melanoma cells, expressing high levels of MCR1. The tissue uptake of radioactivity was determined ex vivo by γ-counter measurements. The intravenous route of administration did not provide a desirable level of radioactivity accumulation in the tumor, possibly, due to a high uptake of the transporter in liver tissue. After i.t. administration 111In-NOTA-MNT-MSH provided a high local retention of radionuclide, ranged from 400 to 350 %ID/g within at least 48 hours post-injection. MNT containing Auger electron emitter and α-MSH peptide as vector ligand could be a promising basis for radiopharmaceutical preparations intended for melanoma treatment.

Safeguarding Stem Cell-Based Regenerative Therapy against Iatrogenic Cancerogenesis: Transgenic Expression of DNASE1, DNASE1L3, DNASE2, DFFB Controlled By POLA1 Promoter in Proliferating and Directed Differentiation Resisting Human Autologous Pluripotent Induced Stem Cells Leads to their Death

PubMed Central

Malecki, Marek; LaVanne, Christine; Alhambra, Dominique; Dodivenaka, Chaitanya; Nagel, Sarah; Malecki, Raf

2014-01-01

Introduction The worst possible complication of using stem cells for regenerative therapy is iatrogenic cancerogenesis. The ultimate goal of our work is to develop a self-triggering feedback mechanism aimed at causing death of all stem cells, which resist directed differentiation, keep proliferating, and can grow into tumors. Specific aim The specific aim was threefold: (1) to genetically engineer the DNA constructs for the human, recombinant DNASE1, DNASE1L3, DNASE2, DFFB controlled by POLA promoter; (2) to bioengineer anti-SSEA-4 antibody guided vectors delivering transgenes to human undifferentiated and proliferating pluripotent stem cells; (3) to cause death of proliferating and directed differentiation resisting stem cells by transgenic expression of the human recombinant the DNases (hrDNases). Methods The DNA constructs for the human, recombinant DNASE1, DNASE1L3, DNASE2, DFFB controlled by POLA promoter were genetically engineered. The vectors targeting specifically SSEA-4 expressing stem cells were bioengineered. The healthy volunteers’ bone marrow mononuclear cells (BMMCs) were induced into human, autologous, pluripotent stem cells with non-integrating plasmids. Directed differentiation of the induced stem cells into endothelial cells was accomplished with EGF and BMP. The anti-SSEA 4 antibodies’ guided DNA vectors delivered the transgenes for the human recombinant DNases’ into proliferating stem cells. Results Differentiation of the pluripotent induced stem cells into the endothelial cells was verified by highlighting formation of tight and adherens junctions through transgenic expression of recombinant fluorescent fusion proteins: VE cadherin, claudin, zona occludens 1, and catenin. Proliferation of the stem cells was determined through highlighting transgenic expression of recombinant fluorescent proteins controlled by POLA promoter, while also reporting expression of the transgenes for the hrDNases. Expression of the transgenes for the DNases resulted in complete collapse of the chromatin architecture and degradation of the proliferating cells’ genomic DNA. The proliferating stem cells, but not the differentiating ones, were effectively induced to die. Conclusion Herein, we describe attaining the proof-of-concept for the strategy, whereby transgenic expression of the genetically engineered human recombinant DNases in proliferating and directed differentiation resisting stem cells leads to their death. This novel strategy reduces the risk of iatrogenic neoplasms in stem cell therapy. PMID:25045589

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.

PubMed

Huang, Mingtao; Bai, Yunpeng; Sjostrom, Staffan L; Hallström, Björn M; Liu, Zihe; Petranovic, Dina; Uhlén, Mathias; Joensson, Haakan N; Andersson-Svahn, Helene; Nielsen, Jens

2015-08-25

There is an increasing demand for biotech-based production of recombinant proteins for use as pharmaceuticals in the food and feed industry and in industrial applications. Yeast Saccharomyces cerevisiae is among preferred cell factories for recombinant protein production, and there is increasing interest in improving its protein secretion capacity. Due to the complexity of the secretory machinery in eukaryotic cells, it is difficult to apply rational engineering for construction of improved strains. Here we used high-throughput microfluidics for the screening of yeast libraries, generated by UV mutagenesis. Several screening and sorting rounds resulted in the selection of eight yeast clones with significantly improved secretion of recombinant α-amylase. Efficient secretion was genetically stable in the selected clones. We performed whole-genome sequencing of the eight clones and identified 330 mutations in total. Gene ontology analysis of mutated genes revealed many biological processes, including some that have not been identified before in the context of protein secretion. Mutated genes identified in this study can be potentially used for reverse metabolic engineering, with the objective to construct efficient cell factories for protein secretion. The combined use of microfluidics screening and whole-genome sequencing to map the mutations associated with the improved phenotype can easily be adapted for other products and cell types to identify novel engineering targets, and this approach could broadly facilitate design of novel cell factories.

A Modular Environment for Geophysical Inversion and Run-time Autotuning using Heterogeneous Computing Systems

NASA Astrophysics Data System (ADS)

Myre, Joseph M.

Heterogeneous computing systems have recently come to the forefront of the High-Performance Computing (HPC) community's interest. HPC computer systems that incorporate special purpose accelerators, such as Graphics Processing Units (GPUs), are said to be heterogeneous. Large scale heterogeneous computing systems have consistently ranked highly on the Top500 list since the beginning of the heterogeneous computing trend. By using heterogeneous computing systems that consist of both general purpose processors and special- purpose accelerators, the speed and problem size of many simulations could be dramatically increased. Ultimately this results in enhanced simulation capabilities that allows, in some cases for the first time, the execution of parameter space and uncertainty analyses, model optimizations, and other inverse modeling techniques that are critical for scientific discovery and engineering analysis. However, simplifying the usage and optimization of codes for heterogeneous computing systems remains a challenge. This is particularly true for scientists and engineers for whom understanding HPC architectures and undertaking performance analysis may not be primary research objectives. To enable scientists and engineers to remain focused on their primary research objectives, a modular environment for geophysical inversion and run-time autotuning on heterogeneous computing systems is presented. This environment is composed of three major components: 1) CUSH---a framework for reducing the complexity of programming heterogeneous computer systems, 2) geophysical inversion routines which can be used to characterize physical systems, and 3) run-time autotuning routines designed to determine configurations of heterogeneous computing systems in an attempt to maximize the performance of scientific and engineering codes. Using three case studies, a lattice-Boltzmann method, a non-negative least squares inversion, and a finite-difference fluid flow method, it is shown that this environment provides scientists and engineers with means to reduce the programmatic complexity of their applications, to perform geophysical inversions for characterizing physical systems, and to determine high-performing run-time configurations of heterogeneous computing systems using a run-time autotuner.

Towards autotrophic tissue engineering: Photosynthetic gene therapy for regeneration.

PubMed

Chávez, Myra Noemi; Schenck, Thilo Ludwig; Hopfner, Ursula; Centeno-Cerdas, Carolina; Somlai-Schweiger, Ian; Schwarz, Christian; Machens, Hans-Günther; Heikenwalder, Mathias; Bono, María Rosa; Allende, Miguel L; Nickelsen, Jörg; Egaña, José Tomás

2016-01-01

The use of artificial tissues in regenerative medicine is limited due to hypoxia. As a strategy to overcome this drawback, we have shown that photosynthetic biomaterials can produce and provide oxygen independently of blood perfusion by generating chimeric animal-plant tissues during dermal regeneration. In this work, we demonstrate the safety and efficacy of photosynthetic biomaterials in vivo after engraftment in a fully immunocompetent mouse skin defect model. Further, we show that it is also possible to genetically engineer such photosynthetic scaffolds to deliver other key molecules in addition to oxygen. As a proof-of-concept, biomaterials were loaded with gene modified microalgae expressing the angiogenic recombinant protein VEGF. Survival of the algae, growth factor delivery and regenerative potential were evaluated in vitro and in vivo. This work proposes the use of photosynthetic gene therapy in regenerative medicine and provides scientific evidence for the use of engineered microalgae as an alternative to deliver recombinant molecules for gene therapy. Copyright © 2015 Elsevier Ltd. All rights reserved.

Model-Based Control of a Nonlinear Aircraft Engine Simulation using an Optimal Tuner Kalman Filter Approach

NASA Technical Reports Server (NTRS)

Connolly, Joseph W.; Csank, Jeffrey Thomas; Chicatelli, Amy; Kilver, Jacob

2013-01-01

This paper covers the development of a model-based engine control (MBEC) methodology featuring a self tuning on-board model applied to an aircraft turbofan engine simulation. Here, the Commercial Modular Aero-Propulsion System Simulation 40,000 (CMAPSS40k) serves as the MBEC application engine. CMAPSS40k is capable of modeling realistic engine performance, allowing for a verification of the MBEC over a wide range of operating points. The on-board model is a piece-wise linear model derived from CMAPSS40k and updated using an optimal tuner Kalman Filter (OTKF) estimation routine, which enables the on-board model to self-tune to account for engine performance variations. The focus here is on developing a methodology for MBEC with direct control of estimated parameters of interest such as thrust and stall margins. Investigations using the MBEC to provide a stall margin limit for the controller protection logic are presented that could provide benefits over a simple acceleration schedule that is currently used in traditional engine control architectures.

Implementation of a Space Communications Cognitive Engine

NASA Technical Reports Server (NTRS)

Hackett, Timothy M.; Bilen, Sven G.; Ferreira, Paulo Victor R.; Wyglinski, Alexander M.; Reinhart, Richard C.

2017-01-01

Although communications-based cognitive engines have been proposed, very few have been implemented in a full system, especially in a space communications system. In this paper, we detail the implementation of a multi-objective reinforcement-learning algorithm and deep artificial neural networks for the use as a radio-resource-allocation controller. The modular software architecture presented encourages re-use and easy modification for trying different algorithms. Various trade studies involved with the system implementation and integration are discussed. These include the choice of software libraries that provide platform flexibility and promote reusability, choices regarding the deployment of this cognitive engine within a system architecture using the DVB-S2 standard and commercial hardware, and constraints placed on the cognitive engine caused by real-world radio constraints. The implemented radio-resource allocation-management controller was then integrated with the larger spaceground system developed by NASA Glenn Research Center (GRC).

Development of an intelligent diagnostic system for reusable rocket engine control

NASA Technical Reports Server (NTRS)

Anex, R. P.; Russell, J. R.; Guo, T.-H.

1991-01-01

A description of an intelligent diagnostic system for the Space Shuttle Main Engines (SSME) is presented. This system is suitable for incorporation in an intelligent controller which implements accommodating closed-loop control to extend engine life and maximize available performance. The diagnostic system architecture is a modular, hierarchical, blackboard system which is particularly well suited for real-time implementation of a system which must be repeatedly updated and extended. The diagnostic problem is formulated as a hierarchical classification problem in which the failure hypotheses are represented in terms of predefined data patterns. The diagnostic expert system incorporates techniques for priority-based diagnostics, the combination of analytical and heuristic knowledge for diagnosis, integration of different AI systems, and the implementation of hierarchical distributed systems. A prototype reusable rocket engine diagnostic system (ReREDS) has been implemented. The prototype user interface and diagnostic performance using SSME test data are described.