High molecular weight DNA assembly in vivo for synthetic biology applications.

PubMed

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

Transportation of part supply improvement in agricultural machinery assembly plant

NASA Astrophysics Data System (ADS)

Saysaman, Anusit; Chutima, Parames

2018-02-01

This research focused on the problem caused by the transportation of part supply in agricultural machinery assembly plant in Thailand, which is one of the processes that are critical to the whole production process. If poorly managed, it will affect transportation of part supply, the emergence of sink cost, quality problems, and the ability to respond to the needs of the customers in time. Since the competition in the agricultural machinery market is more intense, the efficiency of part transportation process has to be improved. In this study, the process of transporting parts of the plant was studied and it was found that the efficiency of the process of transporting parts from the sub assembly line to its main assembly line was 83%. The approach to the performance improvement is done by using the Lean tool to limit wastes based on the ECRS principle and applying pull production system by changing the transportation method to operate as milkrun for transportation of parts to synchronize with the part demands of the main assembly line. After the transportation of parts from sub-assembly line to the main assembly line was improved, the efficiency raised to 98% and transportation process cost was saved to 540,000 Baht per year.

Prediction of phenotypes of missense mutations in human proteins from biological assemblies.

PubMed

Wei, Qiong; Xu, Qifang; Dunbrack, Roland L

2013-02-01

Single nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence-based and structure-based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure-based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X-ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease-associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e-5). When adding this information to sequence-based features such as the difference between wildtype and mutant position-specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence-based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease-associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins. Copyright © 2012 Wiley Periodicals, Inc.

Indentured Parts List Maintenance and Part Assembly Capture Tool - IMPACT

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Jill; Sharpe, Kelly

2004-01-01

Johnson Space Center's (JSC's) indentured parts list (IPL) maintenance and parts assembly capture tool (IMPACT) is an easy-to-use graphical interface for viewing and maintaining the complex assembly hierarchies of large databases. IMPACT, already in use at JSC to support the International Space Station (ISS), queries, updates, modifies, and views data in IPL and associated resource data, functions that it can also perform, with modification, for any large commercial database. By enabling its users to efficiently view and manipulate IPL hierarchical data, IMPACT performs a function unlike that of any other tool. Through IMPACT, users will achieve results quickly, efficiently, and cost effectively.

BioBrick assembly standards and techniques and associated software tools.

PubMed

Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

2014-01-01

The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

Diversity in virus assembly: biology makes things complicated

NASA Astrophysics Data System (ADS)

Zlotnick, Adam

2008-03-01

Icosahedral viruses have an elegance of geometry that implies a general path of assembly. However, structure alone provides insufficient information. Cowpea Chlorotic Mottle Virus (CCMV), an important system for studying virus assembly, consists of 90 coat protein (CP) homodimers condensed around an RNA genome. The crystal structure (Speir et al, 1995) reveals that assembly causes burial of hydrophobic surface and formation of β hexamers, the intertwining of N-termini of the CPs surrounding a quasi-sixfold. This structural view leads to reasonable and erroneous predictions: (i) CCMV capsids are extremely stable, and (ii) β hexamer formation is critical to assembly. Experimentally, we have found that capsids are based on a network of extremely weak (4-5 kT) pairwise interactions and that pentamer formation is the critical step in assembly kinetics. Because of the fragility of CP-Cp interaction, we can redirect assembly to generate and dissociate tubular nanostructures. The dynamic behavior of CCMV reflects the requirements and peculiarities of an evolved biological system; it does not necessarily reflect the behavior predicted from a more static picture of the virus.

Modeling biological problems in computer science: a case study in genome assembly.

PubMed

Medvedev, Paul

2018-01-30

As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment and assembly. In this tutorial, we use the example of the genome assembly problem to demonstrate how to go from a question in the biological realm to a solution in the computer science realm. We show the modeling process step-by-step, including all the intermediate failed attempts. Please note this is not an introduction to how genome assembly algorithms work and, if treated as such, would be incomplete and unnecessarily long-winded. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology.

PubMed

Sarrion-Perdigones, Alejandro; Vazquez-Vilar, Marta; Palací, Jorge; Castelijns, Bas; Forment, Javier; Ziarsolo, Peio; Blanca, José; Granell, Antonio; Orzaez, Diego

2013-07-01

Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects.

Precise Truss Assembly Using Commodity Parts and Low Precision Welding

NASA Technical Reports Server (NTRS)

Komendera, Erik; Reishus, Dustin; Dorsey, John T.; Doggett, W. R.; Correll, Nikolaus

2014-01-01

Hardware and software design and system integration for an intelligent precision jigging robot (IPJR), which allows high precision assembly using commodity parts and low-precision bonding, is described. Preliminary 2D experiments that are motivated by the problem of assembling space telescope optical benches and very large manipulators on orbit using inexpensive, stock hardware and low-precision welding are also described. An IPJR is a robot that acts as the precise "jigging", holding parts of a local structure assembly site in place, while an external low precision assembly agent cuts and welds members. The prototype presented in this paper allows an assembly agent (for this prototype, a human using only low precision tools), to assemble a 2D truss made of wooden dowels to a precision on the order of millimeters over a span on the order of meters. The analysis of the assembly error and the results of building a square structure and a ring structure are discussed. Options for future work, to extend the IPJR paradigm to building in 3D structures at micron precision are also summarized.

Precise Truss Assembly using Commodity Parts and Low Precision Welding

NASA Technical Reports Server (NTRS)

Komendera, Erik; Reishus, Dustin; Dorsey, John T.; Doggett, William R.; Correll, Nikolaus

2013-01-01

We describe an Intelligent Precision Jigging Robot (IPJR), which allows high precision assembly of commodity parts with low-precision bonding. We present preliminary experiments in 2D that are motivated by the problem of assembling a space telescope optical bench on orbit using inexpensive, stock hardware and low-precision welding. An IPJR is a robot that acts as the precise "jigging", holding parts of a local assembly site in place while an external low precision assembly agent cuts and welds members. The prototype presented in this paper allows an assembly agent (in this case, a human using only low precision tools), to assemble a 2D truss made of wooden dowels to a precision on the order of millimeters over a span on the order of meters. We report the challenges of designing the IPJR hardware and software, analyze the error in assembly, document the test results over several experiments including a large-scale ring structure, and describe future work to implement the IPJR in 3D and with micron precision.

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

PubMed Central

Hillier, LaDeana W.; Zody, Michael C.; Goldstein, Steve; She, Xinwe; Bult, Carol J.; Agarwala, Richa; Cherry, Joshua L.; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C.; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C.; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E.; Ponting, Chris P.

2009-01-01

The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non–protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not. PMID:19468303

The precision measurement and assembly for miniature parts based on double machine vision systems

NASA Astrophysics Data System (ADS)

Wang, X. D.; Zhang, L. F.; Xin, M. Z.; Qu, Y. Q.; Luo, Y.; Ma, T. M.; Chen, L.

2015-02-01

In the process of miniature parts' assembly, the structural features on the bottom or side of the parts often need to be aligned and positioned. The general assembly equipment integrated with one vertical downward machine vision system cannot satisfy the requirement. A precision automatic assembly equipment was developed with double machine vision systems integrated. In the system, a horizontal vision system is employed to measure the position of the feature structure at the parts' side view, which cannot be seen with the vertical one. The position measured by horizontal camera is converted to the vertical vision system with the calibration information. By careful calibration, the parts' alignment and positioning in the assembly process can be guaranteed. The developed assembly equipment has the characteristics of easy implementation, modularization and high cost performance. The handling of the miniature parts and assembly procedure were briefly introduced. The calibration procedure was given and the assembly error was analyzed for compensation.

Rapid Assembly of DNA via Ligase Cycling Reaction (LCR).

PubMed

Chandran, Sunil

2017-01-01

The assembly of multiple DNA parts into a larger DNA construct is a requirement in most synthetic biology laboratories. Here we describe a method for the efficient, high-throughput, assembly of DNA utilizing the ligase chain reaction (LCR). The LCR method utilizes non-overlapping DNA parts that are ligated together with the guidance of bridging oligos. Using this method, we have successfully assembled up to 20 DNA parts in a single reaction or DNA constructs up to 26 kb in size.

Assembling new technologies at the interface of materials science and biology

NASA Astrophysics Data System (ADS)

Stendahl, John C.

Molecular self-assembly can be used to construct advanced materials by taking cues from nature and harnessing noncovalent interactions. This bottom-up approach affords molecular level precision that can cultivate pathways to improved materials function. The graduate research presented in this thesis integrates molecular self-assembly with traditional concepts in chemistry and materials science, with the ultimate goal of developing innovative solutions in technology and medicine. In the field of polymer engineering, self-assembly was used to create supramolecular nanoribbons that, when incorporated into polystyrene, modify its microstructure and significantly enhance its toughness and ductility. In medicine, self-assembly was used to create ordered, chemically functional materials to improve interactions with cells and other constituents of the biological environment. One system that was investigated is based on a triblock molecule in which cholesterol is connected to a lysine dendron by a flexible oligo-(L-lactic acid) spacer. These molecules self-assemble into polar surface coatings on fibrous poly(L-lactic acid) scaffolds that improve the scaffold's wettability and increase its retention of cells during seeding. Another self-assembling system that was investigated for biomedical applications is a family of molecules referred to as peptide amphiphiles (PA's). PA's consist of hydrophobic alkyl tails connected to short, hydrophilic peptides that incorporate biological signaling epitopes. These molecules spontaneously assemble into networks of well-defined nanofibers in aqueous environments, with the signaling epitopes presented in high density on the nanofiber exteriors. Nanofiber assembly is triggered by charge screening on the peptides and is able to produce self-supporting gels in concentrations of less than 1.0 wt.-%. The assembly process and mechanical properties of PA gels was investigated in detail with vibrational spectroscopy and oscillatory rheology. PA

Design of Nanostructured Biological Materials Through Self-Assembly of Peptides and Proteins

DTIC Science & Technology

2002-01-01

of applications, including scaffolding for tissue repair in regenerative medicine, drug delivery and biological surface engineering. Tirrell and...colleagues [2] designed artificial proteins that undergo self-assembly to form hydrogels responsive to pH and other environmental changes. Ghadiri and...showed that other β-sheet peptide systems can also undergo self-assembly into regular nanofiber structures. Although they share no sequence

A biological approach to assembling tissue modules through endothelial capillary network formation.

PubMed

Riesberg, Jeremiah J; Shen, Wei

2015-09-01

To create functional tissues having complex structures, bottom-up approaches to assembling small tissue modules into larger constructs have been emerging. Most of these approaches are based on chemical reactions or physical interactions at the interface between tissue modules. Here we report a biological assembly approach to integrate small tissue modules through endothelial capillary network formation. When adjacent tissue modules contain appropriate extracellular matrix materials and cell types that support robust endothelial capillary network formation, capillary tubules form and grow across the interface, resulting in assembly of the modules into a single, larger construct. It was shown that capillary networks formed in modules of dense fibrin gels seeded with human umbilical vein endothelial cells (HUVECs) and mesenchymal stem cells (MSCs); adjacent modules were firmly assembled into an integrated construct having a strain to failure of 117 ± 26%, a tensile strength of 2208 ± 83 Pa and a Young's modulus of 2548 ± 574 Pa. Under the same culture conditions, capillary networks were absent in modules of dense fibrin gels seeded with either HUVECs or MSCs alone; adjacent modules disconnected even when handled gently. This biological assembly approach eliminates the need for chemical reactions or physical interactions and their associated limitations. In addition, the integrated constructs are prevascularized, and therefore this bottom-up assembly approach may also help address the issue of vascularization, another key challenge in tissue engineering. Copyright © 2015 John Wiley & Sons, Ltd.

76 FR 9984 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

..., Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006-(), 174080-(), 174085-(), 174095... manufacturer and part number of the oxygen mask assemblies installed, an inspection to determine the manufacturing date and modification status if certain oxygen mask assemblies are installed, and corrective...

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights.

PubMed

Warnke-Sommer, Julia; Ali, Hesham

2016-05-06

The assembly of Next Generation Sequencing (NGS) reads remains a challenging task. This is especially true for the assembly of metagenomics data that originate from environmental samples potentially containing hundreds to thousands of unique species. The principle objective of current assembly tools is to assemble NGS reads into contiguous stretches of sequence called contigs while maximizing for both accuracy and contig length. The end goal of this process is to produce longer contigs with the major focus being on assembly only. Sequence read assembly is an aggregative process, during which read overlap relationship information is lost as reads are merged into longer sequences or contigs. The assembly graph is information rich and capable of capturing the genomic architecture of an input read data set. We have developed a novel hybrid graph in which nodes represent sequence regions at different levels of granularity. This model, utilized in the assembly and analysis pipeline Focus, presents a concise yet feature rich view of a given input data set, allowing for the extraction of biologically relevant graph structures for graph mining purposes. Focus was used to create hybrid graphs to model metagenomics data sets obtained from the gut microbiomes of five individuals with Crohn's disease and eight healthy individuals. Repetitive and mobile genetic elements are found to be associated with hybrid graph structure. Using graph mining techniques, a comparative study of the Crohn's disease and healthy data sets was conducted with focus on antibiotics resistance genes associated with transposase genes. Results demonstrated significant differences in the phylogenetic distribution of categories of antibiotics resistance genes in the healthy and diseased patients. Focus was also evaluated as a pure assembly tool and produced excellent results when compared against the Meta-velvet, Omega, and UD-IDBA assemblers. Mining the hybrid graph can reveal biological phenomena captured

GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology1[C][W][OA

PubMed Central

Sarrion-Perdigones, Alejandro; Vazquez-Vilar, Marta; Palací, Jorge; Castelijns, Bas; Forment, Javier; Ziarsolo, Peio; Blanca, José; Granell, Antonio; Orzaez, Diego

2013-01-01

Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an ever-growing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects. PMID:23669743

Evaluation of nine popular de novo assemblers in microbial genome assembly.

PubMed

Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher

2017-12-01

Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.

Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

PubMed

Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

2016-02-24

Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural Biology of Supramolecular Assemblies by Magic Angle Spinning NMR Spectroscopy

PubMed Central

Quinn, Caitlin M.; Polenova, Tatyana

2017-01-01

In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic angle spinning (MAS) NMR to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast magic angle spinning, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as HIV-1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology. PMID:28093096

16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR BICYCLE HELMETS Pt. 1203, Fig. 10 Figure 10 to Part 1203—Center of Gravity for Drop Assembly ER10MR98.01...

16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR BICYCLE HELMETS Pt. 1203, Fig. 10 Figure 10 to Part 1203—Center of Gravity for Drop Assembly ER10MR98.01...

16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR BICYCLE HELMETS Pt. 1203, Fig. 10 Figure 10 to Part 1203—Center of Gravity for Drop Assembly ER10MR98.01...

16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR BICYCLE HELMETS Pt. 1203, Fig. 10 Figure 10 to Part 1203—Center of Gravity for Drop Assembly ER10MR98.01...

16 CFR Figure 10 to Part 1203 - Center of Gravity for Drop Assembly

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Center of Gravity for Drop Assembly 10 Figure 10 to Part 1203 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS SAFETY STANDARD FOR BICYCLE HELMETS Pt. 1203, Fig. 10 Figure 10 to Part 1203—Center of Gravity for Drop Assembly ER10MR98.01...

Conformational assembly and biological properties of collagen mimetic peptides and their thermally responsive polymer conjugates

NASA Astrophysics Data System (ADS)

Krishna, Ohm Divyam

2011-12-01

Collagens are one of the most abundant proteins found in body tissues and organs, endowing structural integrity, mechanical strength, and multiple biological functions. Destabilized collagen inside human body leads to various degenerative diseases (ex. osteoarthritis) and ageing. This has continued to motivate the design of synthetic peptides and bio-synthetic polypeptides to closely mimic the native collagens in terms of triple helix structure and stability, potential for higher order assembly, and biological properties. However, the widespread application of de novo collagens has been limited in part by the need for hydroxylated proline in the formation of stable triple helical structures. To address this continued need, a hydroxyproline-free, thermally stable collagen-mimetic peptide (CLP-Cys) was rationally designed via the incorporation of electrostatically stabilized amino acid triplets. CLP-Cys was synthesized via solid phase peptide synthesis. The formation and stability of the triple helical structure were indicated via circular dichroism (CD) experiments and confirmed via differential scanning calorimetry (DSC) results. CLP-Cys also self-assembled into nano-rods and micro-fibrils, as evidenced via a combination of dynamic light scattering and transmission electron microscopy. Given the high thermal stability and its propensity for higher-order assembly, CLP-Cys was further functionalized at both the ends with a thermally responsive polymer, poly(diethylene glycol methyl ether methacrylate), (PDEGMEMA) to synthesize a biohybrid triblock copolymer. The CD results indicated that the triple helical form is retained, the thermal unfolding is sustained and helix to coil transition is reversible in the triblock hybrid context. The LCST of PDEGMEMA homopolymer (26 °C) is increased (to 35 °C) upon conjugation to the hydrophilic collagen peptide domain. Further, a combination of static light scattering, Cryo-SEM, TEM and confocal microscopy elucidated that the

Two sides of the coin. Part 1. Lipid and surfactant self-assembly revisited.

PubMed

Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

2017-04-01

Hofmeister, specific ion effects, hydration and van der Waals forces at and between interfaces are factors that determine curvature and microstructure in self assembled aggregates of surfactants and lipids; and in microemulsions. Lipid and surfactant head group interactions and between aggregates vary enormously and are highly specific. They act on the hydrophilic side of a bilayer, micelle or other self assembled aggregate. It is only over the last three decades that the origin of Hofmeister effects has become generally understood. Knowledge of their systematics now provides much flexibility in designing nanostructured fluids. The other side of the coin involves equally specific forces. These (opposing) forces work on the hydrophobic side of amphiphilic interfaces. They are due to the interaction of hydrocarbons and other "oils" with hydrophobic tails of surfactants and lipids. The specificity of oleophilic solutes in microemulsions and lipid membranes provides a counterpoint to Hofmeister effects and hydration. Together with global packing constraints these effects determine microstructure. Another factor that has hardly been recognised is the role of dissolved gas. This introduces further, qualitative changes in forces that prescribe microstructure. The systematics of these effects and their interplay are elucidated. Awareness of these competing factors facilitates formulation of self assembled nanostructured fluids. New and predictable geometries that emerge naturally provide insights into a variety of biological phenomena like anaesthetic and pheromone action and transmission of the nervous impulse (see Part 2). Copyright © 2017 Elsevier B.V. All rights reserved.

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

Molecular self-assembly for biological investigations and nanoscale lithography

NASA Astrophysics Data System (ADS)

Cheunkar, Sarawut

Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

An Easy-to-Assemble Three-Part Galvanic Cell

ERIC Educational Resources Information Center

Eggen, Per-Odd; Skaugrud, Brit

2015-01-01

The galvanic cell presented in this article is made of only three parts, is easy to assemble, and can light a red light emitting diode (LED). The three cell components consist of a piece of paper with copper sulfate, a piece of paper with sodium sulfate, and a piece of magnesium ribbon. Within less than 1 h, students have time to discuss the…

Blueprints for green biotech: development and application of standards for plant synthetic biology.

PubMed

Patron, Nicola J

2016-06-15

Synthetic biology aims to apply engineering principles to the design and modification of biological systems and to the construction of biological parts and devices. The ability to programme cells by providing new instructions written in DNA is a foundational technology of the field. Large-scale de novo DNA synthesis has accelerated synthetic biology by offering custom-made molecules at ever decreasing costs. However, for large fragments and for experiments in which libraries of DNA sequences are assembled in different combinations, assembly in the laboratory is still desirable. Biological assembly standards allow DNA parts, even those from multiple laboratories and experiments, to be assembled together using the same reagents and protocols. The adoption of such standards for plant synthetic biology has been cohesive for the plant science community, facilitating the application of genome editing technologies to plant systems and streamlining progress in large-scale, multi-laboratory bioengineering projects. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Multi-pose system for geometric measurement of large-scale assembled rotational parts

NASA Astrophysics Data System (ADS)

Deng, Bowen; Wang, Zhaoba; Jin, Yong; Chen, Youxing

2017-05-01

To achieve virtual assembly of large-scale assembled rotational parts based on in-field geometric data, we develop a multi-pose rotative arm measurement system with a gantry and 2D laser sensor (RAMSGL) to measure and provide the geometry of these parts. We mount a 2D laser sensor onto the end of a six-jointed rotative arm to guarantee the accuracy and efficiency, combine the rotative arm with a gantry to measure pairs of assembled rotational parts. By establishing and using the D-H model of the system, the 2D laser data is turned into point clouds and finally geometry is calculated. In addition, we design three experiments to evaluate the performance of the system. Experimental results show that the system’s max length measuring deviation using gauge blocks is 35 µm, max length measuring deviation using ball plates is 50 µm, max single-point repeatability error is 25 µm, and measurement scope is from a radius of 0 mm to 500 mm.

GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.

PubMed

Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

2011-01-01

Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid") topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.

16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION.... 1 Figure 1 to Part 1633—Test Assembly, Shown in Furniture Calorimeter (Configuration A) ER15MR06.000 ...

16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION.... 1 Figure 1 to Part 1633—Test Assembly, Shown in Furniture Calorimeter (Configuration A) ER15MR06.000 ...

16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION.... 1 Figure 1 to Part 1633—Test Assembly, Shown in Furniture Calorimeter (Configuration A) ER15MR06.000 ...

16 CFR Figure 1 to Part 1633 - Test Assembly, Shown in Furniture Calorimeter (Configuration A)

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Test Assembly, Shown in Furniture Calorimeter (Configuration A) 1 Figure 1 to Part 1633 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION.... 1 Figure 1 to Part 1633—Test Assembly, Shown in Furniture Calorimeter (Configuration A) ER15MR06.000 ...

Analyses of Selected Automotive Parts and Assemblies for Cost and Material Impacts

DOT National Transportation Integrated Search

1979-03-01

This is a study of selected automotive parts and assemblies analyzed to determine the elements of manufacturing cost and methods of production. Parts from the 1975 Ford Pinto, 1975 Chevelle, 1976 Audi 100LS, and the VW Rabbit are included in the sele...

Developments in the Tools and Methodologies of Synthetic Biology

PubMed Central

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

2014-01-01

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

GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

PubMed Central

Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I.; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

2011-01-01

Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop (“braid”) topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described. PMID:21750718

EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

PubMed

Moore, Simon J; Lai, Hung-En; Kelwick, Richard J R; Chee, Soo Mei; Bell, David J; Polizzi, Karen Marie; Freemont, Paul S

2016-10-21

Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.

The Design of a Molecular Assembly Line Based on Biological Molecules

DTIC Science & Technology

2003-06-01

and will demonstrate how one can construct a purely synthetic analogue of a polyketide synthase . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF...scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological molecules polyketide synthase and kinesin, and in...stereoselective centers) with any reasonable yield, not including the R&D and process development time. Figure 1.6 shows how a polyketide synthase

Effect of Dendritic Polymer Architecture on Biological Behaviors of Self-Assembled Nanocarriers

NASA Astrophysics Data System (ADS)

Hsu, Hao-Jui

Polymeric self-assembled nanocarriers represent one of the most versatile platforms for drug delivery. Through tailoring the physiochemical properties of amphiphilic block copolymers, self-assembled nanocarriers with great thermodynamic stability and desired biological properties could be achieved. The PEGylated dendron-based copolymers (PDCs) are one of the novel amphiphilic copolymers that have attracted a great deal of scientific interest due to their unique dendritic structure and properties. While the dendritic polymer architecture of PDC has been shown to enhance the thermodynamic stability of the self-assembling PDCs, dendron micelles, the effect of this polymer architecture on the biological properties of dendron micelles has not yet been studied. Therefore, this dissertation research is focused on understanding the role of dendritic polymer structure on moderating the biological properties of various self-assembled nanocarriers. To systematically investigate this, three studies have been designed and performed. First, we studied whether the dendritic structure of PDC allows dendron micelles to behave non-specific cellular interactions in a similar way that dendrimers would do. Second, cell-specific interactions of dendron micelles mediated by conjugated ligands were investigated. Third, we investigated the influence of dendritic PEG outer shell on micelle-serum protein interactions and its subsequent implication. Our results revealed that both non-specific and specific cellular interactions of dendron micelles were controllable through modulation of the PEG corona length. While the non-specific charge-dependent cellular interactions of dendron micelles were tunable through controlling the length of PEG corona, the use of long PEG tether was found to enhance the ligand-mediated cellular interactions of dendron micelles. With the ligand tethers, a 27-fold enhancement in ligand-mediated cellular interactions can be achieved, compared to non-targeted dendron

Biologically templated assembly of hybrid semiconducting nanomesh for high performance field effect transistors and sensors

NASA Astrophysics Data System (ADS)

Byeon, Hye-Hyeon; Lee, Seung-Woo; Lee, Eun-Hee; Kim, Woong; Yi, Hyunjung

2016-10-01

Delicately assembled composites of semiconducting nanomaterials and biological materials provide an attractive interface for emerging applications, such as chemical/biological sensors, wearable health monitoring devices, and therapeutic agent releasing devices. The nanostructure of composites as a channel and a sensing material plays a critical role in the performance of field effect transistors (FETs). Therefore, it is highly desirable to prepare elaborate composite that can allow the fabrication of high performance FETs and also provide high sensitivity and selectivity in detecting specific chemical/biological targets. In this work, we demonstrate that high performance FETs can be fabricated with a hydrodynamically assembled composite, a semiconducting nanomesh, of semiconducting single-walled carbon nanotubes (S-SWNTs) and a genetically engineered M13 phage to show strong binding affinity toward SWNTs. The semiconducting nanomesh enables a high on/off ratio (~104) of FETs. We also show that the threshold voltage and the channel current of the nanomesh FETs are sensitive to the change of the M13 phage surface charge. This biological gate effect of the phage enables the detection of biologically important molecules such as dopamine and bisphenol A using nanomesh-based FETs. Our results provide a new insight for the preparation of composite material platform for highly controllable bio/electronics interfaces.

Optimizing DNA assembly based on statistical language modelling.

PubMed

Fang, Gang; Zhang, Shemin; Dong, Yafei

2017-12-15

By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling more than a few sets of these parts can be expensive, time consuming and error prone. At the last step of assembling it is somewhat difficult to decide which part should be selected. Based on statistical language model, which is a probability distribution P(s) over strings S that attempts to reflect how frequently a string S occurs as a sentence, the most commonly used parts will be selected. Then, a dynamic programming algorithm was designed to figure out the solution of maximum probability. The algorithm optimizes the results of a genetic design based on a grammatical model and finds an optimal solution. In this way, redundant operations can be reduced and the time and cost required for conducting biological experiments can be minimized. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly

PubMed Central

Andreou, Andreas I.

2018-01-01

Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile—simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation. PMID:29293531

Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

PubMed

Andreou, Andreas I; Nakayama, Naomi

2018-01-01

Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

Fourier-Transform Raman Spectroscopy Of Biological Assemblies

NASA Astrophysics Data System (ADS)

Levin, Ira W.; Lewis, E. Neil

1989-12-01

Although the successful coupling of Raman scattered near-infrared radiation to a Michelson interferometer has recently created an outburst of intense interest in Fourier-transform (FT) Raman spectrometry," extended applications of the technique to macromolecular assemblies of biochemical and biophysical relevance have not progressed as rapidly as studies directed primarily at more conventional chemical characterizations. Since biological materials sampled with visible laser excitation sources typically emit a dominant fluorescence signal originating either from the intrinsic fluorescence of the molecular scatterer or from unrelenting contaminants, the use of near-infrared Nd:YAG laser excitation offers a convenient approach for avoiding this frequently overwhelming effect. In addition, the FT-Raman instrumentation provides a means of eliminating the deleterious resonance and decomposition effects often observed with the more accessible green and blue laser emissions. However, in choosing the incident near-infrared wavelength at, for example, 1064nm, the Raman scattered intensity decreases by factors of eighteen to forty from the Raman emissions induced by the shorter, visible excitations. Depending upon the experiment, this disadvantage is offset by the throughput and multiplex advantages afforded by the interferometric design. Thus, for most chemical systems, near-infrared FT-Raman spectroscopy, clearly provides a means for obtaining vibrational Raman spectra from samples intractable to the use of visible laser sources. In particular, for neat liquids, dilute solutions or polycrystalline materials, the ability to achieve high quality, reproducible spectra is, with moderate experience and perhaps relatively high laser powers, as straightforward as the conventional methods used to obtain Raman spectra with visible excitation and dispersive monochromators. In using near-infrared FT techniques to determine the Raman spectra of biological samples, one encounters new

Clean then Assemble Versus Assemble then Clean: Several Comparisons

NASA Technical Reports Server (NTRS)

Welker, Roger W.

2004-01-01

Cleanliness of manufactured parts and assemblies is a significant issue in many industries including disk drives, semiconductors, aerospace, and medical devices. Clean manufacturing requires cleanroom floor space and cleaning technology that are both expensive to own and expensive to operate. Strategies to reduce these costs are an important consideration. One strategy shown to be effective at reducing costs is to assemble parts into subassemblies and then clean the subassembly, rather than clean the individual parts first and then assemble them. One advantage is that assembly outside of the cleanroom reduces the amount of cleanroom floor space and its associated operating cost premium. A second advantage is that this strategy reduces the number of individual parts that must be cleaned prior to assembly, reducing the number of cleaning baskets, handling and, possibly, reducing the number of cleaners. The assemble then clean strategy also results in a part that is significantly cleaner because contamination generated during the assembly steps are more effectively removed that normally can be achieved by hand wiping after assembly in the cleanroom.

76 FR 41669 - Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-15

... Airworthiness Directives; B/E Aerospace, Continuous Flow Passenger Oxygen Mask Assembly, Part Numbers 174006... to prevent the in-line flow indicators of the oxygen mask assembly from fracturing and separating, which could inhibit oxygen flow to the masks. This condition could consequently result in occupants...

Agents, assemblers, and ANTS: scheduling assembly with market and biological software mechanisms

NASA Astrophysics Data System (ADS)

Toth-Fejel, Tihamer T.

2000-06-01

Nanoscale assemblers will need robust, scalable, flexible, and well-understood mechanisms such as software agents to control them. This paper discusses assemblers and agents, and proposes a taxonomy of their possible interaction. Molecular assembly is seen as a special case of general assembly, subject to many of the same issues, such as the advantages of convergent assembly, and the problem of scheduling. This paper discusses the contract net architecture of ANTS, an agent-based scheduling application under development. It also describes an algorithm for least commitment scheduling, which uses probabilistic committed capacity profiles of resources over time, along with realistic costs, to provide an abstract search space over which the agents can wander to quickly find optimal solutions.

Biology is only part of the story ...

PubMed

Read, Dwight; van der Leeuw, Sander

2008-06-12

The origins and development of human cognition constitute one of the most interesting questions to which archaeology can contribute today. In this paper, we do so by presenting an overview of the evolution of artefact technology from the maker's point of view, and linking that development to some hypotheses on the evolution of human cognitive capacity. Our main hypothesis is that these data indicate that, in the first part of the trajectory, biological limits to cognitive capacity were a major constraint that limited technology, whereas, in the second part, this biological constraint seems to have been lifted and others have come in its place. But these are modifiable by means of conceptual frameworks that facilitate concept innovation and therefore enable learning, thereby permitting acceleration in the pace of change in technology. In the last part of the paper, we elaborate on some of the consequences of that acceleration.

From self-organization to self-assembly: a new materialism?

PubMed

Vincent, Bernadette Bensaude

2016-09-01

While self-organization has been an integral part of academic discussions about the distinctive features of living organisms, at least since Immanuel Kant's Critique of Judgement, the term 'self-assembly' has only been used for a few decades as it became a hot research topic with the emergence of nanotechnology. Could it be considered as an attempt at reducing vital organization to a sort of assembly line of molecules? Considering the context of research on self-assembly I argue that the shift of attention from self-organization to self-assembly does not really challenge the boundary between chemistry and biology. Self-assembly was first and foremost investigated in an engineering context as a strategy for manufacturing without human intervention and did not raise new perspectives on the emergence of vital organization itself. However self-assembly implies metaphysical assumptions that this paper tries to disentangle. It first describes the emergence of self-assembly as a research field in the context of materials science and nanotechnology. The second section outlines the metaphysical implications and will emphasize a sharp contrast between the ontology underlying two practices of self-assembly developed under the umbrella of synthetic biology. And unexpectedly, we shall see that chemists are less on the reductionist side than most synthetic biologists. Finally, the third section ventures some reflections on the kind of design involved in self-assembly practices.

Toward scalable parts families for predictable design of biological circuits.

PubMed

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

2008-12-01

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

SPring-8 BL44XU, beamline designed for structure analysis of large biological macromolecular assemblies

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

Higashiura, Akifumi, E-mail: hgsur-a@protein.osaka-u.ac.jp; Yamashita, Eiki; Yoshimura, Masato

2016-07-27

Beamline BL44XU at SPring-8 is operated by the Institute for Protein Research of Osaka University. The beamline is designed for X-ray crystallography of large biological macromolecular assemblies. Here we show its detailed performances, results, and the ongoing upgrade plans.

Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials.

PubMed

Nguyen, Peter Q; Courchesne, Noémie-Manuelle Dorval; Duraj-Thatte, Anna; Praveschotinunt, Pichet; Joshi, Neel S

2018-05-01

Vast potential exists for the development of novel, engineered platforms that manipulate biology for the production of programmed advanced materials. Such systems would possess the autonomous, adaptive, and self-healing characteristics of living organisms, but would be engineered with the goal of assembling bulk materials with designer physicochemical or mechanical properties, across multiple length scales. Early efforts toward such engineered living materials (ELMs) are reviewed here, with an emphasis on engineered bacterial systems, living composite materials which integrate inorganic components, successful examples of large-scale implementation, and production methods. In addition, a conceptual exploration of the fundamental criteria of ELM technology and its future challenges is presented. Cradled within the rich intersection of synthetic biology and self-assembling materials, the development of ELM technologies allows the power of biology to be leveraged to grow complex structures and objects using a palette of bio-nanomaterials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

FLOAT OPERATED RADIAL GATE HOIST ASSEMBLY LIST OF PARTS ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

FLOAT OPERATED RADIAL GATE HOIST ASSEMBLY - LIST OF PARTS - BASE-CRANK. WASTEWAY NO. 1. WELLTON-MOHAWK CANAL - STA. 99+23.50. United States Department of the Interior, Bureau of Reclamation; Gila Project, Arizona, Wellton-Mohawk Division. Drawing No. 50-D-2511, dated May 3, 1949, Denver Colorado. Sheet 1 of 2 - Wellton-Mohawk Irrigation System, Wasteway No. 1, Wellton-Mohawk Canal, North side of Wellton-Mohawk Canal, bounded by Gila River to North & the Union Pacific Railroad & Gila Mountains to south, Wellton, Yuma County, AZ

Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

NASA Technical Reports Server (NTRS)

Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

2017-01-01

This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called digital materials. We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

NASA Technical Reports Server (NTRS)

Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

2017-01-01

This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called "digital materials." We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be

Experiments to evolve toward a tangible user interface for computer-aided design parts assembly

NASA Astrophysics Data System (ADS)

Legardeur, Jeremy; Garreau, Ludovic; Couture, Nadine

2004-05-01

In this paper, we present the concepts of the ESKUA (Experimentation of a Kinesics System Usable for Assembly) platform that allows designers to carry out the assembly of mechanical CAD (Computer Aided Design) parts. This platform, based on tangible user interface lead taking into account assembly constraints from the beginning of the design phase and especially during the phase of CAD models manipulation. Our goal is to propose a working environment where the designer is confronted with real assembly constraints which are currently masked by existing CAD software functionalities. Thus, the platform is based on the handling of physical objects, called tangible interactors, which enable having a physical perception of the assembly constraints. In this goal, we have defined a typology of interactors based on concepts proposed in Design For Assembly methods. We present here the results of studies that led to the evolution of this first interactors set. One is concerning an experiment to evaluate the cognitive aspects of the use of interactors. The other is about an analysis of existing mechanical product and fasteners. We will show how these studies lead to the evolution of the interactors based on the functional surfaces use.

Directed-assembly of ordered nanoparticle arrays exploiting multiple adsorption mechanisms on a self-assembling biological template

NASA Astrophysics Data System (ADS)

Shindel, Matthew M.

Developing processes to fabricate inorganic architectures with designer functionalities at increasingly minute length-scales is of chief concern in the fields of nanotechnology and nanoscience. This enterprise requires assembly mechanisms with the capacity to tailor both the spatial arrangement and material composition of a system's constituent building blocks. To this end, significant advances can be made by turning to biology, as the natural world has evolved the ability to generate intricate nanostructures, which can potentially be employed as templates for inorganic nanosystems. We explore this biotemplating methodology using two-dimensional streptavidin crystals, investigating the ability of the protein lattice to direct the assembly of ordered metallic nanoparticle arrays. We demonstrate that the adsorption of nanoparticles on the protein monolayer can be induced through both electrostatic and molecular recognition (ligand-receptor) interactions. Furthermore, the dynamics of adsorption can be modulated through both environmental factors (e.g. pH), and by tailoring particle surface chemistry. When the characteristic nanoparticle size is on the order of the biotemplate's unit-cell dimension, electrostatically-mediated adsorption occurs in a site-specific manner. The nanoparticles exhibit a pronounced preference for adhering to the areas between protein molecules. The two-dimensional structure of the resultant nanoparticle ensemble consequently conforms to that of the underlying protein crystal. Through theoretical calculations, simulation and experiment, we show that interparticle spacing in the templated array is influenced by the screened-coulombic repulsion between particles, and can thus be tuned by controlling ionic strength during deposition. Templating ordered nanoparticle arrays via ligand-receptor mediated adsorption, and the constrained growth of metallic nanoparticles directly on the protein lattice from ionic precursors are also examined. Overall

Design of polymer motifs for nucleic acid recognition and assembly stabilization

NASA Astrophysics Data System (ADS)

Zhou, Zhun

This dissertation describes the synthesis and assembly of bio-functional polymers and the applications of these polymers to drug encapsulation, delivery, and multivalent biomimetic macromolecular recognition between synthetic polymer and nucleic acids. The main content is divided into three parts: (1) polyacidic domains as strongly stabilizing design elements for aqueous phase polyacrylate diblock assembly; (2) small molecule/polymer recognition triggered macromolecular assembly and drug encapsulation; (3) trizaine derivatized polymer as a novel class of "bifacial polymer nucleic acid" (bPoNA) and applications of bPoNA to nanoparticle loading of DNA/RNA, silencing delivery as well as control of aptamer function. Through the studies in part (1) and part (2), it was demonstrated that well-designed polymer motifs are not only able to enhance assemblies driven by non-specific hydrophobic effect, but are also able to direct assemblies based on specific recognitions. In part (3) of this dissertation, this concept was further extended by the design of polyacrylate polymers that are capable of discrete and robust hybridization with nucleic acids. This surprising finding demonstrated both fundamental and practical applications. Overall, these studies provided insights into the rational design elements for improving the bio-functions of synthetic polymers, and significantly expanded the scope of biological applications in which polymers synthesized via controlled radical polymerization may play a role.

Scar-less multi-part DNA assembly design automation

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

Hillson, Nathan J.

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which tomore » assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.« less

The Eugene language for synthetic biology.

PubMed

Bilitchenko, Lesia; Liu, Adam; Densmore, Douglas

2011-01-01

Synthetic biological systems are currently created by an ad hoc, iterative process of design, simulation, and assembly. These systems would greatly benefit from the introduction of a more formalized and rigorous specification of the desired system components as well as constraints on their composition. In order to do so, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) which allows for both the specification of synthetic biological designs based on biological parts as well as providing a very expressive constraint system to drive the creation of composite devices from collection of parts. This chapter provides an overview of the language primitives as well as instructions on installation and use of Eugene v0.03b. Copyright © 2011 Elsevier Inc. All rights reserved.

Nuclear, biological and chemical warfare. Part I: Medical aspects of nuclear warfare.

PubMed

Kasthuri, A S; Pradhan, A B; Dham, S K; Bhalla, I P; Paul, J S

1990-04-01

Casualties in earlier wars were due much more to diseases than to weapons. Mention has been made in history of the use of biological agents in warfare, to deny the enemy food and water and to cause disease. In the first world war chemical agents were used to cause mass casualties. Nuclear weapons were introduced in the second world war. Several countries are now involved in developing nuclear, biological and chemical weapon systems, for the mass annihilation of human beings, animals and plants, and to destroy the economy of their enemies. Recently, natural calamities and accidents in nuclear, chemical and biological laboratories and industries have caused mass instantaneous deaths in civilian population. The effects of future wars will not be restricted to uniformed persons. It is time that physicians become aware of the destructive potential of these weapons. Awareness, immediate protective measures and first aid will save a large number of persons. This series of articles will outline the medical aspects of nuclear, biological and chemical weapon systems in three parts. Part I will deal with the biological effects of a nuclear explosion. The short and long term effects due to blast, heat and associated radiation are highlighted. In Part II, the role of biological agents which cause commoner or new disease patterns is mentioned. Some of the accidents from biological warfare laboratories are a testimony to its potential deleterious effects. Part III deals with medical aspects of chemical warfare agents, which in view of their mass effects can overwhelm the existing medical resources, both civilian and military.(ABSTRACT TRUNCATED AT 250 WORDS)

Characterisation of minimalist co-assembled fluorenylmethyloxycarbonyl self-assembling peptide systems for presentation of multiple bioactive peptides.

PubMed

Horgan, Conor C; Rodriguez, Alexandra L; Li, Rui; Bruggeman, Kiara F; Stupka, Nicole; Raynes, Jared K; Day, Li; White, John W; Williams, Richard J; Nisbet, David R

2016-07-01

The nanofibrillar structures that underpin self-assembling peptide (SAP) hydrogels offer great potential for the development of finely tuned cellular microenvironments suitable for tissue engineering. However, biofunctionalisation without disruption of the assembly remains a key issue. SAPS present the peptide sequence within their structure, and studies to date have typically focused on including a single biological motif, resulting in chemically and biologically homogenous scaffolds. This limits the utility of these systems, as they cannot effectively mimic the complexity of the multicomponent extracellular matrix (ECM). In this work, we demonstrate the first successful co-assembly of two biologically active SAPs to form a coassembled scaffold of distinct two-component nanofibrils, and demonstrate that this approach is more bioactive than either of the individual systems alone. Here, we use two bioinspired SAPs from two key ECM proteins: Fmoc-FRGDF containing the RGD sequence from fibronectin and Fmoc-DIKVAV containing the IKVAV sequence from laminin. Our results demonstrate that these SAPs are able to co-assemble to form stable hybrid nanofibres containing dual epitopes. Comparison of the co-assembled SAP system to the individual SAP hydrogels and to a mixed system (composed of the two hydrogels mixed together post-assembly) demonstrates its superior stable, transparent, shear-thinning hydrogels at biological pH, ideal characteristics for tissue engineering applications. Importantly, we show that only the coassembled hydrogel is able to induce in vitro multinucleate myotube formation with C2C12 cells. This work illustrates the importance of tissue engineering scaffold functionalisation and the need to develop increasingly advanced multicomponent systems for effective ECM mimicry. Successful control of stem cell fate in tissue engineering applications requires the use of sophisticated scaffolds that deliver biological signals to guide growth and differentiation

Recent advances in synthetic biology of cyanobacteria.

PubMed

Sengupta, Annesha; Pakrasi, Himadri B; Wangikar, Pramod P

2018-05-09

Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO 2 . Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO 2 , diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.

Automated assembly in space

NASA Technical Reports Server (NTRS)

Srivastava, Sandanand; Dwivedi, Suren N.; Soon, Toh Teck; Bandi, Reddy; Banerjee, Soumen; Hughes, Cecilia

1989-01-01

The installation of robots and their use of assembly in space will create an exciting and promising future for the U.S. Space Program. The concept of assembly in space is very complicated and error prone and it is not possible unless the various parts and modules are suitably designed for automation. Certain guidelines are developed for part designing and for an easy precision assembly. Major design problems associated with automated assembly are considered and solutions to resolve these problems are evaluated in the guidelines format. Methods for gripping and methods for part feeding are developed with regard to the absence of gravity in space. The guidelines for part orientation, adjustments, compliances and various assembly construction are discussed. Design modifications of various fasteners and fastening methods are also investigated.

Two sides of the coin. Part 2. Colloid and surface science meets real biointerfaces.

PubMed

Ninham, Barry W; Larsson, Kåre; Lo Nostro, Pierandrea

2017-11-01

Part 1 revisited developments in lipid and surfactant self assembly over the past 40 years [1]. New concepts emerged. Here we explore how these developments can be used to make sense of and bring order to a range of complex biological phenomena. Together with Part 1, this contribution is a fundamental revision of intuition at the boundaries of Colloid Science and Biological interfaces from a perspective of nearly 50 years. We offer new insights on a unified treatment of self assembly of lipids, surfactants and proteins in the light of developments presented in Part 1. These were in the enabling disciplines in molecular forces, hydration, oil and electrolyte specificity; and in the role of non Euclidean geometries-across the whole gammut of physical, colloid and surface chemistry, biophysics and membrane biology and medicine. It is where the early founders of the cell theory of biology and the physiologists expected advances to occur as D'Arcy Thompson predicted us 100 years ago. Copyright © 2017 Elsevier B.V. All rights reserved.

Self-assembly: Misfits unite

NASA Astrophysics Data System (ADS)

Grason, Gregory M.

2017-12-01

The spontaneous assembly of particulate or molecular 'building blocks' into larger architectures underlies structure formation in many biological and synthetic materials. Shape frustration of ill-fitting blocks holds a surprising key to more regular assemblies.

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

PubMed

Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

2017-07-21

Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

Intracellular Peptide Self-Assembly: A Biomimetic Approach for in Situ Nanodrug Preparation.

PubMed

Du, Wei; Hu, Xiaomu; Wei, Weichen; Liang, Gaolin

2018-04-18

Most nanodrugs are preprepared by encapsulating or loading the drugs with nanocarriers (e.g., dendrimers, liposomes, micelles, and polymeric nanoparticles). However, besides the low bioavailability and fast excretion of the nanodrugs in vivo, nanocarriers often exhibit in vitro and in vivo cytotoxicity, oxidative stress, and inflammation. Self-assembly is a ubiquitous process in biology where it plays important roles and underlies the formation of a wide variety of complex biological structures. Inspired by some cellular nanostructures (e.g., actin filaments, microtubules, vesicles, and micelles) in biological systems which are formed via molecular self-assembly, in recent decades, scientists have utilized self-assembly of oligomeric peptide under specific physiological or pathological environments to in situ construct nanodrugs for lesion-targeted therapies. On one hand, peptide-based nanodrugs always have some excellent intrinsic chemical (specificity, intrinsic bioactivity, biodegradability) and physical (small size, conformation) properties. On the other hand, stimuli-regulated intracellular self-assembly of nanodrugs is quite an efficient way to accumulate the drugs in lesion location and can realize an in situ slow release of the drugs. In this review article, we provided an overview on recent design principles for intracellular peptide self-assembly and illustrate how these principles have been applied for the in situ preparation of nanodrugs at the lesion location. In the last part, we list some challenges underlying this strategy and their possible solutions. Moreover, we envision the future possible theranostic applications of this strategy.

Single Day Construction of Multigene Circuits with 3G Assembly.

PubMed

Halleran, Andrew D; Swaminathan, Anandh; Murray, Richard M

2018-05-18

The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly's ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multigene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.

Interest in biology. Part I: A multidimensional construct

NASA Astrophysics Data System (ADS)

Gardner, Paul L.; Tamir, Pinchas

Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There

Application of the Modular Automated Reconfigurable Assembly System (MARAS) concept to adaptable vision gauging and parts feeding

NASA Technical Reports Server (NTRS)

By, Andre Bernard; Caron, Ken; Rothenberg, Michael; Sales, Vic

1994-01-01

This paper presents the first phase results of a collaborative effort between university researchers and a flexible assembly systems integrator to implement a comprehensive modular approach to flexible assembly automation. This approach, named MARAS (Modular Automated Reconfigurable Assembly System), has been structured to support multiple levels of modularity in terms of both physical components and system control functions. The initial focus of the MARAS development has been on parts gauging and feeding operations for cylinder lock assembly. This phase is nearing completion and has resulted in the development of a highly configurable system for vision gauging functions on a wide range of small components (2 mm to 100 mm in size). The reconfigurable concepts implemented in this adaptive Vision Gauging Module (VGM) are now being extended to applicable aspects of the singulating, selecting, and orienting functions required for the flexible feeding of similar mechanical components and assemblies.

A unified convention for biological assemblies with helical symmetry

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

Tsai, Chung-Jung, E-mail: tsaic@mail.nih.gov; Nussinov, Ruth; Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978

A new representation of helical structure by four parameters, [n{sub 1}, n{sub 2}, twist, rise], is able to generate an entire helical construct from asymmetric units, including cases of helical assembly with a seam. Assemblies with helical symmetry can be conveniently formulated in many distinct ways. Here, a new convention is presented which unifies the two most commonly used helical systems for generating helical assemblies from asymmetric units determined by X-ray fibre diffraction and EM imaging. A helical assembly is viewed as being composed of identical repetitive units in a one- or two-dimensional lattice, named 1-D and 2-D helical systems,more » respectively. The unification suggests that a new helical description with only four parameters [n{sub 1}, n{sub 2}, twist, rise], which is called the augmented 1-D helical system, can generate the complete set of helical arrangements, including coverage of helical discontinuities (seams). A unified four-parameter characterization implies similar parameters for similar assemblies, can eliminate errors in reproducing structures of helical assemblies and facilitates the generation of polymorphic ensembles from helical atomic models or EM density maps. Further, guidelines are provided for such a unique description that reflects the structural signature of an assembly, as well as rules for manipulating the helical symmetry presentation.« less

Supramolecular Disassembly of Facially Amphiphilic Dendrimer Assemblies in Response to Physical, Chemical, and Biological Stimuli

PubMed Central

2015-01-01

Conspectus Supramolecular assemblies formed from spontaneous self-assembly of amphiphilic macromolecules are explored as biomimetic architectures and for applications in areas such as sensing, drug delivery, and diagnostics. Macromolecular assemblies are usually preferred, compared with their simpler small molecule counterparts, due to their low critical aggregate concentrations (CAC) and high thermodynamic stability. This Account focuses on the structural and functional aspects of assemblies formed from dendrimers, specifically facially amphiphilic dendrons that form micelle or inverse micelle type supramolecular assemblies depending on the nature of the solvent medium. The micelle type assemblies formed from facially amphiphilic dendrons sequester hydrophobic guest molecules in their interiors. The stability of these assemblies is dependent on the relative compatibility of the hydrophilic and hydrophobic functionalities with water, often referred to as hydrophilic–lipophilic balance (HLB). Disruption of the HLB, using an external stimulus, could lead to disassembly of the aggregates, which can then be utilized to cause an actuation event, such as guest molecule release. Studying these possibilities has led to (i) a robust and general strategy for stimulus-induced disassembly and molecular release and (ii) the introduction of a new approach to protein-responsive supramolecular disassembly. The latter strategy provides a particularly novel avenue for impacting biomedical applications. Most of the stimuli-sensitive supramolecular assemblies have been designed to be responsive to factors such pH, temperature, and redox conditions. The reason for this interest stems from the fact that certain disease microenvironments have aberrations in these factors. However, these variations are the secondary imbalances in biology. Imbalances in protein activity are the primary reasons for most, if not all, human pathology. There have been no robust strategies in stimulus

Structural biological composites: An overview

NASA Astrophysics Data System (ADS)

Meyers, Marc A.; Lin, Albert Y. M.; Seki, Yasuaki; Chen, Po-Yu; Kad, Bimal K.; Bodde, Sara

2006-07-01

Biological materials are complex composites that are hierarchically structured and multifunctional. Their mechanical properties are often outstanding, considering the weak constituents from which they are assembled. They are for the most part composed of brittle (often, mineral) and ductile (organic) components. These complex structures, which have risen from millions of years of evolution, are inspiring materials scientists in the design of novel materials. This paper discusses the overall design principles in biological structural composites and illustrates them for five examples; sea spicules, the abalone shell, the conch shell, the toucan and hornbill beaks, and the sheep crab exoskeleton.

Antifouling aptasensor for the detection of adenosine triphosphate in biological media based on mixed self-assembled aptamer and zwitterionic peptide.

PubMed

Wang, Guixiang; Su, Xiaoli; Xu, Qingjun; Xu, Guiyun; Lin, Jiehua; Luo, Xiliang

2018-03-15

Direct detection of targets in complex biological media with conventional biosensors is an enormous challenge due to the nonspecific adsorption and severe biofouling. In this work, a facile strategy for sensitive and low fouling detection of adenosine triphosphate (ATP) is developed through the construction of a mixed self-assembled biosensing interface, which was composed of zwitterionic peptide (antifouling material) and ATP aptamer (bio-recognition element). The peptide and aptamer (both containing thiol groups) were simultaneously self-assembled onto gold electrode surface electrodeposited with gold nanoparticles. The developed aptasensor possessed high selectivity and sensitivity for ATP, and it showed a wide linear response range towards ATP from 0.1pM to 5nM. Owing to the presence of peptide with excellent antifouling property in the biosensing interface, the aptasensor can detect ATP in complex biological media with remarkably reduced biofouling or nonspecific adsorption effect. Moreover, it can directly detect ATP in 1% human whole blood without suffering from any significant interference, indicating its great potential for practical assaying of ATP in biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Adeno-associated Virus (AAV) Assembly-Activating Protein Is Not an Essential Requirement for Capsid Assembly of AAV Serotypes 4, 5, and 11.

PubMed

Earley, Lauriel F; Powers, John M; Adachi, Kei; Baumgart, Joshua T; Meyer, Nancy L; Xie, Qing; Chapman, Michael S; Nakai, Hiroyuki

2017-02-01

Adeno-associated virus (AAV) vectors have made great progress in their use for gene therapy; however, fundamental aspects of AAV's capsid assembly remain poorly characterized. In this regard, the discovery of assembly-activating protein (AAP) sheds new light on this crucial part of AAV biology and vector production. Previous studies have shown that AAP is essential for assembly; however, how its mechanistic roles in assembly might differ among AAV serotypes remains uncharacterized. Here, we show that biological properties of AAPs and capsid assembly processes are surprisingly distinct among AAV serotypes 1 to 12. In the study, we investigated subcellular localizations and assembly-promoting functions of AAP1 to -12 (i.e., AAPs derived from AAV1 to -12, respectively) and examined the AAP dependence of capsid assembly processes of these 12 serotypes using combinatorial approaches that involved immunofluorescence and transmission electron microscopy, barcode-Seq (i. e., a high-throughput quantitative method using DNA barcodes and a next-generation sequencing technology), and quantitative dot blot assays. This study revealed that AAP1 to -12 are all localized in the nucleus with serotype-specific differential patterns of nucleolar association; AAPs and assembled capsids do not necessarily colocalize; AAPs are promiscuous in promoting capsid assembly of other serotypes, with the exception of AAP4, -5, -11, and -12; assembled AAV5, -8, and -9 capsids are excluded from the nucleolus, in contrast to the nucleolar enrichment of assembled AAV2 capsids; and, surprisingly, AAV4, -5, and -11 capsids are not dependent on AAP for assembly. These observations highlight the serotype-dependent heterogeneity of the capsid assembly process and challenge current notions about the role of AAP and the nucleolus in capsid assembly. Assembly-activating protein (AAP) is a recently discovered adeno-associated virus (AAV) protein that promotes capsid assembly and provides new opportunities

Microfluidic assembly blocks.

PubMed

Rhee, Minsoung; Burns, Mark A

2008-08-01

An assembly approach for microdevice construction using prefabricated microfluidic components is presented. Although microfluidic systems are convenient platforms for biological assays, their use in the life sciences is still limited mainly due to the high-level fabrication expertise required for construction. This approach involves prefabrication of individual microfluidic assembly blocks (MABs) in PDMS that can be readily assembled to form microfluidic systems. Non-expert users can assemble the blocks on glass slides to build their devices in minutes without any fabrication steps. In this paper, we describe the construction and assembly of the devices using the MAB methodology, and demonstrate common microfluidic applications including laminar flow development, valve control, and cell culture.

Self-Assembly: How Nature Builds

ERIC Educational Resources Information Center

Jones, M. Gail; Falvo, Michael R.; Broadwell, Bethany; Dotger, Sharon

2006-01-01

Self-assembly or spontaneous assembly is a process in which materials build themselves without assistance. This process plays a central role in the construction of biological structures and materials such as cells, viruses, and bone, and also in abiotic processes like phase transitions and crystal formation. The principles of self-assembly help…

Tectonic assembly of Gondwana

NASA Astrophysics Data System (ADS)

Rogers, John J. W.; Unrug, Raphael; Sultan, Mohamed

1995-01-01

The Paleozoic assembly of Pangea, with Gondwana as its southern half, completed the last full cycle of growth and dispersal of supercontinents during earth history. This assembly apparently resulted from reorganization of a preceding supercontinent (Rodinia) that existed at ˜1000 Ma. In addition to Laurentia and fragments that formed nuclei for Europe and Asia, the rifting of Rodinia produced: (1) East Gondwana, consisting largely of Western Australia, India, East Antarctica, and possibly part of southern Africa; and (2) various smaller fragments that converged to form West Gondwana, consisting of most of Africa and South America. East Gondwana appears to have been a stable block at a time no younger than ˜1000 Ma and possibly older. West Gondwana accreted largely in the latest Proterozoic and early Paleozoic by closure of the Pharusian Ocean in the north, the Adamaster Ocean in the south, and the ANEKT/Mozambique Ocean between West and East Gondwana. The assembly process was diachronous along numerous mobile belts, accompanied by syn- and post-collisional shearing and magmatism, and led to development of successor basins and rifts. Uncertainties in the timing and mechanism of assembly of Gondwana greatly limit our understanding of the supercontinent cycle. Thus, we propose investigations of Gondwana to determine more precisely the nature and age of apparent cratonic blocks, the locations and ages of orogenic belts, the configuration of former ocean basins, the significance of transcontinental shears, the extent of reactivation of older terranes, and the relationship of Gondwana to North America. Detailed knowledge of the assembly of Gondwana should also provide information on its relationship to other major processes such as mantle evolution and atmospheric, oceanic, and biologic changes.

Digital test assembly of truck parts with the IMMA-tool--an illustrative case.

PubMed

Hanson, L; Högberg, D; Söderholm, M

2012-01-01

Several digital human modelling (DHM) tools have been developed for simulation and visualisation of human postures and motions. In 2010 the DHM tool IMMA (Intelligently Moving Manikins) was introduced as a DHM tool that uses advanced path planning techniques to generate collision free and biomechanically acceptable motions for digital human models (as well as parts) in complex assembly situations. The aim of the paper is to illustrate how the IPS/IMMA tool is used at Scania CV AB in a digital test assembly process, and to compare the tool with other DHM tools on the market. The illustrated case of using the IMMA tool, here combined with the path planner tool IPS, indicates that the tool is promising. The major strengths of the tool are its user friendly interface, the motion generation algorithms, the batch simulation of manikins and the ergonomics assessment methods that consider time.

BASIC: A Simple and Accurate Modular DNA Assembly Method.

PubMed

Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

2017-01-01

Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

AutoAssemblyD: a graphical user interface system for several genome assemblers.

PubMed

Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

2013-01-01

Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

The PLOS ONE Synthetic Biology Collection: Six Years and Counting

PubMed Central

Peccoud, Jean; Isalan, Mark

2012-01-01

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

The PLOS ONE synthetic biology collection: six years and counting.

PubMed

Peccoud, Jean; Isalan, Mark

2012-01-01

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

Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

PubMed Central

Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

2015-01-01

Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

Automated selection of synthetic biology parts for genetic regulatory networks.

PubMed

Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron; Densmore, Douglas; Beal, Jacob

2012-08-17

Raising the level of abstraction for synthetic biology design requires solving several challenging problems, including mapping abstract designs to DNA sequences. In this paper we present the first formalism and algorithms to address this problem. The key steps of this transformation are feature matching, signal matching, and part matching. Feature matching ensures that the mapping satisfies the regulatory relationships in the abstract design. Signal matching ensures that the expression levels of functional units are compatible. Finally, part matching finds a DNA part sequence that can implement the design. Our software tool MatchMaker implements these three steps.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

AFEAP cloning: a precise and efficient method for large DNA sequence assembly.

PubMed

Zeng, Fanli; Zang, Jinping; Zhang, Suhua; Hao, Zhimin; Dong, Jingao; Lin, Yibin

2017-11-14

Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist's toolbox.

Gateway Vectors for Efficient Artificial Gene Assembly In Vitro and Expression in Yeast Saccharomyces cerevisiae

PubMed Central

Giuraniuc, Claudiu V.; MacPherson, Murray; Saka, Yasushi

2013-01-01

Construction of synthetic genetic networks requires the assembly of DNA fragments encoding functional biological parts in a defined order. Yet this may become a time-consuming procedure. To address this technical bottleneck, we have created a series of Gateway shuttle vectors and an integration vector, which facilitate the assembly of artificial genes and their expression in the budding yeast Saccharomyces cerevisiae. Our method enables the rapid construction of an artificial gene from a promoter and an open reading frame (ORF) cassette by one-step recombination reaction in vitro. Furthermore, the plasmid thus created can readily be introduced into yeast cells to test the assembled gene’s functionality. As flexible regulatory components of a synthetic genetic network, we also created new versions of the tetracycline-regulated transactivators tTA and rtTA by fusing them to the auxin-inducible degron (AID). Using our gene assembly approach, we made yeast expression vectors of these engineered transactivators, AIDtTA and AIDrtTA and then tested their functions in yeast. We showed that these factors can be regulated by doxycycline and degraded rapidly after addition of auxin to the medium. Taken together, the method for combinatorial gene assembly described here is versatile and would be a valuable tool for yeast synthetic biology. PMID:23675537

Direct assembling methodologies for high-throughput bioscreening

PubMed Central

Rodríguez-Dévora, Jorge I.; Shi, Zhi-dong; Xu, Tao

2012-01-01

Over the last few decades, high-throughput (HT) bioscreening, a technique that allows rapid screening of biochemical compound libraries against biological targets, has been widely used in drug discovery, stem cell research, development of new biomaterials, and genomics research. To achieve these ambitions, scaffold-free (or direct) assembly of biological entities of interest has become critical. Appropriate assembling methodologies are required to build an efficient HT bioscreening platform. The development of contact and non-contact assembling systems as a practical solution has been driven by a variety of essential attributes of the bioscreening system, such as miniaturization, high throughput, and high precision. The present article reviews recent progress on these assembling technologies utilized for the construction of HT bioscreening platforms. PMID:22021162

Programming biological operating systems: genome design, assembly and activation.

PubMed

Gibson, Daniel G

2014-05-01

The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

[Topical issues of biological safety under current conditions. Part 2. Conceptual, terminological, and definitive framework of biological safety].

PubMed

Onishchenko, G G; Smolenskiĭ, V Iu; Ezhlova, E B; Demina, Iu V; Toporkov, V P; Toporkov, A V; Liapin, M N; Kutyrev, V V

2013-01-01

In accordance with the established conceptual base for the up-to-date broad interpretation of biological safety, and IHR (2005), developed is the notional, terminological, and definitive framework, comprising 33 elements. Key item of the nomenclature is the biological safety that is identified as population safety (individual, social, national) from direct and (or) human environment mediated (occupational, socio-economic, geopolitical infrastructures, ecological system) exposures to hazardous biological factors. Ultimate objective of the biological safety provision is to prevent and liquidate aftermaths of emergency situations of biological character either of natural or human origin (anthropogenic) arising from direct and indirect impact of the biological threats to the public health compatible with national and international security hazard. Elaborated terminological framework allows for the construction of self-sufficient semantic content for biological safety provision, subject to formalization in legislative, normative and methodological respects and indicative of improvement as regards organizational and structural-functional groundwork of the Russian Federation National chemical and biological safety system, which is to become topical issue of Part 3.

An end-to-end workflow for engineering of biological networks from high-level specifications.

PubMed

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

2012-08-17

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

Biological Activation of Inert Ceramics: Recent Advances Using Tailored Self-Assembled Monolayers on Implant Ceramic Surfaces

PubMed Central

Böke, Frederik; Schickle, Karolina; Fischer, Horst

2014-01-01

High-strength ceramics as materials for medical implants have a long, research-intensive history. Yet, especially on applications where the ceramic components are in direct contact with the surrounding tissue, an unresolved issue is its inherent property of biological inertness. To combat this, several strategies have been investigated over the last couple of years. One promising approach investigates the technique of Self-Assembled Monolayers (SAM) and subsequent chemical functionalization to create a biologically active tissue-facing surface layer. Implementation of this would have a beneficial impact on several fields in modern implant medicine such as hip and knee arthroplasty, dental applications and related fields. This review aims to give a summarizing overview of the latest advances in this recently emerging field, along with thorough introductions of the underlying mechanism of SAMs and surface cell attachment mechanics on the cell side. PMID:28788687

Genetically encoded photochemical covalent crosslinking within the Hcp-1 self-assembling bacterial secretion machinery.

PubMed

Antonczak, Alicja K; Milholland, Kedric; Tippmann, Eric M

2018-05-01

The target protein, Hcp1, was first described as part of the bacterial Type VI secretion system from Pseudomonas aeruginosa. The protein first self-assembles into a hexamer and then the hexamers further stack into a nanotubular structure. Hcp1 monomers were targeted for mutagenesis with two widely used photoactivatable amino acids: para-benzoyl phenylalanine or para-azidophenylalanine. The ability of these amino acids to form covalent adducts within the Hcp1 self-assembled system was investigated. Multiple residues, putatively of equal distance between the monomer-monomer interface were targeted. The efficiency of each amino acid to covalently link self-assembled hexamers was determined. The results demonstrate the choice and role of genetically encoded tools applied to complicated biological processes such as self-assembly and also suggested some structural dynamics of the Hcp-1 protein not obvious from crystallographic structures.

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

PubMed

Li, Mingji; Borodina, Irina

2015-02-01

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

Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.

Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Stepanauskas, Ramunas

2018-02-06

DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Chemical synthetic biology: a mini-review.

PubMed

Chiarabelli, Cristiano; Stano, Pasquale; Luisi, Pier Luigi

2013-01-01

Chemical synthetic biology (CSB) is a branch of synthetic biology (SB) oriented toward the synthesis of chemical structures alternative to those present in nature. Whereas SB combines biology and engineering with the aim of synthesizing biological structures or life forms that do not exist in nature - often based on genome manipulation, CSB uses and assembles biological parts, synthetic or not, to create new and alternative structures. A short epistemological note will introduce the theoretical concepts related to these fields, whereas the text will be largely devoted to introduce and comment two main projects of CSB, carried out in our laboratory in the recent years. The "Never Born Biopolymers" project deals with the construction and the screening of RNA and peptide sequences that are not present in nature, whereas the "Minimal Cell" project focuses on the construction of semi-synthetic compartments (usually liposomes) containing the minimal and sufficient number of components to perform the basic function of a biological cell. These two topics are extremely important for both the general understanding of biology in terms of function, organization, and development, and for applied biotechnology.

Simulations of curved assemblies in soft matter and biological systems

NASA Astrophysics Data System (ADS)

Qiao, Cong

Viruses are small infectious agents that replicate only inside living cells of other organisms. In the viral life cycle, the self-assembly of the outer protein shell (capsid) is an essential step. We study this process in the hope of shedding light on development of antiviral drugs, gene therapy and other virus-related technologies that can benefit the humankind. More fundamentally, learning about the process of viral capsid assembly can elucidate the assembly mechanisms of a wide range of complex structures. In this work, we use molecular dynamics simulations and coarse-grained computational models to study viral capsid assembly in several situations where geometric constraints play a role in dictating assembly outcomes. We first focus on icosahedral viruses with single-stranded RNA genomes, in which case the capsid usually assembles around the genomic RNA. It is consistently observed in experiments that such viral particles are ''overcharged'', meaning the net negative charge on the viral genome is greater than the net positive charge on the viral capsid. We computationally investigate the mechanisms that lead to ``overcharging'', and more broadly, how the encapsidated genome length is influenced by the capsid. We perform both dynamical simulations of the assembly process and equilibrium calculations to determine the optimal genome length (meaning that which maximizes the assembly yield and/or minimizes the free energy of the assembled virus). We find that the optimal genome length is determined by the interplay between capsid size, net capsid charge, distribution of capsid charge and nucleic acid structures. Our simulations demonstrate that overcharging results from a combination of electrostatic screening and the geometric constraints associated with encapsulating a nucleic acid inside of a spherical virus. We then study the assembly of the immature HIV. In contrast to icosahedral viruses, the immature HIV forms an asymmetric particle, consisting of continuous

Design of fluidic self-assembly bonds for precise component positioning

NASA Astrophysics Data System (ADS)

Ramadoss, Vivek; Crane, Nathan B.

2008-02-01

Self Assembly is a promising alternative to conventional pick and place robotic assembly of micro components. Its benefits include parallel integration of parts with low equipment costs. Various approaches to self assembly have been demonstrated, yet demanding applications like assembly of micro-optical devices require increased positioning accuracy. This paper proposes a new method for design of self assembly bonds that addresses this need. Current methods have zero force at the desired assembly position and low stiffness. This allows small disturbance forces to create significant positioning errors. The proposed method uses a substrate assembly feature to provide a high accuracy alignment guide to the part. The capillary bond region of the part and substrate are then modified to create a non-zero positioning force to maintain the part in the desired assembly position. Capillary force models show that this force aligns the part to the substrate assembly feature and reduces sensitivity of part position to process variation. Thus, the new configuration can substantially improve positioning accuracy of capillary self-assembly. This will result in a dramatic decrease in positioning errors in the micro parts. Various binding site designs are analyzed and guidelines are proposed for the design of an effective assembly bond using this new approach.

Automatic assembly of micro-optical components

NASA Astrophysics Data System (ADS)

Gengenbach, Ulrich K.

1996-12-01

Automatic assembly becomes an important issue as hybrid micro systems enter industrial fabrication. Moving from a laboratory scale production with manual assembly and bonding processes to automatic assembly requires a thorough re- evaluation of the design, the characteristics of the individual components and of the processes involved. Parts supply for automatic operation, sensitive and intelligent grippers adapted to size, surface and material properties of the microcomponents gain importance when the superior sensory and handling skills of a human are to be replaced by a machine. This holds in particular for the automatic assembly of micro-optical components. The paper outlines these issues exemplified at the automatic assembly of a micro-optical duplexer consisting of a micro-optical bench fabricated by the LIGA technique, two spherical lenses, a wavelength filter and an optical fiber. Spherical lenses, wavelength filter and optical fiber are supplied by third party vendors, which raises the question of parts supply for automatic assembly. The bonding processes for these components include press fit and adhesive bonding. The prototype assembly system with all relevant components e.g. handling system, parts supply, grippers and control is described. Results of first automatic assembly tests are presented.

Information theory in systems biology. Part II: protein-protein interaction and signaling networks.

PubMed

Mousavian, Zaynab; Díaz, José; Masoudi-Nejad, Ali

2016-03-01

By the development of information theory in 1948 by Claude Shannon to address the problems in the field of data storage and data communication over (noisy) communication channel, it has been successfully applied in many other research areas such as bioinformatics and systems biology. In this manuscript, we attempt to review some of the existing literatures in systems biology, which are using the information theory measures in their calculations. As we have reviewed most of the existing information-theoretic methods in gene regulatory and metabolic networks in the first part of the review, so in the second part of our study, the application of information theory in other types of biological networks including protein-protein interaction and signaling networks will be surveyed. Copyright © 2015 Elsevier Ltd. All rights reserved.

M13 Bacteriophage-Based Self-Assembly Structures and Their Functional Capabilities.

PubMed

Moon, Jong-Sik; Kim, Won-Geun; Kim, Chuntae; Park, Geun-Tae; Heo, Jeong; Yoo, So Y; Oh, Jin-Woo

2015-06-01

Controlling the assembly of basic structural building blocks in a systematic and orderly fashion is an emerging issue in various areas of science and engineering such as physics, chemistry, material science, biological engineering, and electrical engineering. The self-assembly technique, among many other kinds of ordering techniques, has several unique advantages and the M13 bacteriophage can be utilized as part of this technique. The M13 bacteriophage (Phage) can easily be modified genetically and chemically to demonstrate specific functions. This allows for its use as a template to determine the homogeneous distribution and percolated network structures of inorganic nanostructures under ambient conditions. Inexpensive and environmentally friendly synthesis can be achieved by using the M13 bacteriophage as a novel functional building block. Here, we discuss recent advances in the application of M13 bacteriophage self-assembly structures and the future of this technology.

M13 Bacteriophage-Based Self-Assembly Structures and Their Functional Capabilities

PubMed Central

Moon, Jong-Sik; Kim, Won-Geun; Kim, Chuntae; Park, Geun-Tae; Heo, Jeong; Yoo, So Y; Oh, Jin-Woo

2015-01-01

Controlling the assembly of basic structural building blocks in a systematic and orderly fashion is an emerging issue in various areas of science and engineering such as physics, chemistry, material science, biological engineering, and electrical engineering. The self-assembly technique, among many other kinds of ordering techniques, has several unique advantages and the M13 bacteriophage can be utilized as part of this technique. The M13 bacteriophage (Phage) can easily be modified genetically and chemically to demonstrate specific functions. This allows for its use as a template to determine the homogeneous distribution and percolated network structures of inorganic nanostructures under ambient conditions. Inexpensive and environmentally friendly synthesis can be achieved by using the M13 bacteriophage as a novel functional building block. Here, we discuss recent advances in the application of M13 bacteriophage self-assembly structures and the future of this technology. PMID:26146494

Self-assembling biomolecular catalysts for hydrogen production

NASA Astrophysics Data System (ADS)

Jordan, Paul C.; Patterson, Dustin P.; Saboda, Kendall N.; Edwards, Ethan J.; Miettinen, Heini M.; Basu, Gautam; Thielges, Megan C.; Douglas, Trevor

2016-02-01

The chemistry of highly evolved protein-based compartments has inspired the design of new catalytically active materials that self-assemble from biological components. A frontier of this biodesign is the potential to contribute new catalytic systems for the production of sustainable fuels, such as hydrogen. Here, we show the encapsulation and protection of an active hydrogen-producing and oxygen-tolerant [NiFe]-hydrogenase, sequestered within the capsid of the bacteriophage P22 through directed self-assembly. We co-opted Escherichia coli for biomolecular synthesis and assembly of this nanomaterial by expressing and maturing the EcHyd-1 hydrogenase prior to expression of the P22 coat protein, which subsequently self assembles. By probing the infrared spectroscopic signatures and catalytic activity of the engineered material, we demonstrate that the capsid provides stability and protection to the hydrogenase cargo. These results illustrate how combining biological function with directed supramolecular self-assembly can be used to create new materials for sustainable catalysis.

Chemical reactions directed Peptide self-assembly.

PubMed

Rasale, Dnyaneshwar B; Das, Apurba K

2015-05-13

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

Self-assembled polyhydroxy fatty acids vesicles: a mechanism for plant cutin synthesis.

PubMed

Heredia-Guerrero, José A; Benítez, José J; Heredia, Antonio

2008-03-01

Despite its biological importance, the mechanism of formation of cutin, the polymeric matrix of plant cuticles, has not yet been fully clarified. Here, for the first time, we show the participation in the process of lipid vesicles formed by the self-assembly of endogenous polyhydroxy fatty acids. The accumulation and fusion of these vesicles (cutinsomes) at the outer part of epidermal cell wall is proposed as the mechanism for early cuticle formation.

Dynamics of assembly production flow

NASA Astrophysics Data System (ADS)

Ezaki, Takahiro; Yanagisawa, Daichi; Nishinari, Katsuhiro

2015-06-01

Despite recent developments in management theory, maintaining a manufacturing schedule remains difficult because of production delays and fluctuations in demand and supply of materials. The response of manufacturing systems to such disruptions to dynamic behavior has been rarely studied. To capture these responses, we investigate a process that models the assembly of parts into end products. The complete assembly process is represented by a directed tree, where the smallest parts are injected at leaves and the end products are removed at the root. A discrete assembly process, represented by a node on the network, integrates parts, which are then sent to the next downstream node as a single part. The model exhibits some intriguing phenomena, including overstock cascade, phase transition in terms of demand and supply fluctuations, nonmonotonic distribution of stockout in the network, and the formation of a stockout path and stockout chains. Surprisingly, these rich phenomena result from only the nature of distributed assembly processes. From a physical perspective, these phenomena provide insight into delay dynamics and inventory distributions in large-scale manufacturing systems.

Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes

NASA Astrophysics Data System (ADS)

Shen, Hsin-Hui; Leyton, Denisse L.; Shiota, Takuya; Belousoff, Matthew J.; Noinaj, Nicholas; Lu, Jingxiong; Holt, Stephen A.; Tan, Khershing; Selkrig, Joel; Webb, Chaille T.; Buchanan, Susan K.; Martin, Lisandra L.; Lithgow, Trevor

2014-10-01

In biological membranes, various protein secretion devices function as nanomachines, and measuring the internal movements of their component parts is a major technological challenge. The translocation and assembly module (TAM) is a nanomachine required for virulence of bacterial pathogens. We have reconstituted a membrane containing the TAM onto a gold surface for characterization by quartz crystal microbalance with dissipation (QCM-D) and magnetic contrast neutron reflectrometry (MCNR). The MCNR studies provided structural resolution down to 1 Å, enabling accurate measurement of protein domains projecting from the membrane layer. Here we show that dynamic movements within the TamA component of the TAM are initiated in the presence of a substrate protein, Ag43, and that these movements recapitulate an initial stage in membrane protein assembly. The reconstituted system provides a powerful new means to study molecular movements in biological membranes, and the technology is widely applicable to studying the dynamics of diverse cellular nanomachines.

Programming function into mechanical forms by directed assembly of silk bulk materials

PubMed Central

Patel, Nereus; Duggan, Thomas; Perotto, Giovanni; Shirman, Elijah; Li, Chunmei; Kaplan, David L.; Omenetto, Fiorenzo G.

2017-01-01

We report simple, water-based fabrication methods based on protein self-assembly to generate 3D silk fibroin bulk materials that can be easily hybridized with water-soluble molecules to obtain multiple solid formats with predesigned functions. Controlling self-assembly leads to robust, machinable formats that exhibit thermoplastic behavior consenting material reshaping at the nanoscale, microscale, and macroscale. We illustrate the versatility of the approach by realizing demonstrator devices where large silk monoliths can be generated, polished, and reshaped into functional mechanical components that can be nanopatterned, embed optical function, heated on demand in response to infrared light, or can visualize mechanical failure through colorimetric chemistries embedded in the assembled (bulk) protein matrix. Finally, we show an enzyme-loaded solid mechanical part, illustrating the ability to incorporate biological function within the bulk material with possible utility for sustained release in robust, programmably shapeable mechanical formats. PMID:28028213

Three-dimensional bioprinting using self-assembling scalable scaffold-free “tissue strands” as a new bioink

PubMed Central

Yu, Yin; Moncal, Kazim K.; Li, Jianqiang; Peng, Weijie; Rivero, Iris; Martin, James A.; Ozbolat, Ibrahim T.

2016-01-01

Recent advances in bioprinting have granted tissue engineers the ability to assemble biomaterials, cells, and signaling molecules into anatomically relevant functional tissues or organ parts. Scaffold-free fabrication has recently attracted a great deal of interest due to the ability to recapitulate tissue biology by using self-assembly, which mimics the embryonic development process. Despite several attempts, bioprinting of scale-up tissues at clinically-relevant dimensions with closely recapitulated tissue biology and functionality is still a major roadblock. Here, we fabricate and engineer scaffold-free scalable tissue strands as a novel bioink material for robotic-assisted bioprinting technologies. Compare to 400 μm-thick tissue spheroids bioprinted in a liquid delivery medium into confining molds, near 8 cm-long tissue strands with rapid fusion and self-assemble capabilities are bioprinted in solid form for the first time without any need for a scaffold or a mold support or a liquid delivery medium, and facilitated native-like scale-up tissues. The prominent approach has been verified using cartilage strands as building units to bioprint articular cartilage tissue. PMID:27346373

Nitrogenase assembly

PubMed Central

Hu, Yilin; Ribbe, Markus W.

2013-01-01

Nitrogenase contains two unique metalloclusters: the P-cluster and the M-cluster. The assembly processes of P- and M-clusters are arguably the most complicated processes in bioinorganic chemistry. There is considerable interest in decoding the biosynthetic mechanisms of the P- and M-clusters, because these clusters are not only biologically important, but also chemically unprecedented. Understanding the assembly mechanisms of these unique metalloclusters is crucial for understanding the structure-function relationship of nitrogenase. Here, we review the recent advances in this research area, with an emphasis on our work that provide important insights into the biosynthetic pathways of these high-nuclearity metal centers. PMID:23232096

Cell-free protein synthesis and assembly on a biochip

NASA Astrophysics Data System (ADS)

Heyman, Yael; Buxboim, Amnon; Wolf, Sharon G.; Daube, Shirley S.; Bar-Ziv, Roy H.

2012-06-01

Biologically active complexes such as ribosomes and bacteriophages are formed through the self-assembly of proteins and nucleic acids. Recapitulating these biological self-assembly processes in a cell-free environment offers a way to develop synthetic biodevices. To visualize and understand the assembly process, a platform is required that enables simultaneous synthesis, assembly and imaging at the nanoscale. Here, we show that a silicon dioxide grid, used to support samples in transmission electron microscopy, can be modified into a biochip to combine in situ protein synthesis, assembly and imaging. Light is used to pattern the biochip surface with genes that encode specific proteins, and antibody traps that bind and assemble the nascent proteins. Using transmission electron microscopy imaging we show that protein nanotubes synthesized on the biochip surface in the presence of antibody traps efficiently assembled on these traps, but pre-assembled nanotubes were not effectively captured. Moreover, synthesis of green fluorescent protein from its immobilized gene generated a gradient of captured proteins decreasing in concentration away from the gene source. This biochip could be used to create spatial patterns of proteins assembled on surfaces.

Protein cage assembly across multiple length scales.

PubMed

Aumiller, William M; Uchida, Masaki; Douglas, Trevor

2018-05-21

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

PubMed

Lai, Hung-En; Moore, Simon; Polizzi, Karen; Freemont, Paul

2018-01-01

Development of advanced synthetic biology tools is always in demand since they act as a platform technology to enable rapid prototyping of biological constructs in a high-throughput manner. EcoFlex is a modular cloning (MoClo) kit for Escherichia coli and is based on the Golden Gate principles, whereby Type IIS restriction enzymes (BsaI, BsmBI, BpiI) are used to construct modular genetic elements (biological parts) in a bottom-up approach. Here, we describe a collection of plasmids that stores various biological parts including promoters, RBSs, terminators, ORFs, and destination vectors, each encoding compatible overhangs allowing hierarchical assembly into single transcription units or a full-length polycistronic operon or biosynthetic pathway. A secondary module cloning site is also available for pathway optimization, in order to limit library size if necessary. Here, we show the utility of EcoFlex using the violacein biosynthesis pathway as an example.

Chemical Reactions Directed Peptide Self-Assembly

PubMed Central

Rasale, Dnyaneshwar B.; Das, Apurba K.

2015-01-01

Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly. PMID:25984603

Characterization of Delayed-Particle Emission Signatures for Pyroprocessing. Part 1: ABTR Fuel Assembly.

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

Durkee, Jr., Joe W.

A three-part study is conducted using the MCNP6 Monte Carlo radiation-transport code to calculate delayed-neutron (DN) and delayed-gamma (DG) emission signatures for nondestructive assay (NDA) metal-fuel pyroprocessing. In Part 1, MCNP6 is used to produce irradiation-induced used nuclear fuel (UNF) isotopic inventories for an Argonne National Laboratory (ANL) Advanced Burner Test Reactor (ABTR) preconceptual design fuel assembly (FA) model. The initial fuel inventory consists of uranium mixed with light-water-reactor transuranic (TRU) waste and 10 wt% zirconium (U-LWR-SFTRU-10%Zr). To facilitate understanding, parametric evaluation is done using models for 3% and 5% initial 235U a% enrichments, burnups of 5, 10, 15, 20,more » 30, …, 120 GWd/MTIHM, and 3-, 5-, 10-, 20-, and 30- year cooling times. Detailed delayed-particle radioisotope source terms for the irradiate FA are created using BAMF-DRT and SOURCES3A. Using simulation tallies, DG activity ratios (DGARs) are developed for 134Cs/ 137Cs 134Cs/ 154Eu, and 154Eu/ 137Cs markers as a function of (1) burnup and (2) actinide mass, including elemental uranium, neptunium, plutonium, americium, and curium. Spectral-integrated DN emission is also tallied. The study reveals a rich assortment of DGAR behavior as a function of DGAR type, enrichment, burnup, and cooling time. Similarly, DN emission plots show variation as a function of burnup and of actinide mass. Sensitivity of DGAR and DN signatures to initial 235U enrichment, burnup, and cooling time is evident. Comparisons of the ABTR radiation signatures and radiation signatures previously reported for a generic Westinghouse oxide-fuel assembly indicate that there are pronounced differences in the ABTR and Westinghouse oxide-fuel DN and DG signatures. These differences are largely attributable to the initial TRU inventory in the ABTR fuel. The actinide and nonactinide inventories for the FA models serve as source materials for the pre- and postelectrorefining

Biocatalytic Self-Assembly on Magnetic Nanoparticles.

PubMed

Conte, Maria P; Sahoo, Jugal Kishore; Abul-Haija, Yousef M; Lau, K H Aaron; Ulijn, Rein V

2018-01-24

Combining (bio)catalysis and molecular self-assembly provides an effective approach for the production and processing of self-assembled materials by exploiting catalysis to direct the assembly kinetics and hence controlling the formation of ordered nanostructures. Applications of (bio)catalytic self-assembly in biologically interfacing systems and in nanofabrication have recently been reported. Inspired by self-assembly in biological cells, efforts to confine catalysts on flat or patterned surfaces to exert spatial control over molecular gelator generation and nanostructure self-assembly have also emerged. Building on our previous work in the area, we demonstrate in this report the use of enzymes immobilized onto magnetic nanoparticles (NPs) to spatially localize the initiation of peptide self-assembly into nanofibers around NPs. The concept is generalized for both an equilibrium biocatalytic system that forms stable hydrogels and a nonequilibrium system that normally has a preset lifetime. Characterization of the hydrogels shows that self-assembly occurs at the site of enzyme immobilization on the NPs to give rise to gels with a "hub-and-spoke" morphology, where the nanofibers are linked through the enzyme-NP conjugates. This NP-controlled arrangement of self-assembled nanofibers enables both remarkable enhancements in the shear strength of hydrogel systems and a dramatic extension of the hydrogel stability in the nonequilibrium system. We are also able to show that the use of magnetic NPs enables the external control of both the formation of the hydrogel and its overall structure by application of an external magnetic field. We anticipate that the enhanced properties and stimuli-responsiveness of our NP-enzyme system will have applications ranging from nanomaterial fabrication to biomaterials and biosensing.

Metagenomic Assembly: Overview, Challenges and Applications

PubMed Central

Ghurye, Jay S.; Cepeda-Espinoza, Victoria; Pop, Mihai

2016-01-01

Advances in sequencing technologies have led to the increased use of high throughput sequencing in characterizing the microbial communities associated with our bodies and our environment. Critical to the analysis of the resulting data are sequence assembly algorithms able to reconstruct genes and organisms from complex mixtures. Metagenomic assembly involves new computational challenges due to the specific characteristics of the metagenomic data. In this survey, we focus on major algorithmic approaches for genome and metagenome assembly, and discuss the new challenges and opportunities afforded by this new field. We also review several applications of metagenome assembly in addressing interesting biological problems. PMID:27698619

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants.

PubMed

Lukan, Tjaša; Machens, Fabian; Coll, Anna; Baebler, Špela; Messerschmidt, Katrin; Gruden, Kristina

2018-01-01

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster

Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

PubMed Central

Machens, Fabian; Coll, Anna; Baebler, Špela; Messerschmidt, Katrin; Gruden, Kristina

2018-01-01

Cloning multiple DNA fragments for delivery of several genes of interest into the plant genome is one of the main technological challenges in plant synthetic biology. Despite several modular assembly methods developed in recent years, the plant biotechnology community has not widely adopted them yet, probably due to the lack of appropriate vectors and software tools. Here we present Plant X-tender, an extension of the highly efficient, scar-free and sequence-independent multigene assembly strategy AssemblX, based on overlap-depended cloning methods and rare-cutting restriction enzymes. Plant X-tender consists of a set of plant expression vectors and the protocols for most efficient cloning into the novel vector set needed for plant expression and thus introduces advantages of AssemblX into plant synthetic biology. The novel vector set covers different backbones and selection markers to allow full design flexibility. We have included ccdB counterselection, thereby allowing the transfer of multigene constructs into the novel vector set in a straightforward and highly efficient way. Vectors are available as empty backbones and are fully flexible regarding the orientation of expression cassettes and addition of linkers between them, if required. We optimised the assembly and subcloning protocol by testing different scar-less assembly approaches: the noncommercial SLiCE and TAR methods and the commercial Gibson assembly and NEBuilder HiFi DNA assembly kits. Plant X-tender was applicable even in combination with low efficient homemade chemically competent or electrocompetent Escherichia coli. We have further validated the developed procedure for plant protein expression by cloning two cassettes into the newly developed vectors and subsequently transferred them to Nicotiana benthamiana in a transient expression setup. Thereby we show that multigene constructs can be delivered into plant cells in a streamlined and highly efficient way. Our results will support faster

Lipid self-assembly and lectin-induced reorganization of the plasma membrane.

PubMed

Sych, Taras; Mély, Yves; Römer, Winfried

2018-05-26

The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

49 CFR 572.186 - Abdomen assembly.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 7 2013-10-01 2013-10-01 false Abdomen assembly. 572.186 Section 572.186... Test Dummy, 50th Percentile Adult Male § 572.186 Abdomen assembly. (a) The abdomen assembly (175-5000) is part of the dummy assembly shown in drawing 175-0000 including load sensors specified in § 572.189...

49 CFR 572.186 - Abdomen assembly.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 7 2011-10-01 2011-10-01 false Abdomen assembly. 572.186 Section 572.186... Dummy, 50th Percentile Adult Male § 572.186 Abdomen assembly. (a) The abdomen assembly (175-5000) is part of the dummy assembly shown in drawing 175-0000 including load sensors specified in § 572.189(e...

49 CFR 572.186 - Abdomen assembly.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 7 2012-10-01 2012-10-01 false Abdomen assembly. 572.186 Section 572.186... Dummy, 50th Percentile Adult Male § 572.186 Abdomen assembly. (a) The abdomen assembly (175-5000) is part of the dummy assembly shown in drawing 175-0000 including load sensors specified in § 572.189(e...

Splice assembly tool and method of splicing

DOEpatents

Silva, Frank A.

1980-01-01

A splice assembly tool for assembling component parts of an electrical conductor while producing a splice connection between electrical cables therewith, comprises a first structural member adaptable for supporting force applying means thereon, said force applying means enabling a rotary force applied manually thereto to be converted to a longitudinal force for subsequent application against a first component part of said electrical connection, a second structural member adaptable for engaging a second component part in a manner to assist said first structural member in assembling the component parts relative to one another and transmission means for conveying said longitudinal force between said first and said second structural members, said first and said second structural members being coupled to one another by said transmission means, wherein at least one of said component parts comprises a tubular elastomeric sleeve and said force applying means provides a relatively high mechanical advantage when said rotary force is applied thereto so as to facilitate assembly of said at least one tubular elastomeric sleeve about said other component part in an interference fit manner.

Information theory in systems biology. Part I: Gene regulatory and metabolic networks.

PubMed

Mousavian, Zaynab; Kavousi, Kaveh; Masoudi-Nejad, Ali

2016-03-01

"A Mathematical Theory of Communication", was published in 1948 by Claude Shannon to establish a framework that is now known as information theory. In recent decades, information theory has gained much attention in the area of systems biology. The aim of this paper is to provide a systematic review of those contributions that have applied information theory in inferring or understanding of biological systems. Based on the type of system components and the interactions between them, we classify the biological systems into 4 main classes: gene regulatory, metabolic, protein-protein interaction and signaling networks. In the first part of this review, we attempt to introduce most of the existing studies on two types of biological networks, including gene regulatory and metabolic networks, which are founded on the concepts of information theory. Copyright © 2015 Elsevier Ltd. All rights reserved.

Planning Assembly Of Large Truss Structures In Outer Space

NASA Technical Reports Server (NTRS)

De Mello, Luiz S. Homem; Desai, Rajiv S.

1992-01-01

Report dicusses developmental algorithm used in systematic planning of sequences of operations in which large truss structures assembled in outer space. Assembly sequence represented by directed graph called "assembly graph", in which each arc represents joining of two parts or subassemblies. Algorithm generates assembly graph, working backward from state of complete assembly to initial state, in which all parts disassembled. Working backward more efficient than working forward because it avoids intermediate dead ends.

Incorporating Biological Mass Spectrometry into Undergraduate Teaching Labs, Part 1: Identifying Proteins Based on Molecular Mass

ERIC Educational Resources Information Center

Arnquist, Isaac J.; Beussman, Douglas J.

2007-01-01

Biological mass spectrometry is an important analytical technique in drug discovery, proteomics, and research at the biology-chemistry interface. Currently, few hands-on opportunities exist for undergraduate students to learn about this technique. With the 2002 Nobel Prize being awarded, in part, for the development of biological mass…

Building biological foundries for next-generation synthetic biology.

PubMed

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

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

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

NASA Astrophysics Data System (ADS)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

Specialty Tier-Level Cost Sharing and Biologic Agent Use in the Medicare Part D Initial Coverage Period Among Beneficiaries With Rheumatoid Arthritis.

PubMed

Doshi, Jalpa A; Hu, Tianyan; Li, Pengxiang; Pettit, Amy R; Yu, Xinyan; Blum, Marissa

2016-11-01

To examine associations between specialty tier-level cost sharing and use of biologic agents for rheumatoid arthritis (RA) during Medicare Part D's initial coverage period (ICP). This was a retrospective study using 2007-2010 5% sample Medicare files to examine RA patients with use of a Part D RA biologic agent in the prior year. Patients without low-income subsidies (non-LIS group), who faced specialty tier-level cost sharing, were compared to a control group of low-income subsidy patients (LIS group), who faced nominal out-of-pocket costs in the ICP. Outcomes included use of a Part D or Part B RA biologic agent during the ICP and presence of a ≥30-day continuous gap in treatment among Part D biologic agent users in the ICP. Risk-adjusted outcomes were estimated using logistic regressions, controlling for patient demographic, clinical, and Part D plan characteristics. On average, a 30-day Part D biologic agent supply cost the non-LIS group $484 out of pocket (29.9% cost sharing) versus $5 (0.3% cost sharing) for the LIS group. The non-LIS group was less likely to fill Part D biologic agents (61.2% versus 72.7%, odds ratio [OR] 0.58 [95% confidence interval (95% CI) 0.46-0.72]; P < 0.001), more than twice as likely to receive Part B biologic agents (9.9% versus 4.4%, OR 2.41 [95% CI 1.61-3.60]; P < 0.001), and less likely to use any biologic agent (70.1% versus 76.9%, OR 0.69 [95% CI 0.55-0.88]; P = 0.002). The non-LIS subgroup filling Part D biologic agents had approximately twice the odds of a gap in both Part D biologic agent and any biologic agent availability. Specialty tier-level cost sharing was associated with interruptions in RA biologic agent treatment among Medicare patients. © 2016, American College of Rheumatology.

Ferromagnetic nanowires: Field-induced self-assembly, magnetotransport and biological applications

NASA Astrophysics Data System (ADS)

Tanase, Monica

In this dissertation, a series of experiments on magnetic nanowires are described. Magnetic nanowires suspended in fluid solutions can be assembled and ordered by taking advantage of their large shape anisotropy. Magnetic manipulation and assembly techniques were developed, using electrodeposited Ni nanowires. Preorienting nanowires in a small magnetic field induced their self-assembly in continuous chains. A new technique of magnetic trapping allowed capture of single nanowires from fluid suspension on lithographically fabricated micromagnets. As described herein, the presence of an external magnetic field plays a fundamental role in all fluid assembly methods used. The dynamics of both chaining and trapping processes is described quantitatively in terms of the interplay of magnetic forces and fluid drag at low Reynolds number. Lithographic methods for addressing single nanowires for transport characterization were developed. Magnetotransport measurements were performed on individual straight and bent PtNiPt nanowires. The Pt end segments provided an oxide-free interface to the magnetic central segment. In straight nanowires, domain reversal was observed to occur via curling mode initiated in a small nucleation volume. Magnetotransport in bent nanowires allowed the investigation of a domain wall trapped at the bend. Magnetic trapping of nanowires on pre-fabricated electrodes was adapted as a successful alternative contacting technique to lithography. The self-assembly and manipulation techniques were adapted for manipulation of cells as nanowires were found to bind to cells through nonspecific adhesion mechanisms. Ni nanowires were found to outperform superparamagnetic beads in magnetic cell separations. Additionally, the large remnant magnetization of the nanowires allowed for low-field manipulation techniques. Self-assembled chains of cells were formed and single cells were localized on substrates patterned with micromagnets. A fluid flow method was developed to

Assembly of objects with not fully predefined shapes

NASA Technical Reports Server (NTRS)

Arlotti, M. A.; Dimartino, V.

1989-01-01

An assembly problem in a non-deterministic environment, i.e., where parts to be assembled have unknown shape, size and location, is described. The only knowledge used by the robot to perform the assembly operation is given by a connectivity rule and geometrical constraints concerning parts. Once a set of geometrical features of parts has been extracted by a vision system, applying such a rule allows the dtermination of the composition sequence. A suitable sensory apparatus allows the control the whole operation.

Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules.

PubMed

Levy, Roie; Borenstein, Elhanan

2014-01-01

The human microbiome is a key contributor to health and development. Yet little is known about the ecological forces that are at play in defining the composition of such host-associated communities. Metagenomics-based studies have uncovered clear patterns of community structure but are often incapable of distinguishing alternative structuring paradigms. In a recent study, we integrated metagenomic analysis with a systems biology approach, using a reverse ecology framework to model numerous human microbiota species and to infer metabolic interactions between species. Comparing predicted interactions with species composition data revealed that the assembly of the human microbiome is dominated at the community level by habitat filtering. Furthermore, we demonstrated that this habitat filtering cannot be accounted for by known host phenotypes or by the metabolic versatility of the various species. Here we provide a summary of our findings and offer a brief perspective on related studies and on future approaches utilizing this metagenomic systems biology framework.

Efficiencies for parts and wholes in biological-motion perception.

PubMed

Bromfield, W Drew; Gold, Jason M

2017-10-01

People can reliably infer the actions, intentions, and mental states of fellow humans from body movements (Blake & Shiffrar, 2007). Previous research on such biological-motion perception has suggested that the movements of the feet may play a particularly important role in making certain judgments about locomotion (Chang & Troje, 2009; Troje & Westhoff, 2006). One account of this effect is that the human visual system may have evolved specialized processes that are efficient for extracting information carried by the feet (Troje & Westhoff, 2006). Alternatively, the motion of the feet may simply be more discriminable than that of other parts of the body. To dissociate these two possibilities, we measured people's ability to discriminate the walking direction of stimuli in which individual body parts (feet, hands) were removed or shown in isolation. We then compared human performance to that of a statistically optimal observer (Gold, Tadin, Cook, & Blake, 2008), giving us a measure of humans' discriminative ability independent of the information available (a quantity known as efficiency). We found that efficiency was highest when the hands and the feet were shown in isolation. A series of follow-up experiments suggested that observers were relying on a form-based cue with the isolated hands (specifically, the orientation of their path through space) and a motion-based cue with the isolated feet to achieve such high efficiencies. We relate our findings to previous proposals of a distinction between form-based and motion-based mechanisms in biological-motion perception.

Interactions regulating the head-to-tail directed assembly of biological Janus rods

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

Greene, A. C.; Bachand, M.; Gomez, A.

We can generalize the directed, head-to-tail self-assembly of microtubule filaments in the context of Janus colloidal rods. Specifically, their assembly at the tens of micron-length scale involves a careful balance between long-range electrostatic repulsion and short-range attractive forces. We show that the addition of counterion salts increases the rate of directed assembly by screening the electrostatic forces and enhancing the effectiveness of short-range interactions at the microtubule ends.

Interactions regulating the head-to-tail directed assembly of biological Janus rods

DOE PAGES

Greene, A. C.; Bachand, M.; Gomez, A.; ...

2017-03-31

We can generalize the directed, head-to-tail self-assembly of microtubule filaments in the context of Janus colloidal rods. Specifically, their assembly at the tens of micron-length scale involves a careful balance between long-range electrostatic repulsion and short-range attractive forces. We show that the addition of counterion salts increases the rate of directed assembly by screening the electrostatic forces and enhancing the effectiveness of short-range interactions at the microtubule ends.

Biosynthesis: Reprogramming assembly lines

NASA Astrophysics Data System (ADS)

Menon, Binuraj R. K.; Jenner, Matthew

2018-03-01

Rational engineering of biosynthetic assembly lines for production of new compounds is an attractive prospect, yet it presents many challenges. Learning from biology, some of the rules for expanding the chemical diversity of non-ribosomal peptides have been uncovered in two recent studies.

Heterocyclic cationic gemini surfactants: a comparative overview of their synthesis, self-assembling, physicochemical, and biological properties.

PubMed

Sharma, Vishnu Dutt; Ilies, Marc A

2014-01-01

Gemini surfactants (GS) are presently receiving substantial attention due to their special self-assembling properties and unique interfacial activity. This comprehensive review is focused on positively charged heterocyclic GS, presenting their major synthetic access routes and examining the impact of structural elements on physicochemical and aggregation properties of this class of amphiphiles. Interaction of geminis surfactants with cells and their biological properties as novel transfection agents are emphasized through a detailed structure-activity relationship analysis. Throughout the review we have also presented the properties of selected ammonium GS, simple surfactants and lipid congeners, in order to emphasize the advantages conferred by using heterocyclic polar heads in GS design. © 2012 Wiley Periodicals, Inc.

The A, C, G, and T of Genome Assembly

PubMed Central

Wajid, Bilal; Sohail, Muhammad U.; Ekti, Ali R.; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research. PMID:27247941

The A, C, G, and T of Genome Assembly.

PubMed

Wajid, Bilal; Sohail, Muhammad U; Ekti, Ali R; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

Pydna: a simulation and documentation tool for DNA assembly strategies using python.

PubMed

Pereira, Filipa; Azevedo, Flávio; Carvalho, Ângela; Ribeiro, Gabriela F; Budde, Mark W; Johansson, Björn

2015-05-02

Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool. We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature. Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.

49 CFR 572.184 - Shoulder assembly.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 7 2012-10-01 2012-10-01 false Shoulder assembly. 572.184 Section 572.184... Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part of...) of this section, the shoulder assembly shall meet performance requirements of paragraph (c) of this...

49 CFR 572.184 - Shoulder assembly.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 7 2011-10-01 2011-10-01 false Shoulder assembly. 572.184 Section 572.184... Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part of...) of this section, the shoulder assembly shall meet performance requirements of paragraph (c) of this...

49 CFR 572.184 - Shoulder assembly.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 7 2014-10-01 2014-10-01 false Shoulder assembly. 572.184 Section 572.184... Test Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part... (b) of this section, the shoulder assembly shall meet performance requirements of paragraph (c) of...

49 CFR 572.184 - Shoulder assembly.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 7 2013-10-01 2013-10-01 false Shoulder assembly. 572.184 Section 572.184... Test Dummy, 50th Percentile Adult Male § 572.184 Shoulder assembly. (a) The shoulder (175-3000) is part... (b) of this section, the shoulder assembly shall meet performance requirements of paragraph (c) of...

Physical Activity: A Tool for Improving Health (Part 1--Biological Health Benefits)

ERIC Educational Resources Information Center

Gallaway, Patrick J.; Hongu, Nobuko

2015-01-01

Extension educators have been promoting and incorporating physical activities into their community-based programs and improving the health of individuals, particularly those with limited resources. This article is the first of a three-part series describing the benefits of physical activity for human health: 1) biological health benefits of…

16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame...

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment...

16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame...

Code of Federal Regulations, 2013 CFR

2013-01-01

... 16 Commercial Practices 2 2013-01-01 2013-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment...

16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame...

Code of Federal Regulations, 2014 CFR

2014-01-01

... 16 Commercial Practices 2 2014-01-01 2014-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws), in Relation to, Portable Frame Allowing Burner Height Adjustment...

Construction and engineering of large biochemical pathways via DNA assembler

PubMed Central

Shao, Zengyi; Zhao, Huimin

2015-01-01

Summary DNA assembler enables rapid construction and engineering of biochemical pathways in a one-step fashion by exploitation of the in vivo homologous recombination mechanism in Saccharomyces cerevisiae. It has many applications in pathway engineering, metabolic engineering, combinatorial biology, and synthetic biology. Here we use two examples including the zeaxanthin biosynthetic pathway and the aureothin biosynthetic gene cluster to describe the key steps in the construction of pathways containing multiple genes using the DNA assembler approach. Methods for construct design, pathway assembly, pathway confirmation, and functional analysis are shown. The protocol for fine genetic modifications such as site-directed mutagenesis for engineering the aureothin gene cluster is also illustrated. PMID:23996442

Representations of mechanical assembly sequences

NASA Technical Reports Server (NTRS)

Homem De Mello, Luiz S.; Sanderson, Arthur C.

1991-01-01

Five types of representations for assembly sequences are reviewed: the directed graph of feasible assembly sequences, the AND/OR graph of feasible assembly sequences, the set of establishment conditions, and two types of sets of precedence relationships. (precedence relationships between the establishment of one connection between parts and the establishment of another connection, and precedence relationships between the establishment of one connection and states of the assembly process). The mappings of one representation into the others are established. The correctness and completeness of these representations are established. The results presented are needed in the proof of correctness and completeness of algorithms for the generation of mechanical assembly sequences.

Quantitative characterization of genetic parts and circuits for plant synthetic biology.

PubMed

Schaumberg, Katherine A; Antunes, Mauricio S; Kassaw, Tessema K; Xu, Wenlong; Zalewski, Christopher S; Medford, June I; Prasad, Ashok

2016-01-01

Plant synthetic biology promises immense technological benefits, including the potential development of a sustainable bio-based economy through the predictive design of synthetic gene circuits. Such circuits are built from quantitatively characterized genetic parts; however, this characterization is a significant obstacle in work with plants because of the time required for stable transformation. We describe a method for rapid quantitative characterization of genetic plant parts using transient expression in protoplasts and dual luciferase outputs. We observed experimental variability in transient-expression assays and developed a mathematical model to describe, as well as statistical normalization methods to account for, this variability, which allowed us to extract quantitative parameters. We characterized >120 synthetic parts in Arabidopsis and validated our method by comparing transient expression with expression in stably transformed plants. We also tested >100 synthetic parts in sorghum (Sorghum bicolor) protoplasts, and the results showed that our method works in diverse plant groups. Our approach enables the construction of tunable gene circuits in complex eukaryotic organisms.

9 CFR 381.78 - Condemnation of carcasses and parts: separation of poultry suspected of containing biological...

Code of Federal Regulations, 2010 CFR

2010-01-01

...: separation of poultry suspected of containing biological residues. 381.78 Section 381.78 Animals and Animal...; MANDATORY MEAT AND POULTRY PRODUCTS INSPECTION AND VOLUNTARY INSPECTION AND CERTIFICATION POULTRY PRODUCTS... carcasses and parts: separation of poultry suspected of containing biological residues. (a) At the time of...

Molecular Precision at Micrometer Length Scales: Hierarchical Assembly of DNA-Protein Nanostructures.

PubMed

Schiffels, Daniel; Szalai, Veronika A; Liddle, J Alexander

2017-07-25

Robust self-assembly across length scales is a ubiquitous feature of biological systems but remains challenging for synthetic structures. Taking a cue from biology-where disparate molecules work together to produce large, functional assemblies-we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method. This process simultaneously shapes the structure at the nanoscale and directs the large-scale geometry. The DNA skeleton guides the assembly of RecA protein filaments, which provides rigidity at the micrometer scale. We use our modular design strategy to assemble tetrahedral, rectangular, and linear shapes of defined dimensions. This method enables the robust construction of complex assemblies, greatly extending the range of DNA-based self-assembly methods.

DNA assembly with error correction on a droplet digital microfluidics platform.

PubMed

Khilko, Yuliya; Weyman, Philip D; Glass, John I; Adams, Mark D; McNeil, Melanie A; Griffin, Peter B

2018-06-01

Custom synthesized DNA is in high demand for synthetic biology applications. However, current technologies to produce these sequences using assembly from DNA oligonucleotides are costly and labor-intensive. The automation and reduced sample volumes afforded by microfluidic technologies could significantly decrease materials and labor costs associated with DNA synthesis. The purpose of this study was to develop a gene assembly protocol utilizing a digital microfluidic device. Toward this goal, we adapted bench-scale oligonucleotide assembly methods followed by enzymatic error correction to the Mondrian™ digital microfluidic platform. We optimized Gibson assembly, polymerase chain reaction (PCR), and enzymatic error correction reactions in a single protocol to assemble 12 oligonucleotides into a 339-bp double- stranded DNA sequence encoding part of the human influenza virus hemagglutinin (HA) gene. The reactions were scaled down to 0.6-1.2 μL. Initial microfluidic assembly methods were successful and had an error frequency of approximately 4 errors/kb with errors originating from the original oligonucleotide synthesis. Relative to conventional benchtop procedures, PCR optimization required additional amounts of MgCl 2 , Phusion polymerase, and PEG 8000 to achieve amplification of the assembly and error correction products. After one round of error correction, error frequency was reduced to an average of 1.8 errors kb - 1 . We demonstrated that DNA assembly from oligonucleotides and error correction could be completely automated on a digital microfluidic (DMF) platform. The results demonstrate that enzymatic reactions in droplets show a strong dependence on surface interactions, and successful on-chip implementation required supplementation with surfactants, molecular crowding agents, and an excess of enzyme. Enzymatic error correction of assembled fragments improved sequence fidelity by 2-fold, which was a significant improvement but somewhat lower than

Large-scale study of the interactions between proteins involved in type IV pilus biology in Neisseria meningitidis: characterization of a subcomplex involved in pilus assembly.

PubMed

Georgiadou, Michaella; Castagnini, Marta; Karimova, Gouzel; Ladant, Daniel; Pelicic, Vladimir

2012-06-01

The functionally versatile type IV pili (Tfp) are one of the most widespread virulence factors in bacteria. However, despite generating much research interest for decades, the molecular mechanisms underpinning the various aspects of Tfp biology remain poorly understood, mainly because of the complexity of the system. In the human pathogen Neisseria meningitidis for example, 23 proteins are dedicated to Tfp biology, 15 of which are essential for pilus biogenesis. One of the important gaps in our knowledge concerns the topology of this multiprotein machinery. Here we have used a bacterial two-hybrid system to identify and quantify the interactions between 11 Pil proteins from N. meningitidis. We identified 20 different binary interactions, many of which are novel. This represents the most complex interaction network between Pil proteins reported to date and indicates, among other things, that PilE, PilM, PilN and PilO, which are involved in pilus assembly, indeed interact. We focused our efforts on this subset of proteins and used a battery of assays to determine the membrane topology of PilN and PilO, map the interaction domains between PilE, PilM, PilN and PilO, and show that a widely conserved N-terminal motif in PilN is essential for both PilM-PilN interactions and pilus assembly. Finally, we show that PilP (another protein involved in pilus assembly) forms a complex with PilM, PilN and PilO. Taken together, these findings have numerous implications for understanding Tfp biology and provide a useful blueprint for future studies. © 2012 Blackwell Publishing Ltd.

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

PubMed

Peck, Evan M; Battles, Paul M; Rice, Douglas R; Roland, Felicia M; Norquest, Kathryn A; Smith, Bradley D

2016-05-18

A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

Oral Mucosal Lesions: Oral Cavity Biology-Part I.

PubMed

Sehgal, Virendra N; Syed, Nazim Hussain; Aggarwal, Ashok; Sehgal, Shruti

2015-01-01

It is important to evaluate the background of oral cavity biology to define morphologic abrasions in oral mucosa following a host of local and/ or systemic disorders. The oral cavity is not only the beginning of the digestive system, but it also plays a significant role in communication; the voice (although the voice is produced in the throat), tongue, lips, and jaw are its essential components to produce the range of sounds. The vestibule and the oral cavity are its major parts, and are usually moist. The lips and the teeth are in approximation, marking its start up. The anatomy of the oral cavity in brief has been reviewed in right prospective for disease related changed morphology, thus facilitating interpretation.

DNA Assembly in 3D Printed Fluidics

PubMed Central

Patrick, William G.; Nielsen, Alec A. K.; Keating, Steven J.; Levy, Taylor J.; Wang, Che-Wei; Rivera, Jaime J.; Mondragón-Palomino, Octavio; Carr, Peter A.; Voigt, Christopher A.; Oxman, Neri; Kong, David S.

2015-01-01

The process of connecting genetic parts—DNA assembly—is a foundational technology for synthetic biology. Microfluidics present an attractive solution for minimizing use of costly reagents, enabling multiplexed reactions, and automating protocols by integrating multiple protocol steps. However, microfluidics fabrication and operation can be expensive and requires expertise, limiting access to the technology. With advances in commodity digital fabrication tools, it is now possible to directly print fluidic devices and supporting hardware. 3D printed micro- and millifluidic devices are inexpensive, easy to make and quick to produce. We demonstrate Golden Gate DNA assembly in 3D-printed fluidics with reaction volumes as small as 490 nL, channel widths as fine as 220 microns, and per unit part costs ranging from $0.61 to $5.71. A 3D-printed syringe pump with an accompanying programmable software interface was designed and fabricated to operate the devices. Quick turnaround and inexpensive materials allowed for rapid exploration of device parameters, demonstrating a manufacturing paradigm for designing and fabricating hardware for synthetic biology. PMID:26716448

BioPartsDB: a synthetic biology workflow web-application for education and research.

PubMed

Stracquadanio, Giovanni; Yang, Kun; Boeke, Jef D; Bader, Joel S

2016-11-15

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones. BioPartsDB is released under the MIT license and available for download at https://github.com/baderzone/biopartsdb Additional documentation and video tutorials are available at https://github.com/baderzone/biopartsdb/wiki An Amazon Web Services image is available from the AWS Market Place (ami-a01d07c8). joel.bader@jhu.edu. © The Author 2016. Published by Oxford University Press.

Construction and biological evaluation of different self-assembled nanoarchitectures of FZU-03,010.

PubMed

Lv, Tingting; Xu, Liang; Wu, Guolin; Li, Cailong; Wen, Yibo; Zhang, Tao; Chen, Haijun; Gao, Yu

2018-06-13

Chemotherapy is currently one of the promising therapeutic methods for non-small-cell lung cancer (NSCLC), but the emergence of multidrug resistance (MDR) is the greatest obstacle to efficient drug delivery for successful chemotherapy. Nanotechnology-based drug delivery holds great promise to promote intracellular drug delivery to reverse MDR. In this work, we used our previously synthesized ursolic acid (UA) derivative, FZU-03,010 (F3), to prepare nanodrugs of F3 with different architectures and study the role of the structure on the physiochemical properties and the biological effects against A549 and its PTX-resistant A549/PTX lung cancer cells. Using different preparation methods, amphiphilic F3 could self-assemble into different structures such as nanoaggregates (F3-NA), vesicles (F3-VC), or nanoparticles (F3-NP) with different physiochemical properties. The self-assembled nanodrugs could be utilized for the entrapment of fluorophores and showed different cellular uptake efficiencies. The cytotoxicity results demonstrated that compared with UA, F3-NA and F3-NP could suppress A549 and A549/PTX cells viability more potently at lower concentration. In addition, F3-NA and F3-NP could induce G1 cell cycle arrest, cell apoptosis and caspase-3 activation more efficiently than that of UA. Furthermore, F3-NA and F3-NP could effectively inhibit PI3K/Akt pathway and decrease the expression of Bcl-2 and the cell cycle-dependent kinase inhibitors p-ERK1/2 and Cyclin D1 in both A549 and A549/PTX cells. In conclusion, our results suggest that the UA derivative F3 is more potent in inhibiting cancer cell proliferation, and F3-NA and F3-NP have the potential to be developed as a therapeutic for resistant NSCLC cells. Copyright © 2017. Published by Elsevier B.V.

Self-Assembly Behavior of Pullulan Abietate

NASA Astrophysics Data System (ADS)

Gradwell, Sheila; Esker, Alan; Glasser, Wolgang; Heinze, Thomas

2003-03-01

Wood is one of nature's most fascinating biological composites due to its toughness and resistance to fracture properties. These properties stem from the self-assembly of cellulose microfibrils in an amorphous matrix of hemicellulose and lignin. In recent years, science has looked to nature for guidance in preparing synthetic materials with desirable physical properties. In order to study the self-assembly process in wood, a model system composed of a polysaccharide, pullulan abietate, and a biomimetic cellulose substrate prepared by the Langmuir-Blodgett technique has been developed. Interfacial tension and surface plasmon resonance measurements used to study the self-assembly process will be discussed for different pullulan derivatives.

Molecular biomimetics: nanotechnology through biology.

PubMed

Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K-Y; Schulten, Klaus; Baneyx, François

2003-09-01

Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

Statistical Tolerance and Clearance Analysis for Assembly

NASA Technical Reports Server (NTRS)

Lee, S.; Yi, C.

1996-01-01

Tolerance is inevitable because manufacturing exactly equal parts is known to be impossible. Furthermore, the specification of tolerances is an integral part of product design since tolerances directly affect the assemblability, functionality, manufacturability, and cost effectiveness of a product. In this paper, we present statistical tolerance and clearance analysis for the assembly. Our proposed work is expected to make the following contributions: (i) to help the designers to evaluate products for assemblability, (ii) to provide a new perspective to tolerance problems, and (iii) to provide a tolerance analysis tool which can be incorporated into a CAD or solid modeling system.

Parallel In Vivo DNA Assembly by Recombination: Experimental Demonstration and Theoretical Approaches

PubMed Central

Shi, Zhenyu; Wedd, Anthony G.; Gras, Sally L.

2013-01-01

The development of synthetic biology requires rapid batch construction of large gene networks from combinations of smaller units. Despite the availability of computational predictions for well-characterized enzymes, the optimization of most synthetic biology projects requires combinational constructions and tests. A new building-brick-style parallel DNA assembly framework for simple and flexible batch construction is presented here. It is based on robust recombination steps and allows a variety of DNA assembly techniques to be organized for complex constructions (with or without scars). The assembly of five DNA fragments into a host genome was performed as an experimental demonstration. PMID:23468883

Our Hidden Past: Biology, Part 1

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

Smith, Ray; Congdon, Charles; Bervin, Barry

After World War II, vacant buildings at Y-12 and a growing new Biology Division for which there was not adequate space at Oak Ridge National Laboratory combined to provide a home for genetic research at Y-12. In January 1949, the Biology Division moved into Building 9210.

Improving Robotic Assembly of Planar High Energy Density Targets

NASA Astrophysics Data System (ADS)

Dudt, D.; Carlson, L.; Alexander, N.; Boehm, K.

2016-10-01

Increased quantities of planar assemblies for high energy density targets are needed with higher shot rates being implemented at facilities such as the National Ignition Facility and the Matter in Extreme Conditions station of the Linac Coherent Light Source. To meet this growing demand, robotics are used to reduce assembly time. This project studies how machine vision and force feedback systems can be used to improve the quantity and quality of planar target assemblies. Vision-guided robotics can identify and locate parts, reducing laborious manual loading of parts into precision pallets and associated teaching of locations. On-board automated inspection can measure part pickup offsets to correct part drop-off placement into target assemblies. Force feedback systems can detect pickup locations and apply consistent force to produce more uniform glue bond thickness, thus improving the performance of the targets. System designs and performance evaluations will be presented. Work supported in part by the US DOE under the Science Undergraduate Laboratory Internships Program (SULI) and ICF Target Fabrication DE-NA0001808.

PREFACE The physics of virus assembly The physics of virus assembly

NASA Astrophysics Data System (ADS)

Stockley, Peter G.; Twarock, Reidun

2010-12-01

Viruses are pathogens in every kingdom of life and are major causes of human disease and suffering. They are known to encompass a size range that overlaps with that of the smallest bacterial cells, and the largest viruses now seem to be hosts of their own viral pathogens. Recent genomic sequencing efforts show that many organisms have genes that are likely to be descended in evolution from viral progenitors. Even more astonishingly, analysis of the world's oceans has shown that some of the simplest viruses, the tailed dsDNA phages, are the most common biological entities on the planet, with estimates of their numbers ranging up to 1031, with ~ 1021 infection events every second, leading to a turnover of around 20% of the biomass in the sea every few days. These cycles of infection and lysis of oceanic bacteria and algae provide the nutrients for the smallest organisms lying at the bottom of the food chain. Without viruses, therefore, life on Earth would probably not be sustainable. These are remarkable facts for systems that are non-living in the strict sense, and are composed of simple materials—nucleic acids, proteins and lipids. Many viruses consist of little more than a protective protein coat surrounding their genomic nucleic acids, which can be either DNA or RNA. Their simplicity leads to highly symmetrical structures with protein containers based on helical or icosahedral lattices. Many simple viruses self-assemble rapidly and with great fidelity, and many groups are busy trying to exploit these properties to make virus-like particles for a wide range of applications, including targeted drug-delivery, medical imaging and even novel materials. This issue of Physical Biology contains a series of papers describing some of the latest experimental and theoretical research on viruses, their structures and assembly, as well as their regulated disassembly during infection. These range from a dissection of the in vivo assembly mechanism of a filamentous virus

Challenging Students' Intuitions--The Influence of a Tangible Model of Virus Assembly on Students' Conceptual Reasoning about the Process of Self-Assembly

ERIC Educational Resources Information Center

Larsson, Caroline; Tibell, Lena A.

2015-01-01

A well-ordered biological complex can be formed by the random motion of its components, i.e. self-assemble. This is a concept that incorporates issues that may contradict students' everyday experiences and intuitions. In previous studies, we have shown that a tangible model of virus self-assembly, used in a group exercise, helps students to grasp…

Backward assembly planning with DFA analysis

NASA Technical Reports Server (NTRS)

Lee, Sukhan (Inventor)

1995-01-01

An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies, and analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans is presented. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc. that must occur during the assembly, and handles nonreversible as well as reversible assembly tasks through backward assembly planning. In order to increase the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

Backward assembly planning with DFA analysis

NASA Technical Reports Server (NTRS)

Lee, Sukhan (Inventor)

1992-01-01

An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies is presented. The planning system analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc., that must occur during the assembly. Additionally, the planning handles nonreversible, as well as reversible, assembly tasks through backward assembly planning. In order to decrease the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

Biology--Chemistry--Physics, Students' Guide, A Three-Year Sequence, Parts I and II.

ERIC Educational Resources Information Center

Scott, Arthur; And Others

Parts I and II of the students' guide to the three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee are contained in this guide. A committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical…

16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to Portable Frame Allowing...

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 2 2011-01-01 2011-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws) in Relation to Portable Frame Allowing Burner Height Adjustment ER15MR06...

16 CFR Figure 6 to Part 1633 - Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to, Portable Frame Allowing...

Code of Federal Regulations, 2012 CFR

2012-01-01

... 16 Commercial Practices 2 2012-01-01 2012-01-01 false Burner Assembly Showing Arms and Pivots (Shoulder Screws) in Relation to, Portable Frame Allowing Burner Height Adjustment 6 Figure 6 to Part 1633... and Pivots (Shoulder Screws) in Relation to, Portable Frame Allowing Burner Height Adjustment ER15MR06...

Emerging Technologies for Assembly of Microscale Hydrogels

PubMed Central

Kavaz, Doga; Demirel, Melik C.; Demirci, Utkan

2013-01-01

Assembly of cell encapsulating building blocks (i.e., microscale hydrogels) has significant applications in areas including regenerative medicine, tissue engineering, and cell-based in vitro assays for pharmaceutical research and drug discovery. Inspired by the repeating functional units observed in native tissues and biological systems (e.g., the lobule in liver, the nephron in kidney), assembly technologies aim to generate complex tissue structures by organizing microscale building blocks. Novel assembly technologies enable fabrication of engineered tissue constructs with controlled properties including tunable microarchitectural and predefined compositional features. Recent advances in micro- and nano-scale technologies have enabled engineering of microgel based three dimensional (3D) constructs. There is a need for high-throughput and scalable methods to assemble microscale units with a complex 3D micro-architecture. Emerging assembly methods include novel technologies based on microfluidics, acoustic and magnetic fields, nanotextured surfaces, and surface tension. In this review, we survey emerging microscale hydrogel assembly methods offering rapid, scalable microgel assembly in 3D, and provide future perspectives and discuss potential applications. PMID:23184717

EDITORIAL: MEMS in biology and medicine MEMS in biology and medicine

NASA Astrophysics Data System (ADS)

Pruitt, Beth L.; Herr, Amy E.

2011-05-01

Stimulating—the first word that springs to mind regarding the emerging and expanding role of MEMS in biological inquiry. When invited to guest-edit this special issue on 'MEMS in biology and medicine' for JMM, we jumped at the opportunity. Partly owing to the breadth of the stimulating research in this nascent area and partly owing to the stimulating of biological function made possible with MEMS accessible length and time scales, we were eager to assemble manuscripts detailing some of the most cutting edge biological research being conducted around the globe. In addition to cutting edge engineering, this special issue features challenging biological questions addressed with innovative MEMS technologies. Topics span from Yetisen and colleagues' inquiry into quantifying pollen tube behaviour in response to pistil tissues [1] to Morimoto and colleagues' engineering efforts to produce monodisperse droplets capable of encapsulating single cells (without surface modification) [2]. Questions are bold, including a means to achieve therapeutically-relevant scaling for enrichment of leukocytes from blood (Inglis et al [3]), assessing the dependence of Escherichia coli biofilm formation on bacterial signalling (Meyer et al [4]), and elucidation of adhesion dynamics of circulating tumour cells (Cheung et al [5]) among others. Technologies are diverse, including microfabricated magnetic actuators (Lee et al [6]), stimuli-responsive polymer nanocomposites (Hess et al [7]), and SU-8 electrothermal microgrippers (Chu et al [8]) to name but a few. Contributing authors do indeed span a large swathe of the globe, with contributions from Australia, Italy, China, Canada, Denmark, Japan, the USA and numerous other locations. Collaboration finds a home here—with researchers from macromolecular science and electrical engineering collaborating with the Veterans Affairs Medical Center or neurosurgery researchers working with biological and electrical engineers. The questions posed by

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper.

PubMed

Cranford, Steven W; Buehler, Markus J

2010-07-02

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper

NASA Astrophysics Data System (ADS)

Cranford, Steven W.; Buehler, Markus J.

2010-07-01

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.

Modular Assembly of the Bacterial Large Ribosomal Subunit

PubMed Central

Davis, Joseph H.; Tan, Yong Zi; Carragher, Bridget; Potter, Clinton S.; Lyumkis, Dmitry; Williamson, James R.

2016-01-01

SUMMARY The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ~4–5Å resolution and could be placed in an assembly pathway. We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be ‘re-routed’ through different pathways as needed. This work reveals the complex landscape of ribosome assembly in vivo and provides the requisite tools to characterize additional assembly pathways for ribosomes and other macromolecular machines. PMID:27912064

Bioinspired synthesis and self-assembly of hybrid organic–inorganic nanomaterials

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

Zhang, Honghu

Nature is replete with complex organic–inorganic hierarchical materials of diverse yet specific functions. These materials are intricately designed under physiological conditions through biomineralization and biological self-assembly processes. Tremendous efforts have been devoted to investigating mechanisms of such biomineralization and biological self-assembly processes as well as gaining inspiration to develop biomimetic methods for synthesis and self-assembly of functional nanomaterials. In this work, we focus on the bioinspired synthesis and self-assembly of functional inorganic nanomaterials templated by specialized macromolecules including proteins, DNA and polymers. The in vitro biomineralization process of the magnetite biomineralizing protein Mms6 has been investigated using small-angle X-ray scattering.more » Templated by Mms6, complex magnetic nanomaterials can be synthesized on surfaces and in the bulk. DNA and synthetic polymers have been exploited to construct macroscopic two- and three-dimensional (2D and 3D) superlattices of gold nanocrystals. Employing X-ray scattering and spectroscopy techniques, the self-assembled structures and the self-assembly mechanisms have been studied, and theoretical models have been developed. Our results show that specialized macromolecules including proteins, DNA and polymers act as effective templates for synthesis and self-assembly of nanomaterials. These bottom-up approaches provide promising routes to fabricate hybrid organic–inorganic nanomaterials with rationally designed hierarchical structures, targeting specific functions.« less

A Versatile Microfluidic Device for Automating Synthetic Biology.

PubMed

Shih, Steve C C; Goyal, Garima; Kim, Peter W; Koutsoubelis, Nicolas; Keasling, Jay D; Adams, Paul D; Hillson, Nathan J; Singh, Anup K

2015-10-16

New microbes are being engineered that contain the genetic circuitry, metabolic pathways, and other cellular functions required for a wide range of applications such as producing biofuels, biobased chemicals, and pharmaceuticals. Although currently available tools are useful in improving the synthetic biology process, further improvements in physical automation would help to lower the barrier of entry into this field. We present an innovative microfluidic platform for assembling DNA fragments with 10× lower volumes (compared to that of current microfluidic platforms) and with integrated region-specific temperature control and on-chip transformation. Integration of these steps minimizes the loss of reagents and products compared to that with conventional methods, which require multiple pipetting steps. For assembling DNA fragments, we implemented three commonly used DNA assembly protocols on our microfluidic device: Golden Gate assembly, Gibson assembly, and yeast assembly (i.e., TAR cloning, DNA Assembler). We demonstrate the utility of these methods by assembling two combinatorial libraries of 16 plasmids each. Each DNA plasmid is transformed into Escherichia coli or Saccharomyces cerevisiae using on-chip electroporation and further sequenced to verify the assembly. We anticipate that this platform will enable new research that can integrate this automated microfluidic platform to generate large combinatorial libraries of plasmids and will help to expedite the overall synthetic biology process.

Modular design of synthetic gene circuits with biological parts and pools.

PubMed

Marchisio, Mario Andrea

2015-01-01

Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

Standardization in synthetic biology: an engineering discipline coming of age.

PubMed

Decoene, Thomas; De Paepe, Brecht; Maertens, Jo; Coussement, Pieter; Peters, Gert; De Maeseneire, Sofie L; De Mey, Marjan

2018-08-01

Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.

Adult Competency Education Kit. Basic Skills in Speaking, Math, and Reading for Employment. Part P: ACE Competency Based Job Descriptions: #77--Secretary; #78--Keypunch Operator; Assembly Worker Core Job Description; #82--Electronics Assembler; #83--Printed Circuit Assembler; #84--Micro Electronics Assembler; #85--Chassis Assembler; #87--Machinist Apprentice.

ERIC Educational Resources Information Center

San Mateo County Office of Education, Redwood City, CA. Career Preparation Centers.

This thirteenth of fifteen sets of Adult Competency Education (ACE) Competency Based Job Descriptions in the ACE kit contains job descriptions for Secretary, Keypunch Operator, Electronics Assembler, Printed Circuit Assembler, Micro Electronincs Assembler, Chassis Assembler, and Machinist Apprentice. Each begins with a fact sheet that includes…

SAGE: String-overlap Assembly of GEnomes.

PubMed

Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

2014-09-15

De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2004-12-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2005-01-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Self-assembly of smallest magnetic particles

PubMed Central

Mehdizadeh Taheri, Sara; Michaelis, Maria; Friedrich, Thomas; Förster, Beate; Drechsler, Markus; Römer, Florian M.; Bösecke, Peter; Narayanan, Theyencheri; Weber, Birgit; Rehberg, Ingo; Rosenfeldt, Sabine; Förster, Stephan

2015-01-01

The assembly of tiny magnetic particles in external magnetic fields is important for many applications ranging from data storage to medical technologies. The development of ever smaller magnetic structures is restricted by a size limit, where the particles are just barely magnetic. For such particles we report the discovery of a kind of solution assembly hitherto unobserved, to our knowledge. The fact that the assembly occurs in solution is very relevant for applications, where magnetic nanoparticles are either solution-processed or are used in liquid biological environments. Induced by an external magnetic field, nanocubes spontaneously assemble into 1D chains, 2D monolayer sheets, and large 3D cuboids with almost perfect internal ordering. The self-assembly of the nanocubes can be elucidated considering the dipole–dipole interaction of small superparamagnetic particles. Complex 3D geometrical arrangements of the nanodipoles are obtained under the assumption that the orientation of magnetization is freely adjustable within the superlattice and tends to minimize the binding energy. On that basis the magnetic moment of the cuboids can be explained. PMID:26554000

Minimus: a fast, lightweight genome assembler.

PubMed

Sommer, Daniel D; Delcher, Arthur L; Salzberg, Steven L; Pop, Mihai

2007-02-26

Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.

SSME component assembly and life management expert system

NASA Technical Reports Server (NTRS)

Ali, M.; Dietz, W. E.; Ferber, H. J.

1989-01-01

The space shuttle utilizes several rocket engine systems, all of which must function with a high degree of reliability for successful mission completion. The space shuttle main engine (SSME) is by far the most complex of the rocket engine systems and is designed to be reusable. The reusability of spacecraft systems introduces many problems related to testing, reliability, and logistics. Components must be assembled from parts inventories in a manner which will most effectively utilize the available parts. Assembly must be scheduled to efficiently utilize available assembly benches while still maintaining flight schedules. Assembled components must be assigned to as many contiguous flights as possible, to minimize component changes. Each component must undergo a rigorous testing program prior to flight. In addition, testing and assembly of flight engines and components must be done in conjunction with the assembly and testing of developmental engines and components. The development, testing, manufacture, and flight assignments of the engine fleet involves the satisfaction of many logistical and operational requirements, subject to many constraints. The purpose of the SSME Component Assembly and Life Management Expert System (CALMES) is to assist the engine assembly and scheduling process, and to insure that these activities utilize available resources as efficiently as possible.

Batch Scheduling for Hybrid Assembly Differentiation Flow Shop to Minimize Total Actual Flow Time

NASA Astrophysics Data System (ADS)

Maulidya, R.; Suprayogi; Wangsaputra, R.; Halim, A. H.

2018-03-01

A hybrid assembly differentiation flow shop is a three-stage flow shop consisting of Machining, Assembly and Differentiation Stages and producing different types of products. In the machining stage, parts are processed in batches on different (unrelated) machines. In the assembly stage, each part of the different parts is assembled into an assembly product. Finally, the assembled products will further be processed into different types of final products in the differentiation stage. In this paper, we develop a batch scheduling model for a hybrid assembly differentiation flow shop to minimize the total actual flow time defined as the total times part spent in the shop floor from the arrival times until its due date. We also proposed a heuristic algorithm for solving the problems. The proposed algorithm is tested using a set of hypothetic data. The solution shows that the algorithm can solve the problems effectively.

Active colloids as assembly machines

NASA Astrophysics Data System (ADS)

Goodrich, Carl; Brenner, Michael

Controlling motion at the microscopic scale is a fundamental goal in the development of biologically-inspired systems. We show that the motion of active, self-propelled colloids can be sufficiently controlled for use as a tool to assemble complex structures such as braids and weaves out of microscopic filaments. Unlike typical self-assembly paradigms, these structures are held together by geometric constraints rather than adhesive bonds. The out-of-equilibrium assembly that we propose involves precisely controlling the two-dimensional motion of active colloids so that their path has a non-trivial topology. We demonstrate with proof-of-principle Brownian dynamics simulations that, when the colloids are attached to long semi-flexible filaments, this motion causes the filaments to braid. The ability of the active particles to provide sufficient force necessary to bend the filaments into a braid depends on a number of factors, including the self-propulsion mechanism, the properties of the filament, and the maximum curvature in the braid. Our work demonstrates that non-equilibrium assembly pathways can be designed using active particles.

Structural performance of light-frame roof assemblies. I, Truss assemblies designed for high variability and wood failure

Treesearch

R.W. Wolfe; Monica McCarthy

1989-01-01

The first report of a three-part series that covers results of a full-scale roof assemblies research program. The focus of this report is the structural performance of truss assemblies comprising trusses with abnormally high stiffness variability and critical joint strength. Results discussed include properties of truss members and connections. individual truss...

Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits.

PubMed

Harbage, David; Kondev, Jané

2016-07-07

Self-assembling filamentous structures made of protein subunits are ubiquitous in cell biology. These structures are often highly dynamic, with subunits in a continuous state of flux, binding to and falling off of filaments. In spite of this constant turnover of their molecular parts, many cellular structures seem to maintain a well-defined size over time, which is often required for their proper functioning. One widely discussed mechanism of size regulation involves the cell maintaining a finite pool of protein subunits available for assembly. This finite pool mechanism can control the length of a single filament by having assembly proceed until the pool of free subunits is depleted to the point when assembly and disassembly are balanced. Still, this leaves open the question of whether the same mechanism can provide size control for multiple filamentous structures that are assembled from a common pool of protein subunits, as is often the case in cells. We address this question by solving the steady-state master equation governing the stochastic assembly and disassembly of multifilament structures made from a shared finite pool of subunits. We find that, while the total number of subunits within a multifilament structure is well-defined, individual filaments within the structure have a wide, power-law distribution of lengths. We also compute the phase diagram for two multifilament structures competing for the same pool of subunits and identify conditions for coexistence when both have a well-defined size. These predictions can be tested in cell experiments in which the size of the subunit pool or the number of filament nucleators is tuned.

Photocontrolled reversible self-assembly of dodecamer nitrilase.

PubMed

Yu, Qiao; Wang, Yong; Zhao, Shengyun; Ren, Yuhong

2017-01-01

Naturally photoswitchable proteins act as a powerful tool for the spatial and temporal control of biological processes by inducing the formation of a photodimerizer. In this study, a method for the precise and reversible inducible self-assembly of dodecamer nitrilase in vivo (in Escherichia coli ) and in vitro (in a cell-free solution) was developed by means of the photoswitch-improved light-inducible dimer (iLID) system which could induce protein-protein dimerization. Nitrilase was fused with the photoswitch protein AsLOV2-SsrA to achieve the photocontrolled self-assembly of dodecamer nitrilase. The fusion protein self-assembled into a supramolecular assembly when illuminated at 470 nm. Scanning electron microscopy showed that the assembly formed a circular sheet structure. Self-assembly was also induced by light in E. coli . Dynamic light scattering and turbidity assay experiments showed that the assemblies formed within a few seconds under 470-nm light and completely disassembled within 5 min in the dark. Assembly and disassembly could be maintained for at least five cycles. Both in vitro and in vivo, the assemblies retained 90% of the initial activity of nitrilase and could be reused at least four times in vitro with 90% activity. An efficient method was developed for the photocontrolled assembly and disassembly of dodecamer nitrilase and for scaffold-free reversible self-assembly of multiple oligomeric enzymes in vivo and in vitro, providing new ideas and methods for immobilization of enzyme without carrier.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome

Assembly Test Article (ATA)

NASA Technical Reports Server (NTRS)

Ricks, Glen A.

1988-01-01

The assembly test article (ATA) consisted of two live loaded redesigned solid rocket motor (RSRM) segments which were assembled and disassembled to simulate the actual flight segment stacking process. The test assembly joint was flight RSRM design, which included the J-joint insulation design and metal capture feature. The ATA test was performed mid-November through 24 December 1987, at Kennedy Space Center (KSC), Florida. The purpose of the test was: certification that vertical RSRM segment mating and separation could be accomplished without any damage; verification and modification of the procedures in the segment stacking/destacking documents; and certification of various GSE to be used for flight assembly and inspection. The RSRM vertical segment assembly/disassembly is possible without any damage to the insulation, metal parts, or seals. The insulation J-joint contact area was very close to the predicted values. Numerous deviations and changes to the planning documents were made to ensure the flight segments are effectively and correctly stacked. Various GSE were also certified for use on flight segments, and are discussed in detail.

Yeast synthetic biology toolbox and applications for biofuel production.

PubMed

Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

2015-02-01

Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes.

PubMed

Olson, Nathan D; Treangen, Todd J; Hill, Christopher M; Cepeda-Espinoza, Victoria; Ghurye, Jay; Koren, Sergey; Pop, Mihai

2017-08-07

Metagenomic samples are snapshots of complex ecosystems at work. They comprise hundreds of known and unknown species, contain multiple strain variants and vary greatly within and across environments. Many microbes found in microbial communities are not easily grown in culture making their DNA sequence our only clue into their evolutionary history and biological function. Metagenomic assembly is a computational process aimed at reconstructing genes and genomes from metagenomic mixtures. Current methods have made significant strides in reconstructing DNA segments comprising operons, tandem gene arrays and syntenic blocks. Shorter, higher-throughput sequencing technologies have become the de facto standard in the field. Sequencers are now able to generate billions of short reads in only a few days. Multiple metagenomic assembly strategies, pipelines and assemblers have appeared in recent years. Owing to the inherent complexity of metagenome assembly, regardless of the assembly algorithm and sequencing method, metagenome assemblies contain errors. Recent developments in assembly validation tools have played a pivotal role in improving metagenomics assemblers. Here, we survey recent progress in the field of metagenomic assembly, provide an overview of key approaches for genomic and metagenomic assembly validation and demonstrate the insights that can be derived from assemblies through the use of assembly validation strategies. We also discuss the potential for impact of long-read technologies in metagenomics. We conclude with a discussion of future challenges and opportunities in the field of metagenomic assembly and validation. © The Author 2017. Published by Oxford University Press.

Systematic, spatial imaging of large multimolecular assemblies and the emerging principles of supramolecular order in biological systems

PubMed Central

Schubert, Walter

2013-01-01

Understanding biological systems at the level of their relational (emergent) molecular properties in functional protein networks relies on imaging methods, able to spatially resolve a tissue or a cell as a giant, non-random, topologically defined collection of interacting supermolecules executing myriads of subcellular mechanisms. Here, the development and findings of parameter-unlimited functional super-resolution microscopy are described—a technology based on the fluorescence imaging cycler (IC) principle capable of co-mapping thousands of distinct biomolecular assemblies at high spatial resolution and differentiation (<40 nm distances). It is shown that the subcellular and transcellular features of such supermolecules can be described at the compositional and constitutional levels; that the spatial connection, relational stoichiometry, and topology of supermolecules generate hitherto unrecognized functional self-segmentation of biological tissues; that hierarchical features, common to thousands of simultaneously imaged supermolecules, can be identified; and how the resulting supramolecular order relates to spatial coding of cellular functionalities in biological systems. A large body of observations with IC molecular systems microscopy collected over 20 years have disclosed principles governed by a law of supramolecular segregation of cellular functionalities. This pervades phenomena, such as exceptional orderliness, functional selectivity, combinatorial and spatial periodicity, and hierarchical organization of large molecular systems, across all species investigated so far. This insight is based on the high degree of specificity, selectivity, and sensitivity of molecular recognition processes for fluorescence imaging beyond the spectral resolution limit, using probe libraries controlled by ICs. © 2013 The Authors. Journal of Molecular Recognition published by John Wiley & Sons, Ltd. PMID:24375580

Modular Assembly of the Bacterial Large Ribosomal Subunit.

PubMed

Davis, Joseph H; Tan, Yong Zi; Carragher, Bridget; Potter, Clinton S; Lyumkis, Dmitry; Williamson, James R

2016-12-01

The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to ∼4-5 Å resolution and could be placed in an assembly pathway. We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be "re-routed" through different pathways as needed. This work reveals the complex landscape of ribosome assembly in vivo and provides the requisite tools to characterize additional assembly pathways for ribosomes and other macromolecular machines. Copyright © 2016 Elsevier Inc. All rights reserved.

Gas Turbine Engine Carbon Oil Seals Computerized Assembly

NASA Technical Reports Server (NTRS)

Lee, Robert

2006-01-01

In a bearing compartment there are a series of parts when assembled determine the location of the bearing and seal as related to the centerline of rotation. We see part datums that do not establish A coincident path from the bearing to the seal. High engine vibration can cause severe oil leakage. The inability of the seal to respond fast enough to the rotating element Radial Seal: Sensitive to housing air pressure Sensitive to seal runout ? Axial Seal: Very sensitive to seal perpendicularity to shaft. Goals include: 1) Repeatable assembly process; 2) Accurate assembly process; 3) Minimize seal runout; 4) Design to engine centerline of rotation, i.e. bearings.

[Nutrition and biological value of food parts of a trade bivalve mollusk Anadara broughtoni].

PubMed

Tabakaeva, O V; Tabakaev, A V

2015-01-01

Currently, the human diet includes different new products of seafishing, including non-fish--bivalves and gastropods, holothurias, echinoderms, jellyfishes that demands careful studying of their chemical composition. The purpose of the study was to determine the nutritional and biological value of all soft parts of the burrowing bivalve MOLLUSK Anadara broughtoni from the Far East region. It was established thatfood parts of a bivalve were significantly flooded (water content--73.5-84.2%), with the minimum water content in the adductor and maximum in the mantle. Dry solids are presented by organic (89-93%) and mineral (7-11%) components. Organic components consist of protein (14.6-20.7%), lipids (1.8-2.3%), carbohydrates (2.1-2.6%). The analysis of amino-acid composition of proteins of food parts of the mollusk of Anadara broughtonishowed the presence of all essential amino acids with slight differences in their content depending on the localization of the protein. All edible parts have tryptophan as the limiting amino acid. Muscle proteins have maximum level of lysine, methionine, cysteine, phenylalanine and tyrosine; mantle proteins--leucine, isoleucine and threonine; adductor proteins--valine, phenylalanine, tyrosine, methionine and cysteine. Predominant nonessential amino acids forproteins of all food pieces are glycine, aspartic acid, glutamic acid, arginine. The coefficient of amino-acid score differences of adductor protein (31.7%) is less than the same of cloak by 3.7%. The indicator "biological value" is maximal for adductor (68.3%), but the differenceformuscle is only 0.83%. Mantle proteins are characterized by minimum biological value (64.6%). The coefficient of utility of amino acid composition of protein is maximalfor muscle (57.83%), and values for a cloak and an adductor differ slightly (55.81 and 55.96%). Taurine content in food parts of a mollusk Anadara broughtoni is rather high compared to with other bivalve mollusks of the Far East region

Synthetic Biology: Putting Synthesis into Biology

PubMed Central

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

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

Telemetry Simulation Assembly Implementation in the DSN

NASA Technical Reports Server (NTRS)

Alberda, M. E.

1984-01-01

The telemetry simulation was implemented as part of the MARK IV network implementation project. The telemetry simulation assembly (TSA) is replacing the Simulation Conversion Assembly (SCA) throughout the DSN. The development of the TSA is discussed, and the design is described to the block diagram level.

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.

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

PubMed

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Shingle assembly with support bracket

DOEpatents

Almy, Charles

2007-01-02

A shingle system, mountable to a support surface, includes overlapping shingle assemblies. Each shingle assembly comprises a support bracket, having upper and lower ends, secured to a shingle body. The upper end has an upper support portion, extending away from the shingle body, and an upper support-surface-engaging part, engageable with a support surface so that the upper edge of the shingle body is positionable at a first distance from the support surface to create a first gap therebetween. The lower end has a lower support portion extending away from the lower surface. The support brackets create: (1) a second gap between shingle bodies of the first and second shingle assemblies, and (2) an open region beneath the first shingle assembly fluidly coupling the first and second gaps.

Multiscale assembly for tissue engineering and regenerative medicine

PubMed Central

Inci, Fatih; Tasoglu, Savas; Erkmen, Burcu; Demirci, Utkan

2015-01-01

Our understanding of cell biology and its integration with materials science has led to technological innovations in the bioengineering of tissue-mimicking grafts that can be utilized in clinical and pharmaceutical applications. Bio-engineering of native-like multiscale building blocks provides refined control over the cellular microenvironment, thus enabling functional tissues. In this review, we focus on assembling building blocks from the biomolecular level to the millimeter scale. We also provide an overview of techniques for assembling molecules, cells, spheroids, and microgels and achieving bottom-up tissue engineering. Additionally, we discuss driving mechanisms for self- and guided assembly to create micro-to-macro scale tissue structures. PMID:25796488

Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios.

PubMed

Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A

2016-03-01

The first part of this review ("Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios") describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction. [Int Microbiol 2016; 19(1):1-1 3]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Scarless assembly of unphosphorylated DNA fragments with a simplified DATEL method.

PubMed

Ding, Wenwen; Weng, Huanjiao; Jin, Peng; Du, Guocheng; Chen, Jian; Kang, Zhen

2017-05-04

Efficient assembly of multiple DNA fragments is a pivotal technology for synthetic biology. A scarless and sequence-independent DNA assembly method (DATEL) using thermal exonucleases has been developed recently. Here, we present a simplified DATEL (sDATEL) for efficient assembly of unphosphorylated DNA fragments with low cost. The sDATEL method is only dependent on Taq DNA polymerase and Taq DNA ligase. After optimizing the committed parameters of the reaction system such as pH and the concentration of Mg 2+ and NAD+, the assembly efficiency was increased by 32-fold. To further improve the assembly capacity, the number of thermal cycles was optimized, resulting in successful assembly 4 unphosphorylated DNA fragments with an accuracy of 75%. sDATEL could be a desirable method for routine manual and automated assembly.

A comprehensive review and update on the biologic treatment of adult noninfectious uveitis: part II.

PubMed

Lee, Kyungmin; Bajwa, Asima; Freitas-Neto, Clovis A; Metzinger, Jamie Lynne; Wentworth, Bailey A; Foster, C Stephen

2014-11-01

Treatment of adult, noninfectious uveitis remains a major challenge for ophthalmologists around the world, especially in regard to recalcitrant cases. It is reported to comprise approximately 10% of preventable blindness in the USA. The cause of uveitis can be idiopathic or associated with infectious and systemic disorders. The era of biologic medical therapies provides new options for patients with otherwise treatment-resistant inflammatory eye disease. This two-part review gives a comprehensive overview of the existing medical treatment options for patients with adult, noninfectious uveitis, as well as important advances for the treatment ocular inflammation. Part I covers classic immunomodulation and latest information on corticosteroid therapy. In part II, emerging therapies are discussed, including biologic response modifiers, experimental treatments and ongoing clinical studies for uveitis. The hazard of chronic corticosteroid use in the treatment of adult, noninfectious uveitis is well documented. Corticosteroid-sparing therapies, which offer a very favorable risk-benefit profile when administered properly, should be substituted. Although nothing is currently approved for on-label use in this indication, many therapies, through either translation or novel basic science research, have the potential to fill the currently exposed gaps.

Metal-directed design of supramolecular protein assemblies

PubMed Central

Bailey, Jake B.; Subramanian, Rohit H.; Churchfield, Lewis A.

2016-01-01

Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive non-covalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, Metal-Directed Protein Self-Assembly (MDPSA) and Metal-Templated Interface Redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution. PMID:27586336

Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

NASA Astrophysics Data System (ADS)

Gazit, Ehud

2013-03-01

The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

Self-assembly from milli- to nanoscales: methods and applications

PubMed Central

Mastrangeli, M; Abbasi, S; Varel, C; Van Hoof, C; Celis, J-P; Böhringer, K F

2009-01-01

The design and fabrication techniques for microelectromechanical systems (MEMS) and nanodevices are progressing rapidly. However, due to material and process flow incompatibilities in the fabrication of sensors, actuators and electronic circuitry, a final packaging step is often necessary to integrate all components of a heterogeneous microsystem on a common substrate. Robotic pick-and-place, although accurate and reliable at larger scales, is a serial process that downscales unfavorably due to stiction problems, fragility and sheer number of components. Self-assembly, on the other hand, is parallel and can be used for device sizes ranging from millimeters to nanometers. In this review, the state-of-the-art in methods and applications for self-assembly is reviewed. Methods for assembling three-dimensional (3D) MEMS structures out of two-dimensional (2D) ones are described. The use of capillary forces for folding 2D plates into 3D structures, as well as assembling parts onto a common substrate or aggregating parts to each other into 2D or 3D structures, is discussed. Shape matching and guided assembly by magnetic forces and electric fields are also reviewed. Finally, colloidal self-assembly and DNA-based self-assembly, mainly used at the nanoscale, are surveyed, and aspects of theoretical modeling of stochastic assembly processes are discussed. PMID:20209016

SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale

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

Meng, Jintao; Seo, Sangmin; Balaji, Pavan

2016-08-16

In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. Inmore » k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.« less

In vitro assembly of catalase.

PubMed

Baureder, Michael; Barane, Elisabeth; Hederstedt, Lars

2014-10-10

Most aerobic organisms contain catalase, which functions to decompose hydrogen peroxide. Typical catalases are structurally complex homo-tetrameric enzymes with one heme prosthetic group buried in each subunit. It is not known how catalase in the cell is assembled from its constituents. The bacterium Enterococcus faecalis cannot synthesize heme but can acquire it from the environment to form a cytoplasmic catalase. We have in E. faecalis monitored production of the enzyme polypeptide (KatA) depending on the availability of heme and used our findings to devise a procedure for the purification of preparative amounts of in vivo-synthesized apocatalase. We show that fully active catalase can be obtained in vitro by incubating isolated apoprotein with hemin. We have characterized features of the assembly process and describe a temperature-trapped hemylated intermediate of the enzyme maturation process. Hemylation of apocatalase does not require auxiliary cell components, but rapid assembly of active enzyme seemingly is assisted in the cell. Our findings provide insight about catalase assembly and offer new experimental possibilities for detailed studies of this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Biomimetic assembly of polypeptide-stabilized CaCO(3) nanoparticles.

PubMed

Zhang, Zhongping; Gao, Daming; Zhao, Hui; Xie, Chenggen; Guan, Guijian; Wang, Dapeng; Yu, Shu-Hong

2006-05-04

In this paper, we report a simple polypeptide-directed strategy for fabricating large spherical assembly of CaCO(3) nanoparticles. Stepwise growth and assembly of a large number of nanoparticles have been observed, from the formation of an amorphous liquidlike CaCO(3)-polypeptide precursor, to the crystallization and stabilization of polypeptide-capped nanoparticles, and eventually, the spherical assembly of nanoparticles. The "soft" poly(aspartate)-capping layer binding on a nanoparticle surface resulted in the unusual soft nature of nanoparticle assembly, providing a reservoir of primary nanoparticles with a moderate mobility, which is the basis of a new strategy for reconstructing nanoparticle assembly into complex nanoparticle architectures. Moreover, the findings of the secondary assembly of nanoparticle microspheres and the morphology transformation of nanoparticle assembly demonstrate a flexible and controllable pathway for manipulating the shapes and structures of nanoparticle assembly. In addition, the combination of the polypeptide with a double hydrophilic block copolymer (DHBC) allows it to possibly further control the shape and complexity of the nanoparticle assembly. A clear perspective is shown here that more complex nanoparticle materials could be created by using "soft" biological proteins or peptides as a mediating template at the organic-inorganic interface.

Chromosome-scale assembly of the Monopterus genome.

PubMed

Zhao, Xueya; Luo, Majing; Li, Zhigang; Zhong, Pei; Cheng, Yibin; Lai, Fengling; Wang, Xin; Min, Jiumeng; Bai, Mingzhou; Yang, Yulan; Cheng, Hanhua; Zhou, Rongjia

2018-05-01

The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (∼689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes. We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.

Rationally engineering natural protein assemblies in nanobiotechnology.

PubMed

Howorka, Stefan

2011-08-01

Multimeric protein assemblies are essential components in viruses, bacteria, eukaryotic cells, and organisms where they act as cytoskeletal scaffold, storage containers, or for directional transport. The bottom-up structures can be exploited in nanobiotechnology by harnessing their built-in properties and combining them with new functional modules. This review summarizes the design principles of natural protein assemblies, highlights recent progress in their structural elucidation, and shows how rational engineering can create new biomaterials for applications in vaccine development, biocatalysis, materials science, and synthetic biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

Method for sealing an oxygen transport membrane assembly

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

Gonzalez, Javier E.; Grant, Arthur F.

An improved method of sealing a ceramic part to a solid part made of ceramic, metal, cermet or a ceramic coated metal is provided. The improved method includes placing a bond agent comprising an Al 2O 3 and SiO 2 based glass-ceramic material and organic binder material on adjoining surfaces of the ceramic part and the solid part. The assembly is heated to a first target temperature that removes or dissolves the organic binder material from the bond agent and the assembly is subjected to a second induction heating step at a temperature ramp rate of between about 100.degree. C.more » and 200.degree. C. per minute to temperatures where the glass-ceramic material flows and wets the interface between adjoining surfaces. The assembly is rapidly cooled at a cooling rate of about 140.degree. C. per minute or more to induce nucleation and re-crystallization of the glass-ceramic material to form a dense, durable and gas-tight seal.« less

Processes For Cleaning a Cathode Tube and Assemblies In A Hollow Cathode Assembly

NASA Technical Reports Server (NTRS)

Patterson, Michael J. (Inventor); Verhey, Timothy R. R. (Inventor); Soulas, George C. (Inventor)

2001-01-01

The present invention is a process for cleaning a cathode tube and other subassemblies in a hollow cathode assembly. In the disclosed process, hand covering elastomer gloves are used for handling all cathode assembly parts. The cathode tube and other subassemblies are cleaned with a lint-free cloth damped with acetone, then wiped with alcohol, immersed in ethyl alcohol or acetone, and ultrasonic agitation is applied, heating to 60 C. for ethyl alcohol or 56 C. for acetone. The cathode tube and other subassemblies are dried by blowing with nitrogen gas.

Software-assisted stacking of gene modules using GoldenBraid 2.0 DNA-assembly framework.

PubMed

Vazquez-Vilar, Marta; Sarrion-Perdigones, Alejandro; Ziarsolo, Peio; Blanca, Jose; Granell, Antonio; Orzaez, Diego

2015-01-01

GoldenBraid (GB) is a modular DNA assembly technology for plant multigene engineering based on type IIS restriction enzymes. GB speeds up the assembly of transcriptional units from standard genetic parts and facilitates the stacking of several genes within the same T-DNA in few days. GBcloning is software-assisted with a set of online tools. The GBDomesticator tool assists in the adaptation of DNA parts to the GBstandard. The combination of GB-adapted parts to build new transcriptional units is assisted by the GB TU Assembler tool. Finally, the assembly of multigene modules is simulated by the GB Binary Assembler. All the software tools are available at www.gbcloning.org . Here, we describe in detail the assembly methodology to create a multigene construct with three transcriptional units for polyphenol metabolic engineering in plants.

Self-assembly in the ferritin nano-cage protein superfamily.

PubMed

Zhang, Yu; Orner, Brendan P

2011-01-01

Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.

Dynamic Nanoparticles Assemblies

PubMed Central

WANG, LIBING; XU, LIGUANG; KUANG, HUA; XU, CHUANLAI; KOTOV, NICHOLAS A.

2012-01-01

in the field may include different size dimensionalities: discrete assemblies (artificial molecules), one-dimensional (spaced chains) and two-dimensional (sheets) and three-dimensional (superlattices, twisted structures) assemblies. Notably, these dimensional attributes must be regarded as primarily topological in nature because all of these superstructures can acquire complex three-dimensional shapes. Preparation We discuss three primary strategies used to prepare NP superstructures: (1) anisotropy-based assemblies utilizing either intrinsic force field anisotropy around NPs or external anisotropy associated with templates and/or applied fields; (2) assembly methods utilizing uniform NPs with isotropic interactions; and (3) methods based on mutual recognition of biomolecules, such as DNA and antigen-antibody interactions. Applications We consider optical, electronic, and magnetic properties of dynamic superstructures, focusing primarily on multiparticle effects in NP superstructures as represented by surface plasmon resonance, NP-NP charge transport, and multibody magnetization. Unique properties of NP superstructures are being applied to biosensing, drug delivery, and nanoelectronics. For both Class 1 and Class 2 dynamic assemblies, biosensing is the most dominant and well-developed area of dynamic nanostructures being successfully transitioned into practice. We can foresee the rapid development of dynamic NP assemblies toward applications in harvesting of dissipated energy, photonics, and electronics. The final part of the review is devoted to the fundamental questions facing dynamic assemblies of NPs in the future. PMID:22449243

Mind the gap; seven reasons to close fragmented genome assemblies.

PubMed

Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

2016-05-01

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

Automatic Assembly of Combined Checkingfixture for Auto-Body Components Based Onfixture Elements Libraries

NASA Astrophysics Data System (ADS)

Jiang, Jingtao; Sui, Rendong; Shi, Yan; Li, Furong; Hu, Caiqi

In this paper 3-D models of combined fixture elements are designed, classified by their functions, and saved in computer as supporting elements library, jointing elements library, basic elements library, localization elements library, clamping elements library, and adjusting elements library etc. Then automatic assembly of 3-D combined checking fixture for auto-body part is presented based on modularization theory. And in virtual auto-body assembly space, Locating constraint mapping technique and assembly rule-based reasoning technique are used to calculate the position of modular elements according to localization points and clamp points of auto-body part. Auto-body part model is transformed from itself coordinate system space to virtual assembly space by homogeneous transformation matrix. Automatic assembly of different functional fixture elements and auto-body part is implemented with API function based on the second development of UG. It is proven in practice that the method in this paper is feasible and high efficiency.

Self-organization: the fundament of cell biology.

PubMed

Wedlich-Söldner, Roland; Betz, Timo

2018-05-26

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order-and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).

Orientation-controlled parallel assembly at the air-water interface

NASA Astrophysics Data System (ADS)

Park, Kwang Soon; Hao Hoo, Ji; Baskaran, Rajashree; Böhringer, Karl F.

2012-10-01

This paper presents an experimental and theoretical study with statistical analysis of a high-yield, orientation-specific fluidic self-assembly process on a preprogrammed template. We demonstrate self-assembly of thin (less than few hundred microns in thickness) parts, which is vital for many applications in miniaturized platforms but problematic for today's pick-and-place robots. The assembly proceeds row-by-row as the substrate is pulled up through an air-water interface. Experiments and analysis are presented with an emphasis on the combined effect of controlled surface waves and magnetic force. For various gap values between a magnet and Ni-patterned parts, magnetic force distributions are generated using Monte Carlo simulation and employed to predict assembly yield. An analysis of these distributions shows that a gradual decline in yield following the probability density function can be expected with degrading conditions. The experimentally determined critical magnetic force is in good agreement with a derived value from a model of competing forces acting on a part. A general set of design guidelines is also presented from the developed model and experimental data.

Coarse-grained Simulations of Viral Assembly

NASA Astrophysics Data System (ADS)

Elrad, Oren M.

2011-12-01

The formation of viral capsids is a marvel of natural engineering and design. A large number (from 60 to thousands) of protein subunits assemble into complete, reproducible structures under a variety of conditions while avoiding kinetic and thermodynamic traps. Small single-stranded RNA viruses not only assemble their coat proteins in this fashion but also package their genome during the self-assembly process. Recent experiments have shown that the coat proteins are competent to assemble not merely around their own genomes but heterologous RNA, synthetic polyanions and even functionalized gold nanoparticles. Remarkably these viruses can even assemble around cargo not commensurate with their native state by adopting different morphologies. Understanding the properties that confer such exquisite precision and flexibility to the assembly process could aid biomedical research in the search for novel antiviral remedies, drug-delivery vehicles and contrast agents used in bioimaging. At the same time, viral assembly provides an excellent model system for the development of a statistical mechanical understanding of biological self-assembly, in the hopes of that we will identify some universal principles that underly such processes. This work consists of computational studies using coarse-grained representations of viral coat proteins and their cargoes. We find the relative strength of protein-cargo and protein-protein interactions has a profound effect on the assembly pathway, in some cases leading to assembly mechanisms that are markedly different from those found in previous work on the assembly of empty capsids. In the case of polymeric cargo, we find the first evidence for a previously theorized mechanism in which the polymer actively participates in recruiting free subunits to the assembly process through cooperative polymer-protein motions. We find that successful assembly is non-monotonic in protein-cargo affinity, such affinity can be detrimental to assembly if it

Programmable assembly of nanoarchitectures using genetically engineered viruses.

PubMed

Huang, Yu; Chiang, Chung-Yi; Lee, Soo Kwan; Gao, Yan; Hu, Evelyn L; De Yoreo, James; Belcher, Angela M

2005-07-01

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

Assembly of the Human Signal Recognition Particle

NASA Astrophysics Data System (ADS)

Menichelli, Elena; Nagai, Kiyoshi

Large RNA-protein complexes (ribonucleoprotein particles or RNPs) control fundamental biological processes. Their correct assembly is essential for function and occurs by the ordered addition of proteins to the RNA. A good model system for studying RNP assembly is provided by the Signal Recognition Particle (SRP), an RNP conserved from bacteria to humans, with different degrees of complexity. Human SRP, composed of a single RNA molecule and six pro teins, is responsible for the co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum membrane. In vitro studies reveal that the SRP proteins need to be added to the RNA sequentially. If the order of addition is altered, non-native particles are formed. The sequential association of proteins causes conformational changes in the RNA, allowing binding of other proteins. The in vivo assembly is regulated by the translocation of precursors between different cellular compartments. In this chapter we review the current understanding of the human SRP assembly mechanism.

Prodrugs as self-assembled hydrogels: a new paradigm for biomaterials.

PubMed

Vemula, Praveen Kumar; Wiradharma, Nikken; Ankrum, James A; Miranda, Oscar R; John, George; Karp, Jeffrey M

2013-12-01

Prodrug-based self-assembled hydrogels represent a new class of active biomaterials that can be harnessed for medical applications, in particular the design of stimuli responsive drug delivery devices. In this approach, a promoiety is chemically conjugated to a known-drug to generate an amphiphilic prodrug that is capable of forming self-assembled hydrogels. Prodrug-based self-assembled hydrogels are advantageous as they alter the solubility of the drug, enhance drug loading, and eliminate the use of harmful excipients. In addition, self-assembled prodrug hydrogels can be designed to undergo controlled drug release or tailored degradation in response to biological cues. Herein we review the development of prodrug-based self-assembled hydrogels as an emerging class of biomaterials that overcome several common limitations encountered in conventional drug delivery. Published by Elsevier Ltd.

High precision optomechanical assembly using threads as mechanical reference

NASA Astrophysics Data System (ADS)

Lamontagne, Frédéric; Desnoyers, Nichola; Bergeron, Guy; Cantin, Mario

2016-09-01

A convenient method to assemble optomechanical components is to use threaded interface. For example, lenses are often secured inside barrels using threaded rings. In other cases, multiple optical sub-assemblies such as lens barrels can be threaded to each other. Threads have the advantage to provide a simple assembly method, to be easy to manufacture, and to offer a compact mechanical design. On the other hand, threads are not considered to provide accurate centering between parts because of the assembly clearance between the inner and outer threads. For that reason, threads are often used in conjunction with precision cylindrical surfaces to limit the radial clearance between the parts to be centered. Therefore, tight manufacturing tolerances are needed on these pilot diameters, which affect the cost of the optical assembly. This paper presents a new optomechanical approach that uses threads as mechanical reference. This innovative method relies on geometric principles to auto-center parts to each other with a very low centering error that is usually less than 5 μm. The method allows to auto-center an optical group in a main barrel, to perform an axial adjustment of an optical group inside a main barrel, and to perform stacking of multiple barrels. In conjunction with the lens auto-centering method that also used threads as a mechanical reference, this novel solution opens new possibilities to realize a variety of different high precision optomechanical assemblies at lower cost.

Flexible, Symmetry-Directed Approach To Assembling Protein Cages (Publisher’s Version Open Access)

DTIC Science & Technology

2016-08-01

widespread in nature and confers new biological properties. Engineered protein assemblies have potential applica- tions in nanotechnology and medicine...and nanotechnology in designing novel self-assembling proteins and adapting natural protein assem- blies for a range of applications broadly

Digital Material Assembly by Passive Means and Modular Isotropic Lattice Extruder System

NASA Technical Reports Server (NTRS)

Gershenfeld, Neil (Inventor); Carney, Matthew Eli (Inventor); Jenett, Benjamin (Inventor)

2017-01-01

A set of machines and related systems build structures by the additive assembly of discrete parts. These digital material assemblies constrain the constituent parts to a discrete set of possible positions and orientations. In doing so, the structures exhibit many of the properties inherent in digital communication such as error correction, fault tolerance and allow the assembly of precise structures with comparatively imprecise tools. Assembly of discrete cellular lattices by a Modular Isotropic Lattice Extruder System (MILES) is implemented by pulling strings of lattice elements through a forming die that enforces geometry constraints that lock the elements into a rigid structure that can then be pushed against and extruded out of the die as an assembled, loadbearing structure.

3D Printing Polymers with Supramolecular Functionality for Biological Applications.

PubMed

Pekkanen, Allison M; Mondschein, Ryan J; Williams, Christopher B; Long, Timothy E

2017-09-11

Supramolecular chemistry continues to experience widespread growth, as fine-tuned chemical structures lead to well-defined bulk materials. Previous literature described the roles of hydrogen bonding, ionic aggregation, guest/host interactions, and π-π stacking to tune mechanical, viscoelastic, and processing performance. The versatility of reversible interactions enables the more facile manufacturing of molded parts with tailored hierarchical structures such as tissue engineered scaffolds for biological applications. Recently, supramolecular polymers and additive manufacturing processes merged to provide parts with control of the molecular, macromolecular, and feature length scales. Additive manufacturing, or 3D printing, generates customizable constructs desirable for many applications, and the introduction of supramolecular interactions will potentially increase production speed, offer a tunable surface structure for controlling cell/scaffold interactions, and impart desired mechanical properties through reinforcing interlayer adhesion and introducing gradients or self-assembled structures. This review details the synthesis and characterization of supramolecular polymers suitable for additive manufacture and biomedical applications as well as the use of supramolecular polymers in additive manufacturing for drug delivery and complex tissue scaffold formation. The effect of supramolecular assembly and its dynamic behavior offers potential for controlling the anisotropy of the printed objects with exquisite geometrical control. The potential for supramolecular polymers to generate well-defined parts, hierarchical structures, and scaffolds with gradient properties/tuned surfaces provides an avenue for developing next-generation biomedical devices and tissue scaffolds.

Multicriteria Analysis of Assembling Buildings from Steel Frame Structures

NASA Astrophysics Data System (ADS)

Miniotaite, Ruta

2017-10-01

Steel frame structures are often used in the construction of public and industrial buildings. They are used for: all types of slope roofs; walls of newly-built public and industrial buildings; load bearing structures; roofs of renovated buildings. The process of assembling buildings from steel frame structures should be analysed as an integrated process influenced by such factors as construction materials and machinery used, the qualification level of construction workers, complexity of work, available finance. It is necessary to find a rational technological design solution for assembling buildings from steel frame structures by conducting a multiple criteria analysis. The analysis provides a possibility to evaluate the engineering considerations and find unequivocal solutions. The rational alternative of a complex process of assembling buildings from steel frame structures was found through multiple criteria analysis and multiple criteria evaluation. In multiple criteria evaluation of technological solutions for assembling buildings from steel frame structures by pairwise comparison method the criteria by significance are distributed as follows: durability is the most important criterion in the evaluation of alternatives; the price (EUR/unit of measurement) of a part of assembly process; construction workers’ qualification level (category); mechanization level of a part of assembling process (%), and complexity of assembling work (in points) are less important criteria.

Peptide-directed self-assembly of functionalized polymeric nanoparticles. Part II: effects of nanoparticle composition on assembly behavior and multiple drug loading ability.

PubMed

Xiang, Xu; Ding, Xiaochu; Moser, Trevor; Gao, Qi; Shokuhfar, Tolou; Heiden, Patricia A

2015-04-01

Peptide-functionalized polymeric nanoparticles were designed and self-assembled into continuous nanoparticle fibers and three-dimensional scaffolds via ionic complementary peptide interaction. Different nanoparticle compositions can be designed to be appropriate for each desired drug, so that the release of each drug is individually controlled and the simultaneous sustainable release of multiple drugs is achieved in a single scaffold. A self-assembled scaffold membrane was incubated with NIH3T3 fibroblast cells in a culture dish that demonstrated non-toxicity and non-inhibition on cell proliferation. This type of nanoparticle scaffold combines the advantages of peptide self-assembly and the versatility of polymeric nanoparticle controlled release systems for tissue engineering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Catalytic diversity in self-propagating peptide assemblies

NASA Astrophysics Data System (ADS)

Omosun, Tolulope O.; Hsieh, Ming-Chien; Childers, W. Seth; Das, Dibyendu; Mehta, Anil K.; Anthony, Neil R.; Pan, Ting; Grover, Martha A.; Berland, Keith M.; Lynn, David G.

2017-08-01

The protein-only infectious agents known as prions exist within cellular matrices as populations of assembled polypeptide phases ranging from particles to amyloid fibres. These phases appear to undergo Darwinian-like selection and propagation, yet remarkably little is known about their accessible chemical and biological functions. Here we construct simple peptides that assemble into well-defined amyloid phases and define paracrystalline surfaces able to catalyse specific enantioselective chemical reactions. Structural adjustments of individual amino acid residues predictably control both the assembled crystalline order and their accessible catalytic repertoire. Notably, the density and proximity of the extended arrays of enantioselective catalytic sites achieve template-directed polymerization of new polymers. These diverse amyloid templates can now be extended as dynamic self-propagating templates for the construction of even more complex functional materials.

Designer nanomaterials using chiral self-assembling peptide systems and their emerging benefit for society.

PubMed

Luo, Zhongli; Zhang, Shuguang

2012-07-07

Chirality is absolutely central in chemistry and biology. The recent findings of chiral self-assembling peptides' remarkable chemical complementarity and structural compatibility make it one of the most inspired designer materials and structures in nanobiotechnology. The emerging field of designer chemistry and biology further explores biological and medical applications of these simple D,L- amino acids through producing marvellous nanostructures under physiological conditions. These self-assembled structures include well-ordered nanofibers, nanotubes and nanovesicles. These structures have been used for 3-dimensional tissue cultures of primary cells and stem cells, sustained release of small molecules, growth factors and monoclonal antibodies, accelerated wound-healing in reparative and regenerative medicine as well as tissue engineering. Recent advances in molecular designs have also led to the development of 3D fine-tuned bioactive tissue culture scaffolds. They are also used to stabilize membrane proteins including difficult G-protein coupled receptors for designing nanobiodevices. One of the self-assembling peptides has been used in human clinical trials for accelerated wound-healings. It is our hope that these peptide materials will open doors for more and diverse clinical uses. The field of chiral self-assembling peptide nanobiotechnology is growing in a number of directions that has led to many surprises in areas of novel materials, synthetic biology, clinical medicine and beyond.

A trait-based approach for examining microbial community assembly

NASA Astrophysics Data System (ADS)

Prest, T. L.; Nemergut, D.

2015-12-01

Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models

PubMed Central

Rajasekaran, Sanguthevar

2013-01-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is Ω(log(n)log(log(n))) (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing Θ(log(n)log(log(n))) unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio (α:β), with high probability, using Θ(α + β) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85–94, 2009)—which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling. This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP ’09, Springer-Verlag, pp 235�

Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.

PubMed

Kundeti, Vamsi; Rajasekaran, Sanguthevar

2012-06-01

Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia).

PubMed

Holt, Carson; Campbell, Michael; Keays, David A; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; T Domyan, Eric; Suh, Alexander; Warren, Wesley C; Yandell, Mark; Gilbert, M Thomas P; Shapiro, Michael D

2018-05-04

The domestic rock pigeon ( Columba livia ) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general. Copyright © 2018 Holt et al.

Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

PubMed Central

Holt, Carson; Campbell, Michael; Keays, David A.; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; T. Domyan, Eric; Suh, Alexander; Warren, Wesley C.; Yandell, Mark; Gilbert, M. Thomas P.; Shapiro, Michael D.

2018-01-01

The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general. PMID:29519939

Self-assembly concepts for multicompartment nanostructures

NASA Astrophysics Data System (ADS)

Gröschel, André H.; Müller, Axel H. E.

2015-07-01

Compartmentalization is ubiquitous to many biological and artificial systems, be it for the separate storage of incompatible matter or to isolate transport processes. Advancements in the synthesis of sequential block copolymers offer a variety of tools to replicate natural design principles with tailor-made soft matter for the precise spatial separation of functionalities on multiple length scales. Here, we review recent trends in the self-assembly of amphiphilic block copolymers to multicompartment nanostructures (MCNs) under (semi-)dilute conditions, with special emphasis on ABC triblock terpolymers. The intrinsic immiscibility of connected blocks induces short-range repulsion into discrete nano-domains stabilized by a third, soluble block or molecular additive. Polymer blocks can be synthesized from an arsenal of functional monomers directing self-assembly through packing frustration or response to various fields. The mobility in solution further allows the manipulation of self-assembly processes into specific directions by clever choice of environmental conditions. This review focuses on practical concepts that direct self-assembly into predictable nanostructures, while narrowing particle dispersity with respect to size, shape and internal morphology. The growing understanding of underlying self-assembly mechanisms expands the number of experimental concepts providing the means to target and manipulate progressively complex superstructures.

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.

PubMed

Papudeshi, Bhavya; Haggerty, J Matthew; Doane, Michael; Morris, Megan M; Walsh, Kevin; Beattie, Douglas T; Pande, Dnyanada; Zaeri, Parisa; Silva, Genivaldo G Z; Thompson, Fabiano; Edwards, Robert A; Dinsdale, Elizabeth A

2017-11-28

Microbiome/host interactions describe characteristics that affect the host's health. Shotgun metagenomics includes sequencing a random subset of the microbiome to analyze its taxonomic and metabolic potential. Reconstruction of DNA fragments into genomes from metagenomes (called metagenome-assembled genomes) assigns unknown fragments to taxa/function and facilitates discovery of novel organisms. Genome reconstruction incorporates sequence assembly and sorting of assembled sequences into bins, characteristic of a genome. However, the microbial community composition, including taxonomic and phylogenetic diversity may influence genome reconstruction. We determine the optimal reconstruction method for four microbiome projects that had variable sequencing platforms (IonTorrent and Illumina), diversity (high or low), and environment (coral reefs and kelp forests), using a set of parameters to select for optimal assembly and binning tools. We tested the effects of the assembly and binning processes on population genome reconstruction using 105 marine metagenomes from 4 projects. Reconstructed genomes were obtained from each project using 3 assemblers (IDBA, MetaVelvet, and SPAdes) and 2 binning tools (GroopM and MetaBat). We assessed the efficiency of assemblers using statistics that including contig continuity and contig chimerism and the effectiveness of binning tools using genome completeness and taxonomic identification. We concluded that SPAdes, assembled more contigs (143,718 ± 124 contigs) of longer length (N50 = 1632 ± 108 bp), and incorporated the most sequences (sequences-assembled = 19.65%). The microbial richness and evenness were maintained across the assembly, suggesting low contig chimeras. SPAdes assembly was responsive to the biological and technological variations within the project, compared with other assemblers. Among binning tools, we conclude that MetaBat produced bins with less variation in GC content (average standard deviation: 1

Amphiphiles for DNA Supramolecular Assemblies

DTIC Science & Technology

2005-11-15

to drug or biomolecule delivery systems. In order to take advantage of forces that hold nucleic acid helices together, (Watson- Crick/Hoogsteen...supramolecular assemblies that highlight the underlying principles are evident in numerous biological (e.g., lipids) and synthetic (e.g., nanofibers ) systems.2...3). Additionally, they form hydrogels and organogels. The supramolecular systems obtained are promising in many aspects and could lead to new types

Ray Meta: scalable de novo metagenome assembly and profiling

PubMed Central

2012-01-01

Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

International Space Station Research Plan, Assembly Sequence Rev., F

DTIC Science & Technology

2000-08-01

muscles ü Higher risk for bone fracture upon return to Earth ü Potential for “slipped discs” ü Diminished ability to quickly respond to emergencies...Office of Biological and Physical Research International Space Station Research Plan Assembly Sequence Rev. F, Aug. 2000l . , . Report...Organization Name(s) and Address(es) NASA, Office of Biological and Physical Research Performing Organization Report Number Sponsoring/Monitoring Agency

Assembly of hydrogel units for 3D microenvironment in a poly(dimethylsiloxane) channel

NASA Astrophysics Data System (ADS)

Cho, Chang Hyun; Kwon, Seyong; Park, Je-Kyun

2017-12-01

Construction of three-dimensional (3D) microenvironment become an important issue in recent biological studies due to their biological relevance compared to conventional two-dimensional (2D) microenvironment. Various fabrication techniques have been employed to construct a 3D microenvironment, however, it is difficult to fully satisfy the biological and mechanical properties required for the 3D cell culture system, such as heterogeneous tissue structures generated from the functional differences or diseases. We propose here an assembly method for facile construction of 3D microenvironment in a poly(dimethylsiloxane) (PDMS) channel using hydrogel units. The high-aspect-ratio of hydrogel units was achieved by fabricating these units using a 2D mold. With this approach, 3D heterogeneous hydrogel units were produced and assembled in a PDMS channel by structural hookup. In vivo-like 3D heterogeneous microenvironment in a precisely controllable fluidic system was also demonstrated using a controlled assembly of different types of hydrogel units, which was difficult to obtain from previous methods. By regulating the flow condition, the mechanical stability of the assembled hydrogel units was verified by the flow-induced deformation of hydrogel units. In addition, in vivo-like cell culture environment was demonstrated using an assembly of cell-coated hydrogel units in the fluidic channel. Based on these features, our method expects to provide a beneficial tool for the 3D cell culture module and biomimetic engineering.

Hierarchical and Helical Self-assembly of ADP-ribosyl Cyclase into Large-scale Protein Microtubes

PubMed Central

Liu, Qun; Kriksunov, Irina A.; Wang, Zhongwu; Graeff, Richard; Lee, Hon Cheung; Hao, Quan

2013-01-01

Proteins are macromolecules with characteristic structures and biological functions. It is extremely challenging to obtain protein microtube structures through self-assembly as proteins are very complex and flexible. Here we present a strategy showing how a specific protein, ADP-ribosyl cyclase, helically self-assembles from monomers into hexagonal nanochains and further to highly ordered crystalline microtubes. The structures of protein nanochains and consequently self-assembled superlattice were determined by X-ray crystallography at 4.5 Å resolution and imaged by Scanning Electron Microscopy. The protein initially forms into dimers that have a fixed size of 5.6 nm, and then, helically self-assembles into 35.6 nm long hexagonal nanochains. One such nanochain consists of six dimers (12 monomers) that stack in order by a pseudo P61 screw axis. Seven nanochains produce a series of largescale assemblies, nanorods, forming the building blocks for microrods. A proposed aging process of microrods results in the formation of hollow microstructures. Synthesis and characterization of large scale self-assembled protein microtubes may pave a new pathway, capable of not only understanding the self-assembly dynamics of biological materials, but also directing design and fabrication of multifunctional nanobuilding blocks with particular applications in biomedical engineering. PMID:18956900

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

PubMed Central

Schneider, Valerie A.; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A.; Murphy, Terence D.; Pruitt, Kim D.; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S.; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T.; Threadgold, Glen; Torrance, James; Wood, Jonathan M.; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M.; Durbin, Richard; Wilson, Richard K.; Flicek, Paul; Eichler, Evan E.; Church, Deanna M.

2017-01-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. PMID:28396521

Forwardly movable assembly for a firearm

DOEpatents

Crandall, David L [Idaho Falls, ID; Watson, Richard W [Blackfoot, ID

2007-06-05

A forwardly movable assembly for a firearm, the forwardly movable assembly adapted to be disposed in operative relationship relative to the other operative parts of a firearm, the firearm having in operative relationship each with one or more of the others: a barrel, a receiver, and at least one firing mechanism; the forwardly movable assembly comprising: the barrel and the receiver operatively connected with each other; a movable hand support structure to which at least one of the barrel and the receiver is connected, the barrel being movable therewith, the movable hand support structure being adapted to be gripped by an operator of the firearm; the forwardly movable assembly being adapted to be moved forward by an operator upon gripping the movable hand support structure and manually maneuvering the hand support structure forwardly; and, as the forwardly movable assembly is moved forwardly, the firing mechanism is completely disengaged therefrom and held substantially stationary relative thereto.

Computational Modeling of Tissue Self-Assembly

NASA Astrophysics Data System (ADS)

Neagu, Adrian; Kosztin, Ioan; Jakab, Karoly; Barz, Bogdan; Neagu, Monica; Jamison, Richard; Forgacs, Gabor

As a theoretical framework for understanding the self-assembly of living cells into tissues, Steinberg proposed the differential adhesion hypothesis (DAH) according to which a specific cell type possesses a specific adhesion apparatus that combined with cell motility leads to cell assemblies of various cell types in the lowest adhesive energy state. Experimental and theoretical efforts of four decades turned the DAH into a fundamental principle of developmental biology that has been validated both in vitro and in vivo. Based on computational models of cell sorting, we have developed a DAH-based lattice model for tissues in interaction with their environment and simulated biological self-assembly using the Monte Carlo method. The present brief review highlights results on specific morphogenetic processes with relevance to tissue engineering applications. Our own work is presented on the background of several decades of theoretical efforts aimed to model morphogenesis in living tissues. Simulations of systems involving about 105 cells have been performed on high-end personal computers with CPU times of the order of days. Studied processes include cell sorting, cell sheet formation, and the development of endothelialized tubes from rings made of spheroids of two randomly intermixed cell types, when the medium in the interior of the tube was different from the external one. We conclude by noting that computer simulations based on mathematical models of living tissues yield useful guidelines for laboratory work and can catalyze the emergence of innovative technologies in tissue engineering.

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

Oxide nanostructures through self-assembly

NASA Astrophysics Data System (ADS)

Aggarwal, S.; Ogale, S. B.; Ganpule, C. S.; Shinde, S. R.; Novikov, V. A.; Monga, A. P.; Burr, M. R.; Ramesh, R.; Ballarotto, V.; Williams, E. D.

2001-03-01

A prominent theme in inorganic materials research is the creation of uniformly flat thin films and heterostructures over large wafers, which can subsequently be lithographically processed into functional devices. This letter proposes an approach that will lead to thin film topographies that are directly counter to the above-mentioned philosophy. Recent years have witnessed considerable research activity in the area of self-assembly of materials, stimulated by observations of self-organized behavior in biological systems. We have fabricated uniform arrays of nonplanar surface features by a spontaneous assembly process involving the oxidation of simple metals, especially under constrained conditions on a variety of substrates, including glass and Si. In this letter we demonstrate the pervasiveness of this process through examples involving the oxidation of Pd, Cu, Fe, and In. The feature sizes can be controlled through the grain size and thickness of the starting metal thin film. Finally, we demonstrate how such submicron scale arrays can serve as templates for the design and development of self-assembled, nanoelectronic devices.

Consistent design schematics for biological systems: standardization of representation in biological engineering

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kitano, Hiroaki

2009-01-01

The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input–output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems. PMID:19493898

An assembly system based on industrial robot with binocular stereo vision

NASA Astrophysics Data System (ADS)

Tang, Hong; Xiao, Nanfeng

2017-01-01

This paper proposes an electronic part and component assembly system based on an industrial robot with binocular stereo vision. Firstly, binocular stereo vision with a visual attention mechanism model is used to get quickly the image regions which contain the electronic parts and components. Secondly, a deep neural network is adopted to recognize the features of the electronic parts and components. Thirdly, in order to control the end-effector of the industrial robot to grasp the electronic parts and components, a genetic algorithm (GA) is proposed to compute the transition matrix and the inverse kinematics of the industrial robot (end-effector), which plays a key role in bridging the binocular stereo vision and the industrial robot. Finally, the proposed assembly system is tested in LED component assembly experiments, and the results denote that it has high efficiency and good applicability.

Self-assembly kinetics of microscale components: A parametric evaluation

NASA Astrophysics Data System (ADS)

Carballo, Jose M.

The goal of the present work is to develop, and evaluate a parametric model of a basic microscale Self-Assembly (SA) interaction that provides scaling predictions of process rates as a function of key process variables. At the microscale, assembly by "grasp and release" is generally challenging. Recent research efforts have proposed adapting nanoscale self-assembly (SA) processes to the microscale. SA offers the potential for reduced equipment cost and increased throughput by harnessing attractive forces (most commonly, capillary) to spontaneously assemble components. However, there are challenges for implementing microscale SA as a commercial process. The existing lack of design tools prevents simple process optimization. Previous efforts have characterized a specific aspect of the SA process. However, the existing microscale SA models do not characterize the inter-component interactions. All existing models have simplified the outcome of SA interactions as an experimentally-derived value specific to a particular configuration, instead of evaluating it outcome as a function of component level parameters (such as speed, geometry, bonding energy and direction). The present study parameterizes the outcome of interactions, and evaluates the effect of key parameters. The present work closes the gap between existing microscale SA models to add a key piece towards a complete design tool for general microscale SA process modeling. First, this work proposes a simple model for defining the probability of assembly of basic SA interactions. A basic SA interaction is defined as the event where a single part arrives on an assembly site. The model describes the probability of assembly as a function of kinetic energy, binding energy, orientation and incidence angle for the component and the assembly site. Secondly, an experimental SA system was designed, and implemented to create individual SA interactions while controlling process parameters independently. SA experiments

Macromolecular assemblies in reduced gravity environments

NASA Technical Reports Server (NTRS)

Moos, Philip J.; Hayes, James W.; Stodieck, Louis S.; Luttges, Marvin W.

1990-01-01

The assembly of protein macro molecules into structures commonly produced within biological systems was achieved using in vitro techniques carried out in nominal as well as reduced gravity environments. Appropriate hardware was designed and fabricated to support such studies. Experimental protocols were matched to the available reduced gravity test opportunities. In evaluations of tubulin, fibrin and collagen assembly products the influence of differing gravity test conditions are apparent. Product homogeneity and organization were characteristic enhancements documented in reduced gravity samples. These differences can be related to the fluid flow conditions that exist during in vitro product formation. Reduced gravity environments may provide a robust opportunity for directing the products formed in a variety of bioprocessing applications.

Sequential self-assembly of DNA functionalized droplets

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

Zhang, Yin; McMullen, Angus; Pontani, Lea-Laetitia

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Though biology relies on such schemes, they have not been available in materials science. We demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activatesmore » the next droplet in the sequence, akin to living polymerization. This strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.« less

Sequential self-assembly of DNA functionalized droplets

DOE PAGES

Zhang, Yin; McMullen, Angus; Pontani, Lea-Laetitia; ...

2017-06-16

Complex structures and devices, both natural and manmade, are often constructed sequentially. From crystallization to embryogenesis, a nucleus or seed is formed and built upon. Sequential assembly allows for initiation, signaling, and logical programming, which are necessary for making enclosed, hierarchical structures. Though biology relies on such schemes, they have not been available in materials science. We demonstrate programmed sequential self-assembly of DNA functionalized emulsions. The droplets are initially inert because the grafted DNA strands are pre-hybridized in pairs. Active strands on initiator droplets then displace one of the paired strands and thus release its complement, which in turn activatesmore » the next droplet in the sequence, akin to living polymerization. This strategy provides time and logic control during the self-assembly process, and offers a new perspective on the synthesis of materials.« less

Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

PubMed

Carter, Joshua D; LaBean, Thomas H

2011-03-22

An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

Assembly of Colloidal Materials Using Bioadhesive Interactions

NASA Technical Reports Server (NTRS)

Hammer, Daniel A.; Hiddessen, Amy L.; Tohver, Valeria; Crocker, John C.; Weitz, David A.

2002-01-01

We have pursued the use of biological crosslinking molecules of several types to make colloidal materials at relatively low volume fraction of colloidal particles. The objective is to make binary alloys of colloidal particles, made of two different colloidal particles coated with complementary biological lock-and-key binding molecules, which assemble due to the biological specificity. The long-term goal is to use low affinity lock-and-key biological interactions, so that the can anneal to form crystalline states. We have used a variety of different surface chemistries in order to make colloidal materials. Our first system involved using selectin-carbohydrate (sialyl-Lewis) interactions; this chemistry is derived from immune system. This chemical interaction is of relatively low affinity, with timescales for dissociation of several seconds. Furthermore, the adhesion mediated by these molecules can be reversed by the chelation of calcium atoms; thus assembled structures can be disassembled reversibly. Our second system employed avidin-biotin chemistry. This well-studied system is of high affinity, and is generally irreversible on a laboratory time-scale. Thus, we would expect selectin-carbohydrate interactions at high molecular density and avidin-biotin interactions to give kinetically-trapped structures; however, at low densities, we would expect significant differences in the structure and dynamics of the two materials, owing to their very different release rates. We have also begun to use a third chemistry - DNA hybridization. By attaching single stranded DNA oligonucleotide chains to beads, we can drive the assembly of colloidal materials by hybridization of complementary DNA chains. It is well known that DNA adenosine-thymine (A-T) and guanine-cytosine (G-C) bases hybridize pairwise with a Gibbs free energy change of 1.7 kcal/mol per base; thus, the energy of the assembly can be modulated by altering the number of complementary bases in the DNA chains. Using

Modular robotic assembly of small devices.

PubMed

Frauenfelder, M

2000-01-01

The use of robots for the automatic assembly of devices of up to 100 x 100 x 100 mm is relatively uncommon today. Insufficient return on investment and the long lead times that are required have been limiting factors. Innovations in vision technology have led to the development of robotic assembly systems that employ flexible part-feeding. The benefits of these systems are described, which suggest that better ratios of price to productivity and deployment times are now achievable.

Integrative, Dynamic Structural Biology at Atomic Resolution—It’s About Time

PubMed Central

van den Bedem, Henry; Fraser, James S.

2015-01-01

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and other techniques are helping us realize the dream of seeing—in atomic detail—how different parts of biomolecules exchange between functional sub-states using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR, and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution. PMID:25825836

Self-assembled Tunable Photonic Hyper-crystals

DTIC Science & Technology

2014-07-16

a cobalt nanoparticle-based ferrofluid. Unique spectral properties of photonic hyper-crystals lead to extreme sensitivity of the material to...monolayer coatings of cobalt nanoparticles, which should find numerous applications in biological and chemical sensing. 2 Approved for public release...assembly of photonic hyper crystals has been achieved by application of external magnetic field to a cobalt nanoparticle based ferrofluid. Unique spectral

Self-assembly of keratin peptides: Its implication on the performance of electrospun PVA nanofibers

PubMed Central

Kadirvelu, Kavitha; Fathima, Nishter Nishad

2016-01-01

Drawing inspiration from the field of designer self-assembling materials, this work is aimed to focus on the self-assembling nature of extracted peptides. Hair keratin, a proteinacious reject in tanning industry has been chosen since they have been extracted and used for wide range of applications. Keratin source was subjected to five hydrolysis treatments (viz., sulphitolysis, β-mercaptoethanol, ionic liquid, thioglycolic acid and alkali) and assayed for functional groups. This was followed by the prediction of secondary structure using circular dichroism, determining the microstructural level to which the extracted peptide has self-assembled. Sulphitolysis and thioglycolic acid based hydrolysates exist in monomeric conformation, whereas β-mercaptoethanol based hydrolysate exhibited dimeric conformation. The subsequent part of the study is to incorporate these peptides into the nanofibers to study the structural implication of keratin peptides on its characteristics. Accordingly, the peptides were electrospun with PVA and subjected to morphological, mechanical, thermal and biological characterizations. Monomeric nanofiber mat has high tensile strength of around 5.5 MPa and offered lower mass transport resistance, whereas dimeric mat has high Tm of around 290 °C and was more biocompatible. These results help in understanding the extraction-structure-function aspect of the hydrolysates stressing the role of extraction methods on the choice of application. PMID:27812004

Morphology and Pattern Control of Diphenylalanine Self-Assembly via Evaporative Dewetting.

PubMed

Chen, Jiarui; Qin, Shuyu; Wu, Xinglong; Chu, And Paul K

2016-01-26

Self-assembled peptide nanostructures have unique physical and biological properties and promising applications in electrical devices and functional molecular recognition. Although solution-based peptide molecules can self-assemble into different morphologies, it is challenging to control the self-assembly process. Herein, controllable self-assembly of diphenylalanine (FF) in an evaporative dewetting solution is reported. The fluid mechanical dimensionless numbers, namely Rayleigh, Marangoni, and capillary numbers, are introduced to control the interaction between the solution and FF molecules in the self-assembly process. The difference in the film thickness reflects the effects of Rayleigh and Marangoni convection, and the water vapor flow rate reveals the role of viscous fingering in the emergence of aligned FF flakes. By employing dewetting, various FF self-assembled patterns, like concentric and spokelike, and morphologies, like strips and hexagonal tubes/rods, can be produced, and there are no significant lattice structural changes in the FF nanostructures.

Helically assembled π-conjugated polymers with circularly polarized luminescence.

PubMed

Watanabe, Kazuyoshi; Akagi, Kazuo

2014-08-01

We review the recent progress in the field of helically assembled π -conjugated polymers, focusing on aromatic conjugated polymers with interchain helical π -stacking that exhibit circularly polarized luminescence (CPL). In Part 1, we discuss optically active polymers with white-colored CPL and the amplification of the circular polarization through liquid crystallinity. In Part 2, we focus on the stimuli-responsive CPL that results from changes in the conformation and aggregation state of π -conjugated molecules and polymers. In Part 3, we discuss the self-assembly of achiral cationic π -conjugated polymers into circularly polarized luminescent supramolecular nanostructures with the aid of other chiral molecules.

Mitochondrial ribosome assembly in health and disease

PubMed Central

De Silva, Dasmanthie; Tu, Ya-Ting; Amunts, Alexey; Fontanesi, Flavia; Barrientos, Antoni

2015-01-01

The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health. PMID:26030272

Self-Assembly of Two-Dimensional Patchy Colloidal Dumbbells

NASA Astrophysics Data System (ADS)

Nakamura, Kanji; Sato, Masahide

2018-06-01

We study the self-assembly of two-dimensional patchy colloidal dumbbells, which are composed of attractive and repulsive circles. The shape of a colloidal dumbbell is characterized by the ratio of the diameters of the two circles forming it, q, and the dimensionless distance between the centers of mass of the two circles, l. We carry out Monte Carlo simulations and show that various self-assembled structures, micelles, elongated micelles, straight string, a meshlike structure, and large clusters with voids, are formed by changing the combination of q and l. q represents the steric effect of the repulsive part of colloidal dumbbells. l represents the anisotropy of the particle shape and increasing the periphery of attractive part. From our simulations, we find that the shapes of self-assembled structures are more sensitive to q than to l.

Our Hidden Past: Biology, Part 2

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

Smith, Ray; Russell, Liane; Mazur, Peter

In their new home at "The Mouse House" at Y-12, researchers from ORNL's Biology Division conducted studies that led to standards such as dose rate effects that form the basis for current international standards for radiation exposure in humans.

Multidimensional Self-Assembled Structures of Alkylated Cellulose Oligomers Synthesized via in Vitro Enzymatic Reactions.

PubMed

Yataka, Yusuke; Sawada, Toshiki; Serizawa, Takeshi

2016-10-04

The self-assembly of biomolecules into highly ordered nano-to-macroscale structures is essential in the construction of biological tissues and organs. A variety of biomolecular assemblies composed of nucleic acids, peptides, and lipids have been used as molecular building units for self-assembled materials. However, crystalline polysaccharides have rarely been utilized in self-assembled materials. In this study, we describe multidimensional self-assembled structures of alkylated cellulose oligomers synthesized via in vitro enzymatic reactions. We found that the alkyl chain length drastically affected the assembled morphologies and allomorphs of cellulose moieties. The modulation of the intermolecular interactions of cellulose oligomers by alkyl substituents was highly effective at controlling their assembly into multidimensional structures. This study proposes a new potential of crystalline oligosaccharides for structural components of molecular assemblies with controlled morphologies and crystal structures.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

PubMed

Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M

2017-05-01

The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. © 2017 Schneider et al.; Published by Cold Spring Harbor Laboratory Press.

Micro/nano-particles and Cells: Manipulation, Transport, and Self-assembly

DTIC Science & Technology

2014-10-23

SECURITY CLASSIFICATION OF: Technologies that control nano- and micron- sized inert as well as biological materials are crucial to realizing engineered...that control nano- and micron- sized inert as well as biological materials are crucial to realizing engineered systems that can assemble, transport, and...nano-scale particles offer several advantages as building blocks of artificial materials . The relative ease of modifying their charge states

Rho1- and Pkc1-dependent phosphorylation of the F-BAR protein Syp1 contributes to septin ring assembly.

PubMed

Merlini, Laura; Bolognesi, Alessio; Juanes, Maria Angeles; Vandermoere, Franck; Courtellemont, Thibault; Pascolutti, Roberta; Séveno, Martial; Barral, Yves; Piatti, Simonetta

2015-09-15

In many cell types, septins assemble into filaments and rings at the neck of cellular appendages and/or at the cleavage furrow to help compartmentalize the plasma membrane and support cytokinesis. How septin ring assembly is coordinated with membrane remodeling and controlled by mechanical stress at these sites is unclear. Through a genetic screen, we uncovered an unanticipated link between the conserved Rho1 GTPase and its effector protein kinase C (Pkc1) with septin ring stability in yeast. Both Rho1 and Pkc1 stabilize the septin ring, at least partly through phosphorylation of the membrane-associated F-BAR protein Syp1, which colocalizes asymmetrically with the septin ring at the bud neck. Syp1 is displaced from the bud neck upon Pkc1-dependent phosphorylation at two serines, thereby affecting the rigidity of the new-forming septin ring. We propose that Rho1 and Pkc1 coordinate septin ring assembly with membrane and cell wall remodeling partly by controlling Syp1 residence at the bud neck. © 2015 Merlini et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

TOPICAL REVIEW: Self-assembly from milli- to nanoscales: methods and applications

NASA Astrophysics Data System (ADS)

Mastrangeli, M.; Abbasi, S.; Varel, C.; Van Hoof, C.; Celis, J.-P.; Böhringer, K. F.

2009-08-01

The design and fabrication techniques for microelectromechanical systems (MEMS) and nanodevices are progressing rapidly. However, due to material and process flow incompatibilities in the fabrication of sensors, actuators and electronic circuitry, a final packaging step is often necessary to integrate all components of a heterogeneous microsystem on a common substrate. Robotic pick-and-place, although accurate and reliable at larger scales, is a serial process that downscales unfavorably due to stiction problems, fragility and sheer number of components. Self-assembly, on the other hand, is parallel and can be used for device sizes ranging from millimeters to nanometers. In this review, the state-of-the-art in methods and applications for self-assembly is reviewed. Methods for assembling three-dimensional (3D) MEMS structures out of two-dimensional (2D) ones are described. The use of capillary forces for folding 2D plates into 3D structures, as well as assembling parts onto a common substrate or aggregating parts to each other into 2D or 3D structures, is discussed. Shape matching and guided assembly by magnetic forces and electric fields are also reviewed. Finally, colloidal self-assembly and DNA-based self-assembly, mainly used at the nanoscale, are surveyed, and aspects of theoretical modeling of stochastic assembly processes are discussed.

Initial condition of stochastic self-assembly

NASA Astrophysics Data System (ADS)

Davis, Jason K.; Sindi, Suzanne S.

2016-02-01

The formation of a stable protein aggregate is regarded as the rate limiting step in the establishment of prion diseases. In these systems, once aggregates reach a critical size the growth process accelerates and thus the waiting time until the appearance of the first critically sized aggregate is a key determinant of disease onset. In addition to prion diseases, aggregation and nucleation is a central step of many physical, chemical, and biological process. Previous studies have examined the first-arrival time at a critical nucleus size during homogeneous self-assembly under the assumption that at time t =0 the system was in the all-monomer state. However, in order to compare to in vivo biological experiments where protein constituents inherited by a newly born cell likely contain intermediate aggregates, other possibilities must be considered. We consider one such possibility by conditioning the unique ergodic size distribution on subcritical aggregate sizes; this least-informed distribution is then used as an initial condition. We make the claim that this initial condition carries fewer assumptions than an all-monomer one and verify that it can yield significantly different averaged waiting times relative to the all-monomer condition under various models of assembly.

Modeling Protein Self Assembly

ERIC Educational Resources Information Center

Baker, William P.; Jones, Carleton Buck; Hull, Elizabeth

2004-01-01

Understanding the structure and function of proteins is an important part of the standards-based science curriculum. Proteins serve vital roles within the cell and malfunctions in protein self assembly are implicated in degenerative diseases. Experience indicates that this topic is a difficult one for many students. We have found that the concept…

Cross counter-based adaptive assembly scheme in optical burst switching networks

NASA Astrophysics Data System (ADS)

Zhu, Zhi-jun; Dong, Wen; Le, Zi-chun; Chen, Wan-jun; Sun, Xingshu

2009-11-01

A novel adaptive assembly algorithm called Cross-counter Balance Adaptive Assembly Period (CBAAP) is proposed in this paper. The major difference between CBAAP and other adaptive assembly algorithms is that the threshold of CBAAP can be dynamically adjusted according to the cross counter and step length value. In terms of assembly period and the burst loss probability, we compare the performance of CBAAP with those of three typical algorithms FAP (Fixed Assembly Period), FBL (Fixed Burst Length) and MBMAP (Min-Burst length-Max-Assembly-Period) in the simulation part. The simulation results demonstrate the effectiveness of our algorithm.

Advances in Structural Biology and the Application to Biological Filament Systems.

PubMed

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Demisable Reaction-Wheel Assembly

NASA Technical Reports Server (NTRS)

Roder, Russell; Ahronovich, Eliezer; Davis, Milton C., III

2008-01-01

A document discusses the concept of a demisable motor-drive-and-flywheel assembly [reaction-wheel assembly (RWA)] used in controlling the attitude of a spacecraft. Demisable as used here does not have its traditional legal meaning; instead, it signifies susceptible to melting, vaporizing, and/or otherwise disintegrating during re-entry of the spacecraft into the atmosphere of the Earth so as not to pose a hazard to anyone or anything on the ground. Prior RWAs include parts made of metals (e.g., iron, steel, and titanium) that melt at high temperatures and include structures of generally closed character that shield some parts (e.g., magnets) against re-entry heating. In a demisable RWA, the flywheel would be made of aluminum, which melts at a lower temperature. The flywheel web would not be a solid disk but would have a more open, nearly-spoke-like structure so that it would disintegrate more rapidly; hence, the flywheel rim would separate more rapidly so that parts shielded by the rim would be exposed sooner to re-entry heating. In addition, clearances between the flywheel and other components would be made greater, imparting a more open character and thus increasing the exposure of those components.

Bacteriophage lambda: The path from biology to theranostic agent.

PubMed

Catalano, Carlos E

2018-03-13

Viral particles provide an attractive platform for the engineering of semisynthetic therapeutic nanoparticles. They can be modified both genetically and chemically in a defined manner to alter their surface characteristics, for targeting specific cell types, to improve their pharmacokinetic features and to attenuate (or enhance) their antigenicity. These advantages derive from a detailed understanding of virus biology, gleaned from decades of fundamental genetic, biochemical, and structural studies that have provided mechanistic insight into virus assembly pathways. In particular, bacteriophages offer significant advantages as nanoparticle platforms and several have been adapted toward the design and engineering of "designer" nanoparticles for therapeutic and diagnostic (theranostic) applications. The present review focuses on one such virus, bacteriophage lambda; I discuss the biology of lambda, the tools developed to faithfully recapitulate the lambda assembly reactions in vitro and the observations that have led to cooptation of the lambda system for nanoparticle design. This discussion illustrates how a fundamental understanding of virus assembly has allowed the rational design and construction of semisynthetic nanoparticles as potential theranostic agents and illustrates the concept of benchtop to bedside translational research. This article is categorized under: Biology-Inspired Nanomaterials> Protein and Virus-Based Structures Biology-Inspired Nanomaterials> Nucleic Acid-Based Structures. © 2018 Wiley Periodicals, Inc.

Self-Organization in Coordination-Driven Self-Assembly

PubMed Central

Northrop, Brian H.; Zheng, Yao-Rong; Chi, Ki-Whan; Stang, Peter J.

2009-01-01

Conspectus Self-assembly allows for the preparation of highly complex molecular and supramolecular systems from relatively simple starting materials. Typically, self-assembled supramolecules are constructed by combining complementary pairs of two highly symmetric molecular components, thus limiting the chances of forming unwanted side products. Combining asymmetric molecular components or multiple complementary sets of molecules in one complex mixture can produce myriad different ordered and disordered supramolecular assemblies. Alternatively, spontaneous self-organization phenomena can promote the formation of specific product(s) out of a collection of multiple possibilities. Self-organization processes are common throughout much of nature and are especially common in biological systems. Recently, researchers have studied self-organized self-assembly in purely synthetic systems. This Account describes our investigations of self-organization in the coordination-driven self-assembly of platinum(II)-based metallosupramolecules. The modularity of the coordination-driven approach to self-assembly has allowed us to systematically study a wide variety of different factors that can control the extent of supramolecular self-organization. In particular, we have evaluated the effects of the symmetry and polarity of ambidentate donor subunits, differences in geometrical parameters (e.g. the size, angularity, and dimensionality) of Pt(II)-based acceptors and organic donors, the influence of temperature and solvent, and the effects of intermolecular steric interactions and hydrophobic interactions on self-organization. Our studies have shown that the extent of self-organization in the coordination-driven self-assembly of both 2D polygons and 3D polyhedra ranges from no organization (a statistical mixture of multiple products), to amplified organization (wherein a particular product or products are favored over others), and all the way to the absolute self-organization of

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

WHO: World Health Assembly.

PubMed

McGregor, A

1992-05-23

1200 delegates from 175 member countries attended the 45th World Health Assembly in Geneva. Everyone at the Assembly ratified measures to prevent and control AIDS. 12 countries intended to do long term planning for community based care for AIDS patients. Further the Assembly denounced instances where countries and individuals denied the gravity of the AIDS pandemic. In fact, it expressed the importance for urgent and intensive action against HIV/AIDS. The assembly backed proposals to prevent and control sexually transmitted diseases that affect AIDS patients, especially hepatitis B. For example, in countries with hepatitis B prevalence 8% (many countries in Sub-Sahara Africa, Asia, the Pacific region, and South America), health officials should introduce hepatitis B vaccine into their existing immunization programs by 1995. By 1997, this vaccine should be part of all immunization programs. The Assembly was aware of the obstacles of establishing reliable cold chains for nationwide distribution, however. Delegates in Committee A objected to the fact that 50% of the populations of developing countries continued to have limited access to essential drugs. They also expressed disapproval in implementation of WHO's 1988 ethical criteria for promotion of drugs which WHO entrusted to the Council for International Organisations of Medical Sciences (CIOMS). CIOMS lacked WHO's status and thus could not effectively monitor drug advertising. In fact, the pharmaceutical industry as well as WHO provided the funds for a meeting of 25 experts to discuss principles included in the ethical criteria. At least 4 countries insisted that WHO have the ultimate authority in monitoring drug advertising. Delegates did adopt a compromise resolution on this topic which required that industry promotion methods be reported to the 1994 Assembly via the Executive Board. The Assembly requested WHO to establish an international advisory committee on nursing and midwifery and to improve the network of

Self-assembly of polyelectrolyte surfactant complexes using large scale MD simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby

2014-03-01

Polyelectrolytes (PE) and surfactants are known to form interesting structures with varied properties in aqueous solutions. The morphological details of the PE-surfactant complexes depend on a combination of polymer backbone, electrostatic interactions and hydrophobic interactions. We study the self-assembly of cationic PE and anionic surfactants complexes in dilute condition. The importance of such complexes of PE with oppositely charged surfactants can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate which has applications in industry. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered pearl-necklace structures that have been observed experimentally in biological systems. We investigate many different properties of PE-surfactant complexation for different parameter ranges that are useful for pharmaceutical, engineering and biological applications.

Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

PubMed

Lee, Kyung-Ho; Kim, Dong-Myung

2013-11-01

Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Imaging enzyme-triggered self-assembly of small molecules inside live cells

PubMed Central

Gao, Yuan; Shi, Junfeng; Yuan, Dan; Xu, Bing

2012-01-01

Self-assembly of small molecules in water to form nanofibers, besides generating sophisticated biomaterials, promises a simple system inside cells for regulating cellular processes. But lack of a convenient approach for studying the self-assembly of small molecules inside cells hinders the development of such systems. Here we report a method to image enzyme-triggered self-assembly of small molecules inside live cells. After linking a fluorophore to a self-assembly motif to make a precursor, we confirmed by 31P NMR and rheology that enzyme-triggered conversion of the precursor to a hydrogelator results in the formation of a hydrogel via self-assembly. The imaging contrast conferred by the nanofibers of the hydrogelators allowed the evaluation of intracellular self-assembly; the dynamics, and the localization of the nanofibers of the hydrogelators in live cells. This approach explores supramolecular chemistry inside cells and may lead to new insights, processes, or materials at the interface of chemistry and biology. PMID:22929790

40 CFR 1048.612 - What is the exemption for delegated final assembly?

Code of Federal Regulations, 2012 CFR

2012-07-01

... final assembly? 1048.612 Section 1048.612 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Compliance Provisions § 1048.612 What is the exemption for delegated final assembly? The provisions of 40 CFR 1068.261 related to delegated final assembly apply for engines certified under this part 1048, with the...

40 CFR 1048.612 - What is the exemption for delegated final assembly?

Code of Federal Regulations, 2010 CFR

2010-07-01

... final assembly? 1048.612 Section 1048.612 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Compliance Provisions § 1048.612 What is the exemption for delegated final assembly? The provisions of 40 CFR 1068.261 related to delegated final assembly apply for engines certified under this part 1048, with the...

40 CFR 1048.612 - What is the exemption for delegated final assembly?

Code of Federal Regulations, 2013 CFR

2013-07-01

... final assembly? 1048.612 Section 1048.612 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Compliance Provisions § 1048.612 What is the exemption for delegated final assembly? The provisions of 40 CFR 1068.261 related to delegated final assembly apply for engines certified under this part 1048, with the...

40 CFR 1048.612 - What is the exemption for delegated final assembly?

Code of Federal Regulations, 2011 CFR

2011-07-01

... final assembly? 1048.612 Section 1048.612 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Compliance Provisions § 1048.612 What is the exemption for delegated final assembly? The provisions of 40 CFR 1068.261 related to delegated final assembly apply for engines certified under this part 1048, with the...

40 CFR 1048.612 - What is the exemption for delegated final assembly?

Code of Federal Regulations, 2014 CFR

2014-07-01

... final assembly? 1048.612 Section 1048.612 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Compliance Provisions § 1048.612 What is the exemption for delegated final assembly? The provisions of 40 CFR 1068.261 related to delegated final assembly apply for engines certified under this part 1048, with the...

Diverse Supramolecular Nanofiber Networks Assembled by Functional Low-Complexity Domains.

PubMed

An, Bolin; Wang, Xinyu; Cui, Mengkui; Gui, Xinrui; Mao, Xiuhai; Liu, Yan; Li, Ke; Chu, Cenfeng; Pu, Jiahua; Ren, Susu; Wang, Yanyi; Zhong, Guisheng; Lu, Timothy K; Liu, Cong; Zhong, Chao

2017-07-25

Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multiblock, and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities. We demonstrate the utilities of these networks in the templated, spatially controlled assembly of ligand-decorated gold nanoparticles, quantum dots, nanorods, DNA origami, and hybrid structures. Owing to the distinguishable nanoarchitectures of these nanofibers, this assembly is structure-dependent. By coupling a modular genetic strategy with kinetically controlled complex supramolecular self-assembly, we demonstrate that a single type of protein molecule can be used to engineer diverse one-dimensional supramolecular nanostructures with distinct functionalities.

Hepatitis C Virus Particle Assembly Involves Phosphorylation of NS5A by the c-Abl Tyrosine Kinase.

PubMed

Yamauchi, Shota; Takeuchi, Kenji; Chihara, Kazuyasu; Sun, Xuedong; Honjoh, Chisato; Yoshiki, Hatsumi; Hotta, Hak; Sada, Kiyonao

2015-09-04

Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is thought to regulate the replication of viral RNA and the assembly of virus particles in a serine/threonine phosphorylation-dependent manner. However, the host kinases that phosphorylate NS5A have not been fully identified. Here, we show that HCV particle assembly involves the phosphorylation of NS5A by the c-Abl tyrosine kinase. Pharmacological inhibition or knockdown of c-Abl reduces the production of infectious HCV (J6/JFH1) particles in Huh-7.5 cells without markedly affecting viral RNA translation and replication. NS5A is tyrosine-phosphorylated in HCV-infected cells, and this phosphorylation is also reduced by the knockdown of c-Abl. Mutational analysis reveals that NS5A tyrosine phosphorylation is dependent, at least in part, on Tyr(330) (Tyr(2306) in polyprotein numbering). Mutation of this residue to phenylalanine reduces the production of infectious HCV particles but does not affect the replication of the JFH1 subgenomic replicon. These findings suggest that c-Abl promotes HCV particle assembly by phosphorylating NS5A at Tyr(330). © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Biological control is more than just natural enemies

Treesearch

Dean E. Pearson

2005-01-01

The past decade has given rise to exciting new developments in the field of community ecology that have profound implications for biological control. The recognition that biological invasions offer unprecedented opportunities to investigate the nature of community assembly has swept invasive species studies to the forefront of popular ecology. Meanwhile,...

Terminal Supraparticle Assemblies from Similarly Charged Protein Molecules and Nanoparticles

PubMed Central

Park, Jai Il; Nguyen, Trung Dac; de Queirós Silveira, Gleiciani; Bahng, Joong Hwan; Srivastava, Sudhanshu; Sun, Kai; Zhao, Gongpu; Zhang, Peijun; Glotzer, Sharon C.; Kotov, Nicholas A.

2015-01-01

Self-assembly of proteins and inorganic nanoparticles into terminal assemblies makes possible a large family of uniformly sized hybrid colloids. These particles can be compared in terms of utility, versatility and multifunctionality to other known types of terminal assemblies. They are simple to make and offer theoretical tools for designing their structure and function. To demonstrate such assemblies, we combine cadmium telluride nanoparticles with cytochrome C protein and observe spontaneous formation of spherical supraparticles with a narrow size distribution. Such self-limiting behaviour originates from the competition between electrostatic repulsion and non-covalent attractive interactions. Experimental variation of supraparticle diameters for several assembly conditions matches predictions obtained in simulations. Similar to micelles, supraparticles can incorporate other biological components as exemplified by incorporation of nitrate reductase. Tight packing of nanoscale components enables effective charge and exciton transport in supraparticles as demonstrated by enzymatic nitrate reduction initiated by light absorption in the nanoparticle. PMID:24845400

Lipid membrane-assisted condensation and assembly of amphiphilic Janus particles

DOE PAGES

Chambers, Mariah; Mallory, Stewart Anthony; Malone, Heather; ...

2016-01-01

Amphiphilic Janus particles self-assemble into complex metastructures, but little is known about how their assembly might be modified by weak interactions with a nearby biological membrane surface. Here, we report an integrated experimental and molecular dynamics simulation study to investigate the self-assembly of amphiphilic Janus particles on a lipid membrane. We created an experimental system in which Janus particles are allowed to self-assemble in the same medium where zwitterionic lipids form giant unilamellar vesicles (GUVs). Janus particles spontaneously concentrated on the inner leaflet of the GUVs. They exhibited biased orientation and heterogeneous rotational dynamics as revealed by single particle rotationalmore » tracking. The combined experimental and simulation results show that Janus particles concentrate on the lipid membranes due to weak particle–lipid attraction, whereas the biased orientation of particles is driven predominantly by inter-particle interactions. Furthermore, this study demonstrates the potential of using lipid membranes to influence the self-assembly of Janus particles.« less

Self-Assembled Peptide-Lanthanide Nanoclusters for Safe Tumor Therapy: Overcoming and Utilizing Biological Barriers to Peptide Drug Delivery.

PubMed

Yan, Jin; He, Wangxiao; Yan, Siqi; Niu, Fan; Liu, Tianya; Ma, Bohan; Shao, Yongping; Yan, Yuwei; Yang, Guang; Lu, Wuyuan; Du, Yaping; Lei, Bo; Ma, Peter X

2018-02-27

Developing a sophisticated nanomedicine platform to deliver therapeutics effectively and safely into tumor/cancer cells remains challenging in the field of nanomedicine. In particular, reliable peptide drug delivery systems capable of overcoming biological barriers are still lacking. Here, we developed a simple, rapid, and robust strategy to manufacture nanoclusters of ∼90 nm in diameter that are self-assembled from lanthanide-doped nanoparticles (5 nm), two anticancer peptides with different targets (BIM and PMI), and one cyclic peptide iNGR targeted to cancer cells. The peptide-lanthanide nanoclusters (LDC-PMI-BIM-iNGR) enhanced the resistance of peptide drugs to proteolysis, disassembled in response to reductive conditions that are present in the tumor microenvironment and inhibited cancer cell growth in vitro and in vivo. Notably, LDC-PMI-BIM-iNGR exhibited extremely low systemic toxicity and side effects in vivo. Thus, the peptide-lanthanide nanocluster may serve as an ideal multifunctional platform for safe, targeted, and efficient peptide drug delivery in cancer therapy.

Light-activated control of protein channel assembly mediated by membrane mechanics

NASA Astrophysics Data System (ADS)

Miller, David M.; Findlay, Heather E.; Ces, Oscar; Templer, Richard H.; Booth, Paula J.

2016-12-01

Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.

Assembly considerations for large reflectors

NASA Technical Reports Server (NTRS)

Bush, H.

1988-01-01

The technologies developed at LaRC in the area of erectable instructures are discussed. The information is of direct value to the Large Deployable Reflector (LDR) because an option for the LDR backup structure is to assemble it in space. The efforts in this area, which include development of joints, underwater assembly simulation tests, flight assembly/disassembly tests, and fabrication of 5-meter trusses, led to the use of the LaRC concept as the baseline configuration for the Space Station Structure. The Space Station joint is linear in the load and displacement range of interest to Space Station; the ability to manually assemble and disassemble a 45-foot truss structure was demonstrated by astronauts in space as part of the ACCESS Shuttle Flight Experiment. The structure was built in 26 minutes 46 seconds, and involved a total of 500 manipulations of untethered hardware. Also, the correlation of the space experience with the neutral buoyancy simulation was very good. Sections of the proposed 5-meter bay Space Station truss have been built on the ground. Activities at LaRC have included the development of mobile remote manipulator systems (which can traverse the Space Station 5-meter structure), preliminary LDR sun shield concepts, LDR construction scenarios, and activities in robotic assembly of truss-type structures.

Neutronics Investigations for the Lower Part of a Westinghouse SVEA-96+ Assembly

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

Murphy, M.F.; Luethi, A.; Seiler, R.

2002-05-15

Accurate critical experiments have been performed for the validation of total fission (F{sub tot}) and {sup 238}U-capture (C{sub 8}) reaction rate distributions obtained with CASMO-4, HELIOS, BOXER, and MCNP4B for the lower axial region of a real Westinghouse SVEA-96+ fuel assembly. The assembly comprised fresh fuel with an average {sup 235}U enrichment of 4.02 wt%, a maximum enrichment of 4.74 wt%, 14 burnable-absorber fuel pins, and full-density water moderation. The experimental configuration investigated was core 1A of the LWR-PROTEUS Phase I project, where 61 different fuel pins, representing {approx}64% of the assembly, were gamma-scanned individually. Calculated (C) and measured (E)more » values have been compared in terms of C/E distributions. For F{sub tot}, the standard deviations are 1.2% for HELIOS, 0.9% for CASMO-4, 0.8% for MCNP4B, and 1.7% for BOXER. Standard deviations of 1.1% for HELIOS, CASMO-4, and MCNP4B and 1.2% for BOXER were obtained in the case of C{sub 8}. Despite the high degree of accuracy observed on the average, it was found that the five burnable-absorber fuel pins investigated showed a noticeable underprediction of F{sub tot}, quite systematically, for the deterministic codes evaluated (average C/E for the burnable-absorber fuel pins in the range 0.974 to 0.988, depending on the code)« less

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

PubMed Central

Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

2011-01-01

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

The Assembly of Cell-Encapsulating Microscale Hydrogels Using Acoustic Waves

PubMed Central

Xu, Feng; Finley, Thomas Dylan; Turkaydin, Muge; Sung, Yuree; Gurkan, Umut Atakan; Yavuz, Ahmet Sinan; Guldiken, Rasim; Demirci, Utkan

2011-01-01

Microscale hydrogels find widespread applications in medicine and biology, e.g., as building blocks for tissue engineering and regenerative medicine. In these applications, these microgels are assembled to fabricate large complex 3D constructs. The success of this approach requires non-destructive and high throughput assembly of the microgels. Although various assembly methods have been developed based on modifying interfaces, and using microfluidics, so far, none of the available assembly technologies have shown the ability to assembly microgels using non-invasive fields rapidly within seconds in an efficient way. Acoustics has been widely used in biomedical area to manipulatedroplets, cells and biomolecules. In this study, we developed a simple, non-invasiveacoustic assembler for cell-encapsulating microgels with maintained cell viability (>93%). We assessed the assembler for both microbeads (with diameter of 50 µm and 100 µm) and microgels of different sizes and shapes (e.g., cubes, lock-and-key shapes, tetris, saw) in microdroplets (with volume of 10 µL, 20 µL, 40 µL, 80 µL). The microgels were assembled in second sin a non-invasive manner. These results indicate that the developed acoustic approach could become an enabling biotechnology tool for tissue engineering, regenerative medicine, pharmacology studies and high throughput screening applications. PMID:21820734

Three-dimensional fit-to-flow microfluidic assembly.

PubMed

Chen, Arnold; Pan, Tingrui

2011-12-01

Three-dimensional microfluidics holds great promise for large-scale integration of versatile, digitalized, and multitasking fluidic manipulations for biological and clinical applications. Successful translation of microfluidic toolsets to these purposes faces persistent technical challenges, such as reliable system-level packaging, device assembly and alignment, and world-to-chip interface. In this paper, we extended our previously established fit-to-flow (F2F) world-to-chip interconnection scheme to a complete system-level assembly strategy that addresses the three-dimensional microfluidic integration on demand. The modular F2F assembly consists of an interfacial chip, pluggable alignment modules, and multiple monolithic layers of microfluidic channels, through which convoluted three-dimensional microfluidic networks can be easily assembled and readily sealed with the capability of reconfigurable fluid flow. The monolithic laser-micromachining process simplifies and standardizes the fabrication of single-layer pluggable polymeric modules, which can be mass-produced as the renowned Lego(®) building blocks. In addition, interlocking features are implemented between the plug-and-play microfluidic chips and the complementary alignment modules through the F2F assembly, resulting in facile and secure alignment with average misalignment of 45 μm. Importantly, the 3D multilayer microfluidic assembly has a comparable sealing performance as the conventional single-layer devices, providing an average leakage pressure of 38.47 kPa. The modular reconfigurability of the system-level reversible packaging concept has been demonstrated by re-routing microfluidic flows through interchangeable modular microchannel layers.

The mathematics of virus shell assembly. Progress report 1995--1996

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

Berger, B.

1996-08-01

This research focuses on applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding. Significant progress has been made in the following areas relating to virus shell assembly: the local rules theory has been further developed; development has begun on a second-generation simulator which provides a more physically realistic model of assembly, collaborative efforts have continued with an experimental biologist to verify and inspire the local rules theory; an investigation has been initiated into the mechanics of virus shell assembly; laboratory experiments have been conducted on bacteriophage T4 which verify that the previouslymore » believed structure for the core may be incorrect.« less

Reversible Self-Assembly of 3D Architectures Actuated by Responsive Polymers.

PubMed

Zhang, Cheng; Su, Jheng-Wun; Deng, Heng; Xie, Yunchao; Yan, Zheng; Lin, Jian

2017-11-29

An assembly of three-dimensional (3D) architectures with defined configurations has important applications in broad areas. Among various approaches of constructing 3D structures, a stress-driven assembly provides the capabilities of creating 3D architectures in a broad range of functional materials with unique merits. However, 3D architectures built via previous methods are simple, irreversible, or not free-standing. Furthermore, the substrates employed for the assembly remain flat, thus not involved as parts of the final 3D architectures. Herein, we report a reversible self-assembly of various free-standing 3D architectures actuated by the self-folding of smart polymer substrates with programmed geometries. The strategically designed polymer substrates can respond to external stimuli, such as organic solvents, to initiate the 3D assembly process and subsequently become the parts of the final 3D architectures. The self-assembly process is highly controllable via origami and kirigami designs patterned by direct laser writing. Self-assembled geometries include 3D architectures such as "flower", "rainbow", "sunglasses", "box", "pyramid", "grating", and "armchair". The reported self-assembly also shows wide applicability to various materials including epoxy, polyimide, laser-induced graphene, and metal films. The device examples include 3D architectures integrated with a micro light-emitting diode and a flex sensor, indicting the potential applications in soft robotics, bioelectronics, microelectromechanical systems, and others.

Self-Assembly of Nanoparticles and Origin of Life

NASA Astrophysics Data System (ADS)

Kotov, Nicholas

Inorganic nanoparticles (NPs) have the ability to self-organize into variety of extended and terminal structures, as do many molecular and nanoscale compounds, given a sufficient number of translational and rotational degrees of freedom. Analysis of experimental data for all NPs (metal, semiconductor, ceramic ..) indicate a general trend of self-assembly under a much wider range of conditions and having much broader structural variability than building blocks from organic matter. Remarkably, the internal organization of self-assembled structures spontaneously produced by NPs rival in complexity and functional sophistication to those found in biology. Multiscale collective effects make NP-NP interactions no less fascinating than those of naturally occurring proteins. In this talk, I will address the following questions: 1. What are the differences and similarities of NP self-organization compared with similar phenomena involving organic and biological building blocks? 2. What are the forces and related theoretical assumptions essential for NP interactions? 3. What is the significance of NP self-assembly for understanding emergence of life? In this context, self-organization of chiral nanostructures will illustrate the importance of subtle anisotropic effects stemming from collective behavior of NPs and non-additivity of their interactions. Chirality transfer from circularly-polarized photons to NPs and its relationship to the origin of homochirality on Earth, spontaneous compartmentalization (protocells), and out-of-equilibrium chemical synthesis in nanoassemblies.

The self-assembled behavior of DNA bases on the interface.

PubMed

Liu, Lei; Xia, Dan; Klausen, Lasse H; Dong, Mingdong

2014-01-27

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

The Self-Assembled Behavior of DNA Bases on the Interface

PubMed Central

Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

2014-01-01

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

The logic of automated glycan assembly.

PubMed

Seeberger, Peter H

2015-05-19

Carbohydrates are the most abundant biopolymers on earth and part of every living creature. Glycans are essential as materials for nutrition and for information transfer in biological processes. To date, in few cases a detailed correlation between glycan structure and glycan function has been established. A molecular understanding of glycan function will require pure glycans for biological, immunological, and structural studies. Given the immense structural complexity of glycans found in living organisms and the lack of amplification methods or expression systems, chemical synthesis is the only means to access usable quantities of pure glycan molecules. While the solid-phase synthesis of DNA and peptides has become routine for decades, access to glycans has been technically difficult, time-consuming and confined to a few expert laboratories. In this Account, the development of a comprehensive approach to the automated synthesis of all classes of mammalian glycans, including glycosaminoglycans and glycosylphosphatidyl inositol (GPI) anchors, as well as bacterial and plant carbohydrates is described. A conceptual advance concerning the logic of glycan assembly was required in order to enable automated execution of the synthetic process. Based on the central glycosidic bond forming reaction, a general concept for the protecting groups and leaving groups has been developed. Building blocks that can be procured on large scale, are stable for prolonged periods of time, but upon activation result in high yields and selectivities were identified. A coupling-capping and deprotection cycle was invented that can be executed by an automated synthesis instrument. Straightforward postsynthetic protocols for cleavage from the solid support as well as purification of conjugation-ready oligosaccharides have been established. Introduction of methods to install selectively a wide variety of glycosidic linkages has enabled the rapid assembly of linear and branched oligo- and

Amorphous Metals and Composites as Mirrors and Mirror Assemblies

NASA Technical Reports Server (NTRS)

Hofmann, Douglas C. (Inventor); Davis, Gregory L. (Inventor); Agnes, Gregory S. (Inventor); Shapiro, Andrew A. (Inventor)

2016-01-01

A mirror or mirror assembly fabricated by molding, pressing, assembling, or depositing one or more bulk metal glass (BMG), bulk metal glass composite (BMGMC), or amorphous metal (AM) parts and where the optical surface and backing of the mirror can be fabricated without machining or polishing by utilizing the unique molding capabilities of this class of materials.

Electrochemical assembly of organic molecules by the reduction of iodonium salts

DOEpatents

Dirk, Shawn M [Albuquerque, NM; Howell, Stephen W [Albuquerque, NM; Wheeler, David R [Albuquerque, NM

2009-06-23

Methods are described for the electrochemical assembly of organic molecules on silicon, or other conducting or semiconducting substrates, using iodonium salt precursors. Iodonium molecules do not assemble on conducting surfaces without a negative bias. Accordingly, the iodonium salts are preferred for patterning applications that rely on direct writing with negative bias. The stability of the iodonium molecule to acidic conditions allows them to be used with standard silicon processing. As a directed assembly process, the use of iodonium salts provides for small features while maintaining the ability to work on a surface and create structures on a wafer level. Therefore, the process is amenable for mass production. Furthermore, the assembled monolayer (or multilayer) is chemically robust, allowing for subsequent chemical manipulations and the introduction of various molecular functionalities for various chemical and biological applications.

Seeing Circuits Assemble

PubMed Central

Lichtman, Jeff W.; Smith, Stephen J.

2009-01-01

Developmental neurobiology has been greatly invigorated by a recent string of breakthroughs in molecular biology and optical physics that permit direct in vivo observation of neural circuit assembly. The imaging done thus far suggests that as brains are built, a significant amount of unbuilding is also occurring. We offer the view that this tumult is the result of the intersecting behaviors of the many single-celled creatures (i.e., neurons, glia, and progenitors) that inhabit brains. New tools will certainly be needed if we wish to monitor the myriad cooperative and competitive interactions at play in the cellular society that builds brains. PMID:18995818

Cell-cycle regulation of formin-mediated actin cable assembly

PubMed Central

Miao, Yansong; Wong, Catherine C. L.; Mennella, Vito; Michelot, Alphée; Agard, David A.; Holt, Liam J.; Yates, John R.; Drubin, David G.

2013-01-01

Assembly of appropriately oriented actin cables nucleated by formin proteins is necessary for many biological processes in diverse eukaryotes. However, compared with knowledge of how nucleation of dendritic actin filament arrays by the actin-related protein-2/3 complex is regulated, the in vivo regulatory mechanisms for actin cable formation are less clear. To gain insights into mechanisms for regulating actin cable assembly, we reconstituted the assembly process in vitro by introducing microspheres functionalized with the C terminus of the budding yeast formin Bni1 into extracts prepared from yeast cells at different cell-cycle stages. EM studies showed that unbranched actin filament bundles were reconstituted successfully in the yeast extracts. Only extracts enriched in the mitotic cyclin Clb2 were competent for actin cable assembly, and cyclin-dependent kinase 1 activity was indispensible. Cyclin-dependent kinase 1 activity also was found to regulate cable assembly in vivo. Here we present evidence that formin cell-cycle regulation is conserved in vertebrates. The use of the cable-reconstitution system to test roles for the key actin-binding proteins tropomyosin, capping protein, and cofilin provided important insights into assembly regulation. Furthermore, using mass spectrometry, we identified components of the actin cables formed in yeast extracts, providing the basis for comprehensive understanding of cable assembly and regulation. PMID:24133141

Oxygen Generation Assembly Technology Development

NASA Technical Reports Server (NTRS)

Bagdigian, Robert; Cloud, Dale

1999-01-01

Hamilton Standard Space Systems International (HSSI) is under contract to NASA Marshall Space Flight Center (MSFC) to develop an Oxygen Generation Assembly (OGA) for the International Space Station (ISS). The International Space Station Oxygen Generation Assembly (OGA) electrolyzes potable water from the Water Recovery System (WRS) to provide gaseous oxygen to the Space Station module atmosphere. The OGA produces oxygen for metabolic consumption by crew and biological specimens. The OGA also replenishes oxygen lost by experiment ingestion, airlock depressurization, CO2 venting, and leakage. As a byproduct, gaseous hydrogen is generated. The hydrogen will be supplied at a specified pressure range above ambient to support future utilization. Initially, the hydrogen will be vented overboard to space vacuum. This paper describes the OGA integration into the ISS Node 3. It details the development history supporting the design and describes the OGA System characteristics and its physical layout.

Artificial transmembrane ion channels from self-assembling peptide nanotubes

NASA Astrophysics Data System (ADS)

Ghadiri, M. Reza; Granja, Juan R.; Buehler, Lukas K.

1994-05-01

NATURALLY occurring membrane channels and pores are formed from a large family of diverse proteins, peptides and organic secon-dary metabolites whose vital biological functions include control of ion flow, signal transduction, molecular transport and produc-tion of cellular toxins. But despite the availability of a large amount of biochemical information about these molecules1, the design and synthesis of artificial systems that can mimic the bio-logical function of natural compounds remains a formidable task2-12. Here we present a simple strategy for the design of artifi-cial membrane ion channels based on a self-assembled cylindrical β-sheet peptide architecture13. Our systems-essentially stacks of peptide rings-display good channel-mediated ion-transport activ-ity with rates exceeding 107 ions s-1, rivalling the performance of many naturally occurring counterparts. Such molecular assemblies should find use in the design of novel cytotoxic agents, membrane transport vehicles and drug-delivery systems.

Coordinate Transformation Assembly

NASA Astrophysics Data System (ADS)

Huang, C.-C.; Barney, J.

1983-08-01

The coordinate transformation assembly (CTA) is a non-contact electro-optical device designed to link the angular coordinates between two remote platforms to a high degree of accuracy. Each assembly, which is compact and without moving parts, consists of two units: the transmitter and the receiver. The transmitter consists of one polarizing beamsplitter and two laser diodes with polarized output. The receiver consists of a polarizing beam-splitter, two lenses, a dual-axis photodetector and a regular photodetector. The angular roll is measured about the line-of-sight between two assemblies using a polarizing sensing method. Accuracy is calculated to be better than 0.01 degrees with a signal-to-noise ratio of 35 db. Pitch and yaw are measured relative to the line-of-sight at each assembly by locating a laser spot in the field-of-view of a dual-axis photodetector located in the focal plane of a small lens. The coordinate transformation parameter most difficult to obtain is the roll coordinate because high resolution involves observing a small variation in the difference of two strong signals. Under such an arrangement, any variation in source strength or detector sensitivity will cause an error. In the scheme devised for the CTA, this source of error has been eliminated through a paring and signal processing arrangement wherein the detector sensitivity and the source intensity are made common to the paired measurements and thus eliminated. The ±0.01 degree accuracy of the angular roll as well as the pitch and yaw measurements over ±2 degrees angular range has been demonstrated. An attractive feature of the CTA is that paired assemblies can be deployed to relay coordinates around corners and over extended distances.

The Assembly-Activating Protein Promotes Stability and Interactions between AAV's Viral Proteins to Nucleate Capsid Assembly.

PubMed

Maurer, Anna C; Pacouret, Simon; Cepeda Diaz, Ana Karla; Blake, Jessica; Andres-Mateos, Eva; Vandenberghe, Luk H

2018-05-08

The adeno-associated virus (AAV) vector is a preferred delivery platform for in vivo gene therapy. Natural and engineered variations of the AAV capsid affect a plurality of phenotypes relevant to gene therapy, including vector production and host tropism. Fundamental to these aspects is the mechanism of AAV capsid assembly. Here, the role of the viral co-factor assembly-activating protein (AAP) was evaluated in 12 naturally occurring AAVs and 9 putative ancestral capsid intermediates. The results demonstrate increased capsid protein stability and VP-VP interactions in the presence of AAP. The capsid's dependence on AAP can be partly overcome by strengthening interactions between monomers within the assembly, as illustrated by the transfer of a minimal motif defined by a phenotype-to-phylogeny mapping method. These findings suggest that the emergence of AAP within the Dependovirus genus relaxes structural constraints on AAV assembly in favor of increasing the degrees of freedom for the capsid to evolve. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Visualization of Bacterial Microcompartment Facet Assembly Using High-Speed Atomic Force Microscopy

DOE PAGES

Sutter, Markus; Faulkner, Matthew; Aussignargues, Clément; ...

2015-11-30

Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla. They compartmentalize enzymes within a selectively permeable shell and play important roles in CO 2 fixation, pathogenesis, and microbial ecology. Here, we combine X-ray crystallography and high-speed atomic force microscopy to characterize, at molecular resolution, the structure and dynamics of BMC shell facet assembly. Our results show that preformed hexamers assemble into uniformly oriented shell layers, a single hexamer thick. We also observe the dynamic process of shell facet assembly. Shell hexamers can dissociate from and incorporate into assembled sheets, indicating a flexible intermolecular interaction. Furthermore, we demonstrate that themore » self-assembly and dynamics of shell proteins are governed by specific contacts at the interfaces of shell proteins. Our study provides novel insights into the formation, interactions, and dynamics of BMC shell facets, which are essential for the design and engineering of self-assembled biological nanoreactors and scaffolds based on BMC architectures.« less

Controlled surface-induced flows from the motion of self-assembled colloidal walkers.

PubMed

Sing, Charles E; Schmid, Lothar; Schneider, Matthias F; Franke, Thomas; Alexander-Katz, Alfredo

2010-01-12

Biological flows at the microscopic scale are important for the transport of nutrients, locomotion, and differentiation. Here, we present a unique approach for creating controlled, surface-induced flows inspired by a ubiquitous biological system, cilia. Our design is based on a collection of self-assembled colloidal rotors that "walk" along surfaces in the presence of a rotating magnetic field. These rotors are held together solely by magnetic forces that allow for reversible assembly and disassembly of the chains. Furthermore, rotation of the magnetic field allows for straightforward manipulation of the shape and motion of these chains. This system offers a simple and versatile approach for designing microfluidic devices as well as for studying fundamental questions in cooperative-driven motion and transport at the microscopic level.

Building block synthesis using the polymerase chain assembly method.

PubMed

Marchand, Julie A; Peccoud, Jean

2012-01-01

De novo gene synthesis allows the creation of custom DNA molecules without the typical constraints of traditional cloning assembly: scars, restriction site incompatibility, and the quest to find all the desired parts to name a few. Moreover, with the help of computer-assisted design, the perfect DNA molecule can be created along with its matching sequence ready to download. The challenge is to build the physical DNA molecules that have been designed with the software. Although there are several DNA assembly methods, this section presents and describes a method using the polymerase chain assembly (PCA).

jsc2018m000297_Investigation_Seeks_to_Create_Self-Assembling_Materials-MP4

NASA Image and Video Library

2018-05-14

Investigation Seeks to Create Self-Assembling Materials------ As we travel farther into space, clever solutions to problems like engine part malfunctions and other possible mishaps will be a vital part of the planning process. 3D printing, or additive manufacturing, is an emerging technology that may be used to custom-create mission-critical parts. An integral piece of this process is understanding how particle shape, size distribution and packing behavior affect the manufacturing process. The Advanced Colloids Experiment-Temperature-7 investigation (ACE-T-7) aboard the International Space Station explores the feasibility of creating self-assembling microscopic particles for use in the manufacturing of materials during spaceflight. Read more about ACE-T-& here: https://www.nasa.gov/feature/investigation-seeks-to-create-self-assembling-materials

Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare.

ERIC Educational Resources Information Center

Tribe, Michael; Pritchard, Alan J.

This five-chapter document (part of a series on biology and human welfare) focuses on biological systems as energy sources and on the teaching of this subject area. Chapter 1 discusses various topics related to energy and ecology, including biomass, photosynthesis and world energy balances, energy flow through ecosystems, and others. Chapter 2…

Comparison of multiple gene assembly methods for metabolic engineering

Treesearch

Chenfeng Lu; Karen Mansoorabadi; Thomas Jeffries

2007-01-01

A universal, rapid DNA assembly method for efficient multigene plasmid construction is important for biological research and for optimizing gene expression in industrial microbes. Three different approaches to achieve this goal were evaluated. These included creating long complementary extensions using a uracil-DNA glycosylase technique, overlap extension polymerase...

The polymeric nanofilm of triazinedithiolsilane fabricated by self-assembled technique on copper surface. Part 2: Characterization of composition and morphology

NASA Astrophysics Data System (ADS)

Wang, Yabin; Liu, Zhong; Huang, Yudong; Qi, Yutai

2015-11-01

In the first part, a novel design route for metal protection against corrosion was proposed, and a class of triazinedithiolsilane compounds was conceived as protector for copper. The protective capability of the polymeric nanofilm, fabricated by self-assembling one representative (abbreviated as TESPA) of triazinedithiolsilane compounds onto copper surface, has been investigated and evaluated by electrochemical tests. The results show that the polymeric nanofilm significantly inhibits copper corrosion. This study, on the one hand, concentrates on the chemical composition of the TESPA polymeric nanofilm by means of X-ray photoelectron spectroscopy (XPS). The XPS results reveal that the chemical bonds between copper and TESPA monomers, three dimensional disulfide units and siloxane networks are responsible for the satisfactory protection of TESPA polymeric nanofilm against copper corrosion. On the other hand, scanning electron microscope (SEM) and energy-dispersive spectroscopy (EDS) are utilized to reveal the morphology and the uniformity of the TESPA polymeric nanofilm. The SEM-EDS results demonstrate that the copper surfaces are uniformly covered with TESPA self-assembled monolayer and the polymeric nanofilm. The TESPA-covered copper surfaces turn out to be smoother than that of the bare copper surface.

AND/OR graph representation of assembly plans

NASA Astrophysics Data System (ADS)

Homem de Mello, Luiz S.; Sanderson, Arthur C.

1990-04-01

A compact representation of all possible assembly plans of a product using AND/OR graphs is presented as a basis for efficient planning algorithms that allow an intelligent robot to pick a course of action according to instantaneous conditions. The AND/OR graph is equivalent to a state transition graph but requires fewer nodes and simplifies the search for feasible plans. Three applications are discussed: (1) the preselection of the best assembly plan, (2) the recovery from execution errors, and (3) the opportunistic scheduling of tasks. An example of an assembly with four parts illustrates the use of the AND/OR graph representation in assembly-plan preselection, based on the weighting of operations according to complexity of manipulation and stability of subassemblies. A hypothetical error situation is discussed to show how a bottom-up search of the AND/OR graph leads to an efficient recovery.

AND/OR graph representation of assembly plans

NASA Technical Reports Server (NTRS)

Homem De Mello, Luiz S.; Sanderson, Arthur C.

1990-01-01

A compact representation of all possible assembly plans of a product using AND/OR graphs is presented as a basis for efficient planning algorithms that allow an intelligent robot to pick a course of action according to instantaneous conditions. The AND/OR graph is equivalent to a state transition graph but requires fewer nodes and simplifies the search for feasible plans. Three applications are discussed: (1) the preselection of the best assembly plan, (2) the recovery from execution errors, and (3) the opportunistic scheduling of tasks. An example of an assembly with four parts illustrates the use of the AND/OR graph representation in assembly-plan preselection, based on the weighting of operations according to complexity of manipulation and stability of subassemblies. A hypothetical error situation is discussed to show how a bottom-up search of the AND/OR graph leads to an efficient recovery.

Self-organization: the fundament of cell biology

PubMed Central

Betz, Timo

2018-01-01

Self-organization refers to the emergence of an overall order in time and space of a given system that results from the collective interactions of its individual components. This concept has been widely recognized as a core principle in pattern formation for multi-component systems of the physical, chemical and biological world. It can be distinguished from self-assembly by the constant input of energy required to maintain order—and self-organization therefore typically occurs in non-equilibrium or dissipative systems. Cells, with their constant energy consumption and myriads of local interactions between distinct proteins, lipids, carbohydrates and nucleic acids, represent the perfect playground for self-organization. It therefore comes as no surprise that many properties and features of self-organized systems, such as spontaneous formation of patterns, nonlinear coupling of reactions, bi-stable switches, waves and oscillations, are found in all aspects of modern cell biology. Ultimately, self-organization lies at the heart of the robustness and adaptability found in cellular and organismal organization, and hence constitutes a fundamental basis for natural selection and evolution. This article is part of the theme issue ‘Self-organization in cell biology’. PMID:29632257

Proton-Fueled, Reversible DNA Hybridization Chain Assembly for pH Sensing and Imaging.

PubMed

Liu, Lan; Liu, Jin-Wen; Huang, Zhi-Mei; Wu, Han; Li, Na; Tang, Li-Juan; Jiang, Jian-Hui

2017-07-05

Design of DNA self-assembly with reversible responsiveness to external stimuli is of great interest for diverse applications. We for the first time develop a pH-responsive, fully reversible hybridization chain reaction (HCR) assembly that allows sensitive sensing and imaging of pH in living cells. Our design relies on the triplex forming sequences that form DNA triplex with toehold regions under acidic conditions and then induce a cascade of strand displacement and DNA assembly. The HCR assembly has shown dynamic responses in physiological pH ranges with excellent reversibility and demonstrated the potential for in vitro detection and live-cell imaging of pH. Moreover, this method affords HCR assemblies with highly localized fluorescence responses, offering advantages of improving sensitivity and better selectivity. The proton-fueled, reversible HCR assembly may provide a useful approach for pH-related cell biology study and disease diagnostics.

GFinisher: a new strategy to refine and finish bacterial genome assemblies

NASA Astrophysics Data System (ADS)

Guizelini, Dieval; Raittz, Roberto T.; Cruz, Leonardo M.; Souza, Emanuel M.; Steffens, Maria B. R.; Pedrosa, Fabio O.

2016-10-01

Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

GFinisher: a new strategy to refine and finish bacterial genome assemblies.

PubMed

Guizelini, Dieval; Raittz, Roberto T; Cruz, Leonardo M; Souza, Emanuel M; Steffens, Maria B R; Pedrosa, Fabio O

2016-10-10

Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.

Peptide assemblies: from cell scaffolds to immune adjuvants

NASA Astrophysics Data System (ADS)

Collier, Joel

2011-03-01

This talk will discuss two interrelated aspects of peptide self-assemblies in biological applications: their use as matrices for regenerative medicine, and their use as chemically defined adjuvants for directing immune responses against engineered antigens. In the first half of the presentation, the design of peptide self-assemblies as analogues for the extracellular matrix will be described, with a focus on self-assemblies displaying multiple different cell-binding peptides. We conducted multi-factorial investigations of peptide co-assemblies containing several different ligand-bearing peptides using statistical ``design of experiments'' (DoE). Using the DoE techniques of factorial experimentation and response surface modeling, we systematically explored how precise combinations of ligand-bearing peptides modulated endothelial cell growth, in the process finding interactions between ligands not previously appreciated. By investigating immune responses against the materials intended for tissue engineering applications, we discovered that the basic self-assembling peptides were minimally immunogenic or non-immunogenic, even when delivered in strong adjuvants. -But when they were appended to an appropriately restricted epitope peptide, these materials raised strong and persistent antibody responses. These responses were dependent on covalent conjugation between the epitope and self-assembling domains of the peptides, were mediated by T cells, and could be directed towards both peptide epitopes and conjugated protein antigens. In addition to their demonstrated utility as scaffolds for regenerative medicine, peptide self-assemblies may also be useful as chemically defined adjuvants for vaccines and immunotherapies. This work was funded by NIH/NIDCR (1 R21 DE017703-03), NIH/NIBIB (1 R01 EB009701-01), and NSF (CHE-0802286).

Synthetic biology engineering of biofilms as nanomaterials factories.

PubMed

Nguyen, Peter Q

2017-06-15

Bottom-up fabrication of nanoscale materials has been a significant focus in materials science for expanding our technological frontiers. This assembly concept, however, is old news to biology - all living organisms fabricate themselves using bottom-up principles through a vast self-organizing system of incredibly complex biomolecules, a marvelous dynamic that we are still attempting to unravel. Can we use what we have gleaned from biology thus far to illuminate alternative strategies for designer nanomaterial manufacturing? In the present review article, new synthetic biology efforts toward using bacterial biofilms as platforms for the synthesis and secretion of programmable nanomaterials are described. Particular focus is given to self-assembling functional amyloids found in bacterial biofilms as re-engineerable modular nanomolecular components. Potential applications and existing challenges for this technology are also explored. This novel approach for repurposing biofilm systems will enable future technologies for using engineered living systems to grow artificial nanomaterials. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

PubMed

Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Advanced composite applications for sub-micron biologically derived microstructures

NASA Technical Reports Server (NTRS)

Schnur, J. M.; Price, R. R.; Schoen, P. E.; Bonanventura, Joseph; Kirkpatrick, Douglas

1991-01-01

A major thrust of advanced material development is in the area of self-assembled ultra-fine particulate based composites (micro-composites). The application of biologically derived, self-assembled microstructures to form advanced composite materials is discussed. Hollow 0.5 micron diameter cylindrical shaped microcylinders self-assemble from diacetylenic lipids. These microstructures have a multiplicity of potential applications in the material sciences. Exploratory development is proceeding in application areas such as controlled release for drug delivery, wound repair, and biofouling as well as composites for electronic and magnetic applications, and high power microwave cathodes.

Interrogating viral capsid assembly with ion mobility-mass spectrometry

NASA Astrophysics Data System (ADS)

Uetrecht, Charlotte; Barbu, Ioana M.; Shoemaker, Glen K.; van Duijn, Esther; Heck, Albert J. R.

2011-02-01

Most proteins fulfil their function as part of large protein complexes. Surprisingly, little is known about the pathways and regulation of protein assembly. Several viral coat proteins can spontaneously assemble into capsids in vitro with morphologies identical to the native virion and thus resemble ideal model systems for studying protein complex formation. Even for these systems, the mechanism for self-assembly is still poorly understood, although it is generally thought that smaller oligomeric structures form key intermediates. This assembly nucleus and larger viral assembly intermediates are typically low abundant and difficult to monitor. Here, we characterised small oligomers of Hepatitis B virus (HBV) and norovirus under equilibrium conditions using native ion mobility mass spectrometry. This data in conjunction with computational modelling enabled us to elucidate structural features of these oligomers. Instead of more globular shapes, the intermediates exhibit sheet-like structures suggesting that they are assembly competent. We propose pathways for the formation of both capsids.

Collaborated measurement of three-dimensional position and orientation errors of assembled miniature devices with two vision systems

NASA Astrophysics Data System (ADS)

Wang, Xiaodong; Zhang, Wei; Luo, Yi; Yang, Weimin; Chen, Liang

2013-01-01

In assembly of miniature devices, the position and orientation of the parts to be assembled should be guaranteed during or after assembly. In some cases, the relative position or orientation errors among the parts can not be measured from only one direction using visual method, because of visual occlusion or for the features of parts located in a three-dimensional way. An automatic assembly system for precise miniature devices is introduced. In the modular assembly system, two machine vision systems were employed for measurement of the three-dimensionally distributed assembly errors. High resolution CCD cameras and high position repeatability precision stages were integrated to realize high precision measurement in large work space. The two cameras worked in collaboration in measurement procedure to eliminate the influence of movement errors of the rotational or translational stages. A set of templates were designed for calibration of the vision systems and evaluation of the system's measurement accuracy.

Elastic-Plastic Nonlinear Response of a Space Shuttle External Tank Stringer. Part 1; Stringer-Feet Imperfections and Assembly

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Song, Kyongchan; Elliott, Kenny B.; Raju, Ivatury S.; Warren, Jerry E.

2012-01-01

Elastic-plastic, large-deflection nonlinear stress analyses are performed for the external hat-shaped stringers (or stiffeners) on the intertank portion of the Space Shuttle s external tank. These stringers are subjected to assembly strains when the stringers are initially installed on an intertank panel. Four different stringer-feet configurations including the baseline flat-feet, the heels-up, the diving-board, and the toes-up configurations are considered. The assembly procedure is analytically simulated for each of these stringer configurations. The location, size, and amplitude of the strain field associated with the stringer assembly are sensitive to the assumed geometry and assembly procedure. The von Mises stress distributions from these simulations indicate that localized plasticity will develop around the first eight fasteners for each stringer-feet configuration examined. However, only the toes-up configuration resulted in high assembly hoop strains.

Programmable self-assembly of three-dimensional nanostructures from 104 unique components

PubMed Central

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron A.; Zhu, Allen; Jungmann, Ralf

2017-01-01

Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity1–14 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 102 unique DNA strands6,7,10,13 . Aiming for even larger DNA origami structures is in principle possible15,16, but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly8,9, which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 102 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success.9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 104 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove

Invasion Ecology and School Biology--Part II.

ERIC Educational Resources Information Center

Wells, R. V.

1981-01-01

Suggests that invasion biology can supply subject matter for teaching evolution, genetics, ecological relationships, and conservation. Describes flowering and non-flowering plant invaders, vertebrates and invertebrates, and two ecological invasions on the southern coast of England. (JN)

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

PubMed

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical

Haptic feedback for virtual assembly

NASA Astrophysics Data System (ADS)

Luecke, Greg R.; Zafer, Naci

1998-12-01

Assembly operations require high speed and precision with low cost. The manufacturing industry has recently turned attenuation to the possibility of investigating assembly procedures using graphical display of CAD parts. For these tasks, some sort of feedback to the person is invaluable in providing a real sense of interaction with virtual parts. This research develops the use of a commercial assembly robot as the haptic display in such tasks. For demonstration, a peg-hole insertion task is studied. Kane's Method is employed to derive the dynamics of the peg and the contact motions between the peg and the hole. A handle modeled as a cylindrical peg is attached to the end effector of a PUMA 560 robotic arm. The arm is handle modeled as a cylindrical peg is attached to the end effector of a PUMA 560 robotic arm. The arm is equipped with a six axis force/torque transducer. The use grabs the handle and the user-applied forces are recorded. A 300 MHz Pentium computer is used to simulate the dynamics of the virtual peg and its interactions as it is inserted in the virtual hole. The computed torque control is then employed to exert the full dynamics of the task to the user hand. Visual feedback is also incorporated to help the user in the process of inserting the peg into the hole. Experimental results are presented to show several contact configurations for this virtually simulated task.

Self-assembly of Janus dendrimers into uniform dendrimersomes and other complex architectures.

PubMed

Percec, Virgil; Wilson, Daniela A; Leowanawat, Pawaret; Wilson, Christopher J; Hughes, Andrew D; Kaucher, Mark S; Hammer, Daniel A; Levine, Dalia H; Kim, Anthony J; Bates, Frank S; Davis, Kevin P; Lodge, Timothy P; Klein, Michael L; DeVane, Russell H; Aqad, Emad; Rosen, Brad M; Argintaru, Andreea O; Sienkowska, Monika J; Rissanen, Kari; Nummelin, Sami; Ropponen, Jarmo

2010-05-21

Self-assembled nanostructures obtained from natural and synthetic amphiphiles serve as mimics of biological membranes and enable the delivery of drugs, proteins, genes, and imaging agents. Yet the precise molecular arrangements demanded by these functions are difficult to achieve. Libraries of amphiphilic Janus dendrimers, prepared by facile coupling of tailored hydrophilic and hydrophobic branched segments, have been screened by cryogenic transmission electron microscopy, revealing a rich palette of morphologies in water, including vesicles, denoted dendrimersomes, cubosomes, disks, tubular vesicles, and helical ribbons. Dendrimersomes marry the stability and mechanical strength obtainable from polymersomes with the biological function of stabilized phospholipid liposomes, plus superior uniformity of size, ease of formation, and chemical functionalization. This modular synthesis strategy provides access to systematic tuning of molecular structure and of self-assembled architecture.

Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

NASA Technical Reports Server (NTRS)

Holloway, Nancy M. (Inventor); Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor); Leong, Kam W. (Inventor); Kulangara, Karina (Inventor)

2015-01-01

A scaffold assembly and related methods of manufacturing and/or using the scaffold for stem cell culture and tissue engineering applications are disclosed which at least partially mimic a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold

NASA Technical Reports Server (NTRS)

Kulangara, Karina (Inventor); Scott Carnell, Lisa A. (Inventor); Holloway, Nancy M. (Inventor); Leong, Kam W. (Inventor); Siochi, Emilie J. (Inventor)

2017-01-01

A method of manufacturing and/or using a scaffold assembly for stem cell culture and tissue engineering applications is disclosed. The scaffold at least partially mimics a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation that uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

Large surface-enhanced Raman scattering from self-assembled gold nanosphere monolayers

NASA Astrophysics Data System (ADS)

Fontana, Jake; Livenere, John; Bezares, Francisco J.; Caldwell, Joshua D.; Rendell, Ronald; Ratna, Banahalli R.

2013-05-01

We demonstrate an average surface-enhanced Raman scattering enhancement on the order of 108 from benzenethiol molecules using self-assembled, macroscopic, and tunable gold nanosphere monolayers on non-templated substrates. The self-assembly of the nanosphere monolayers uses a simple and efficient technique that allows for the creation of a high-density, chemically functionalized gold nanosphere monolayers with enhancement factors comparable to those produced using top-down fabrication techniques. These films may provide an approach for the future development of portable chemical/biological sensors.

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

Sequencing and assembly of the 22-gb loblolly pine genome.

PubMed

Zimin, Aleksey; Stevens, Kristian A; Crepeau, Marc W; Holtz-Morris, Ann; Koriabine, Maxim; Marçais, Guillaume; Puiu, Daniela; Roberts, Michael; Wegrzyn, Jill L; de Jong, Pieter J; Neale, David B; Salzberg, Steven L; Yorke, James A; Langley, Charles H

2014-03-01

Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer "super-reads," rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp.

Additive Manufacturing of Parts and Tooling in Robotic Systems

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

Love, Lonnie J.; Hassen, Ahmed A.; Chesser, Phillip C.

ORNL worked with Transcend Robotics, LLC to explore additive manufacturing of the two-piece compression body for their ARTI mobile robot platform. Extrusion compression molding was identified as an effective means of manufacturing these parts. ORNL consulted on modifications to the housing design to accommodate the selected manufacturing process. Parts were printed using ORNL's FDM machines for testing and evaluation of the design as a precursor to molding the parts. The assembly and evaluation of the parts proved favorable and minor design changes to improve assembly and performance were identified.The goal is to develop a light weight and rugged two-part roboticmore » enclosure for an unmanned ground vehicle UGV) that will be used in search and rescue applications. The FDM parts fabricated by ORNL allowed Transcend Robotics to assemble a prototype robot and verify that the new parts will meet the performance requirements. ORNL fabricated enclosure parts out of ABS and Nylon 12 materials such that the design could be tested prior to fabricating tooling for compression molding of Nylon 6 with carbon fiber fill. The robot was performance tested and compared with the previous manufacturing techniques and found to have superior performance.« less

Marine biology, intertidal ecology, and a new place for biology.

PubMed

Benson, Keith R

2015-01-01

At the present time, there is considerable interest for the physical setting of science, that is, its actual 'place' of practice. Among historians of biology, place has been considered to be a crucial component for the study of ecology. Other historians have noted the 'built' environments (laboratories) for the study of biology along the seashore, even referring to these places in terms more applicable to vacation sites. In this paper, I examine the place of intertidal ecology investigations, both in terms of the physical space and the built space. Part of the examination will investigate the aesthetic aspect of the Pacific Coast, part will evaluate the unique character of the intertidal zone, and part will consider the construction of natural laboratories and built laboratories as characteristic places for biology.

Single haplotype assembly of the human genome from a hydatidiform mole

PubMed Central

Steinberg, Karyn Meltz; Schneider, Valerie A.; Graves-Lindsay, Tina A.; Fulton, Robert S.; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A.; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C.; Church, Deanna M.; Eichler, Evan E.; Wilson, Richard K.

2014-01-01

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. PMID:25373144

Assembly constraints drive co-evolution among ribosomal constituents.

PubMed

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Supramolecular domains in mixed peptide self-assembled monolayers on gold nanoparticles.

PubMed

Duchesne, Laurence; Wells, Geoff; Fernig, David G; Harris, Sarah A; Lévy, Raphaël

2008-09-01

Self-organization in mixed self-assembled monolayers of small molecules provides a route towards nanoparticles with complex molecular structures. Inspired by structural biology, a strategy based on chemical cross-linking is introduced to probe proximity between functional peptides embedded in a mixed self-assembled monolayer at the surface of a nanoparticle. The physical basis of the proximity measurement is a transition from intramolecular to intermolecular cross-linking as the functional peptides get closer. Experimental investigations of a binary peptide self-assembled monolayer show that this transition happens at an extremely low molar ratio of the functional versus matrix peptide. Molecular dynamics simulations of the peptide self-assembled monolayer are used to calculate the volume explored by the reactive groups. Comparison of the experimental results with a probabilistic model demonstrates that the peptides are not randomly distributed at the surface of the nanoparticle, but rather self-organize into supramolecular domains.

Self-assemblies of luminescent rare earth compounds in capsules and multilayers.

PubMed

Zhang, Renjie; Shang, Juanjuan; Xin, Jing; Xie, Beibei; Li, Ya; Möhwald, Helmuth

2014-05-01

This review addresses luminescent rare earth compounds assembled in microcapsules as well as in planar films fabricated by the layer-by-layer (LbL) technique, the Langmuir-Blodgett (LB) method and in self-assembled monolayers. Chemical precipitation, electrostatic, van der Waals interactions and covalent bonds are involved in the assembly of these compounds. Self-organized ring patterns of rare earth complexes in Langmuir monolayers and on planar surfaces with stripe patterns, as well as fluorescence enhancement due to donor-acceptor pairs, microcavities, enrichment of rare earth compounds, and shell protection against water are described. Recent information on the tuning of luminescence intensity and multicolors by the excitation wavelength and the ratio of rare earth ions, respectively, are also reviewed. Potential applications of luminescent rare earth complex assemblies serving as biological probes, temperature and gas sensors are pointed out. Copyright © 2014 Elsevier B.V. All rights reserved.

Sequential bottom-up assembly of mechanically stabilized synthetic cells by microfluidics

NASA Astrophysics Data System (ADS)

Weiss, Marian; Frohnmayer, Johannes Patrick; Benk, Lucia Theresa; Haller, Barbara; Janiesch, Jan-Willi; Heitkamp, Thomas; Börsch, Michael; Lira, Rafael B.; Dimova, Rumiana; Lipowsky, Reinhard; Bodenschatz, Eberhard; Baret, Jean-Christophe; Vidakovic-Koch, Tanja; Sundmacher, Kai; Platzman, Ilia; Spatz, Joachim P.

2018-01-01

Compartments for the spatially and temporally controlled assembly of biological processes are essential towards cellular life. Synthetic mimics of cellular compartments based on lipid-based protocells lack the mechanical and chemical stability to allow their manipulation into a complex and fully functional synthetic cell. Here, we present a high-throughput microfluidic method to generate stable, defined sized liposomes termed `droplet-stabilized giant unilamellar vesicles (dsGUVs)’. The enhanced stability of dsGUVs enables the sequential loading of these compartments with biomolecules, namely purified transmembrane and cytoskeleton proteins by microfluidic pico-injection technology. This constitutes an experimental demonstration of a successful bottom-up assembly of a compartment with contents that would not self-assemble to full functionality when simply mixed together. Following assembly, the stabilizing oil phase and droplet shells are removed to release functional self-supporting protocells to an aqueous phase, enabling them to interact with physiologically relevant matrices.

Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers

PubMed Central

Wajid, Bilal; Serpedin, Erchin

2012-01-01

In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity. PMID:22768980

Enzymatically Active Microgels from Self-Assembling Protein Nanofibrils for Microflow Chemistry.

PubMed

Zhou, Xiao-Ming; Shimanovich, Ulyana; Herling, Therese W; Wu, Si; Dobson, Christopher M; Knowles, Tuomas P J; Perrett, Sarah

2015-06-23

Amyloid fibrils represent a generic class of protein structure associated with both pathological states and with naturally occurring functional materials. This class of protein nanostructure has recently also emerged as an excellent foundation for sophisticated functional biocompatible materials including scaffolds and carriers for biologically active molecules. Protein-based materials offer the potential advantage that additional functions can be directly incorporated via gene fusion producing a single chimeric polypeptide that will both self-assemble and display the desired activity. To succeed, a chimeric protein system must self-assemble without the need for harsh triggering conditions which would damage the appended functional protein molecule. However, the micrometer to nanoscale patterning and morphological control of protein-based nanomaterials has remained challenging. This study demonstrates a general approach for overcoming these limitations through the microfluidic generation of enzymatically active microgels that are stabilized by amyloid nanofibrils. The use of scaffolds formed from biomaterials that self-assemble under mild conditions enables the formation of catalytic microgels while maintaining the integrity of the encapsulated enzyme. The enzymatically active microgel particles show robust material properties and their porous architecture allows diffusion in and out of reactants and products. In combination with microfluidic droplet trapping approaches, enzymatically active microgels illustrate the potential of self-assembling materials for enzyme immobilization and recycling, and for biological flow-chemistry. These design principles can be adopted to create countless other bioactive amyloid-based materials with diverse functions.

Enzymatically Active Microgels from Self-Assembling Protein Nanofibrils for Microflow Chemistry

PubMed Central

2015-01-01

Amyloid fibrils represent a generic class of protein structure associated with both pathological states and with naturally occurring functional materials. This class of protein nanostructure has recently also emerged as an excellent foundation for sophisticated functional biocompatible materials including scaffolds and carriers for biologically active molecules. Protein-based materials offer the potential advantage that additional functions can be directly incorporated via gene fusion producing a single chimeric polypeptide that will both self-assemble and display the desired activity. To succeed, a chimeric protein system must self-assemble without the need for harsh triggering conditions which would damage the appended functional protein molecule. However, the micrometer to nanoscale patterning and morphological control of protein-based nanomaterials has remained challenging. This study demonstrates a general approach for overcoming these limitations through the microfluidic generation of enzymatically active microgels that are stabilized by amyloid nanofibrils. The use of scaffolds formed from biomaterials that self-assemble under mild conditions enables the formation of catalytic microgels while maintaining the integrity of the encapsulated enzyme. The enzymatically active microgel particles show robust material properties and their porous architecture allows diffusion in and out of reactants and products. In combination with microfluidic droplet trapping approaches, enzymatically active microgels illustrate the potential of self-assembling materials for enzyme immobilization and recycling, and for biological flow-chemistry. These design principles can be adopted to create countless other bioactive amyloid-based materials with diverse functions. PMID:26030507

Polymeric amphiphile branching leads to rare nanodisc shaped planar self-assemblies.

PubMed

Qu, Xiaozhong; Omar, Leila; Le, Thi Bich Hang; Tetley, Laurence; Bolton, Katherine; Chooi, Kar Wai; Wang, Wei; Uchegbu, Ijeoma F

2008-09-16

Self-assembly is fundamental to the biological function of cells and the fabrication of nanomaterials. However, the origin of the shape of various self-assemblies, such as the shape of cells, is not altogether clear. Polymeric, oligomeric, or low molecular weight amphiphiles are a rich source of nanomaterials, and controlling their self-assembly is the route to tailored nanosystems with specific functionalities. Here, we provide direct evidence that a particular molecular architecture, polymeric branching, leads to a rare form of self-assembly, the planar nanodisc. Cholesterol containing self-assemblies formed from amphiphilic linear or branched cetyl poly(ethylenimine) (Mn approximately 1000 Da) or amphiphilic cetyl poly(propylenimine) dendrimer derivatives (Mn approximately 2000 Da) show that branching, by reducing the hydrophilic headgroup area, alters the shape of the self-assemblies transforming closed 60 nm spherical bilayer vesicles to rare 50 nm x 10 nm planar bilayer discs. Increasing the hydrophilic headgroup area, by the inclusion of methoxy poly(ethylene glycol) moieties into the amphiphilic headgroup, transforms the planar discs to 100 nm spherical bilayer vesicles. This study provides insight into the key role played by molecular shape on molecular self-organization into rare nanodiscs.

The Naegleria genome: a free-living microbial eukaryote lends unique insights into core eukaryotic cell biology

PubMed Central

Fritz-Laylin, Lillian K.; Ginger, Michael L.; Walsh, Charles; Dawson, Scott C.; Fulton, Chandler

2016-01-01

Naegleria gruberi, a free-living protist, has long been treasured as a model for basal body and flagellar assembly due to its ability to differentiate from crawling amoebae into swimming flagellates. The full genome sequence of Naegleria gruberi has recently been used to estimate gene families ancestral to all eukaryotes and to identify novel aspects of Naegleria biology, including likely facultative anaerobic metabolism, extensive signaling cascades, and evidence for sexuality. Distinctive features of the Naegleria genome and nuclear biology provide unique perspectives for comparative cell biology, including cell division, RNA processing and nucleolar assembly. We highlight here exciting new and novel aspects of Naegleria biology identified through genomic analysis. PMID:21392573

Tilt assembly for tracking solar collector assembly

DOEpatents

Almy, Charles; Peurach, John; Sandler, Reuben

2012-01-24

A tilt assembly is used with a solar collector assembly of the type comprising a frame, supporting a solar collector, for movement about a tilt axis by pivoting a drive element between first and second orientations. The tilt assembly comprises a drive element coupler connected to the drive element and a driver, the driver comprising a drive frame, a drive arm and a drive arm driver. The drive arm is mounted to the drive frame for pivotal movement about a drive arm axis. Movement on the drive arm mimics movement of the drive element. Drive element couplers can extend in opposite directions from the outer portion of the drive arm, whereby the assembly can be used between adjacent solar collector assemblies in a row of solar collector assemblies.

Computational Design of Self-Assembling Cyclic Protein Homo-oligomers

PubMed Central

Fallas, Jorge A.; Ueda, George; Sheffler, William; Nguyen, Vanessa; McNamara, Dan E.; Sankaran, Banumathi; Pereira, Jose Henrique; Parmeggiani, Fabio; Brunette, TJ; Cascio, Duilio; Yeates, Todd R.; Zwart, Peter; Baker, David

2016-01-01

Self-assembling cyclic protein homo-oligomers play important roles in biology and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue pair transform method for assessing the design ability of a protein-protein interface. This method is sufficiently rapid to enable systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were experimentally characterized, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (4 homodimers, 6 homotrimers, 6 homotetramers and 1 homopentamer) had solution small angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each of these were shown to be very close to their design model. PMID:28338692

Protocols for self-assembly and imaging of DNA nanostructures.

PubMed

Sobey, Thomas L; Simmel, Friedrich C

2011-01-01

Programed molecular structures allow us to research and make use of physical, chemical, and biological effects at the nanoscale. They are an example of the "bottom-up" approach to nanotechnology, with structures forming through self-assembly. DNA is a particularly useful molecule for this purpose, and some of its advantages include parallel (as opposed to serial) assembly, naturally occurring "tools," such as enzymes and proteins for making modifications and attachments, and structural dependence on base sequence. This allows us to develop one, two, and three dimensional structures that are interesting for their fundamental physical and chemical behavior, and for potential applications such as biosensors, medical diagnostics, molecular electronics, and efficient light-harvesting systems. We describe five techniques that allow one to assemble and image such structures: concentration measurement by ultraviolet absorption, titration gel electrophoresis, thermal annealing, fluorescence microscopy, and atomic force microscopy in fluids.

Internal Aspects of the Skill Transfer of Manual Assembly Work

ERIC Educational Resources Information Center

Doyo, Daisuke

2009-01-01

In manual assembly work, parts are often assembled by applying force with a simple tool or by hand. A worker thus needs control the force he or she applies in working, as an appropriate level of force is requisite for minimizing work failures and improving efficiency. The object of this study is to clarify the relationship between the level of…

Finding Nemo: hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the clownfish (Amphiprion ocellaris) genome assembly.

PubMed

Tan, Mun Hua; Austin, Christopher M; Hammer, Michael P; Lee, Yin Peng; Croft, Laurence J; Gan, Han Ming

2018-03-01

Some of the most widely recognized coral reef fishes are clownfish or anemonefish, members of the family Pomacentridae (subfamily: Amphiprioninae). They are popular aquarium species due to their bright colours, adaptability to captivity, and fascinating behavior. Their breeding biology (sequential hermaphrodites) and symbiotic mutualism with sea anemones have attracted much scientific interest. Moreover, there are some curious geographic-based phenotypes that warrant investigation. Leveraging on the advancement in Nanopore long read technology, we report the first hybrid assembly of the clown anemonefish (Amphiprion ocellaris) genome utilizing Illumina and Nanopore reads, further demonstrating the substantial impact of modest long read sequencing data sets on improving genome assembly statistics. We generated 43 Gb of short Illumina reads and 9 Gb of long Nanopore reads, representing approximate genome coverage of 54× and 11×, respectively, based on the range of estimated k-mer-predicted genome sizes of between 791 and 967 Mbp. The final assembled genome is contained in 6404 scaffolds with an accumulated length of 880 Mb (96.3% BUSCO-calculated genome completeness). Compared with the Illumina-only assembly, the hybrid approach generated 94% fewer scaffolds with an 18-fold increase in N50 length (401 kb) and increased the genome completeness by an additional 16%. A total of 27 240 high-quality protein-coding genes were predicted from the clown anemonefish, 26 211 (96%) of which were annotated functionally with information from either sequence homology or protein signature searches. We present the first genome of any anemonefish and demonstrate the value of low coverage (∼11×) long Nanopore read sequencing in improving both genome assembly contiguity and completeness. The near-complete assembly of the A. ocellaris genome will be an invaluable molecular resource for supporting a range of genetic, genomic, and phylogenetic studies specifically for clownfish and

Self-assembled bionanostructures: proteins following the lead of DNA nanostructures

PubMed Central

2014-01-01

Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction. PMID:24491139

Interconnect assembly for an electronic assembly and assembly method therefor

DOEpatents

Gerbsch, Erich William

2003-06-10

An interconnect assembly and method for a semiconductor device, in which the interconnect assembly can be used in lieu of wirebond connections to form an electronic assembly. The interconnect assembly includes first and second interconnect members. The first interconnect member has a first surface with a first contact and a second surface with a second contact electrically connected to the first contact, while the second interconnect member has a flexible finger contacting the second contact of the first interconnect member. The first interconnect member is adapted to be aligned and registered with a semiconductor device having a contact on a first surface thereof, so that the first contact of the first interconnect member electrically contacts the contact of the semiconductor device. Consequently, the assembly method does not require any wirebonds, but instead merely entails aligning and registering the first interconnect member with the semiconductor device so that the contacts of the first interconnect member and the semiconductor device make electrically contact, and then contacting the second contact of the first interconnect member with the flexible finger of the second interconnect member.

DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways

PubMed Central

Shao, Zengyi; Zhao, Hua; Zhao, Huimin

2009-01-01

The assembly of large recombinant DNA encoding a whole biochemical pathway or genome represents a significant challenge. Here, we report a new method, DNA assembler, which allows the assembly of an entire biochemical pathway in a single step via in vivo homologous recombination in Saccharomyces cerevisiae. We show that DNA assembler can rapidly assemble a functional d-xylose utilization pathway (∼9 kb DNA consisting of three genes), a functional zeaxanthin biosynthesis pathway (∼11 kb DNA consisting of five genes) and a functional combined d-xylose utilization and zeaxanthin biosynthesis pathway (∼19 kb consisting of eight genes) with high efficiencies (70–100%) either on a plasmid or on a yeast chromosome. As this new method only requires simple DNA preparation and one-step yeast transformation, it represents a powerful tool in the construction of biochemical pathways for synthetic biology, metabolic engineering and functional genomics studies. PMID:19074487

Nanoscale device architectures derived from biological assemblies: The case of tobacco mosaic virus and (apo)ferritin

NASA Astrophysics Data System (ADS)

Calò, Annalisa; Eiben, Sabine; Okuda, Mitsuhiro; Bittner, Alexander M.

2016-03-01

Virus particles and proteins are excellent examples of naturally occurring structures with well-defined nanoscale architectures, for example, cages and tubes. These structures can be employed in a bottom-up assembly strategy to fabricate repetitive patterns of hybrid organic-inorganic materials. In this paper, we review methods of assembly that make use of protein and virus scaffolds to fabricate patterned nanostructures with very high spatial control. We chose (apo)ferritin and tobacco mosaic virus (TMV) as model examples that have already been applied successfully in nanobiotechnology. Their interior space and their exterior surfaces can be mineralized with inorganic layers or nanoparticles. Furthermore, their native assembly abilities can be exploited to generate periodic architectures for integration in electrical and magnetic devices. We introduce the state of the art and describe recent advances in biomineralization techniques, patterning and device production with (apo)ferritin and TMV.

Ebola virus VP35 blocks stress granule assembly.

PubMed

Le Sage, Valerie; Cinti, Alessandro; McCarthy, Stephen; Amorim, Raquel; Rao, Shringar; Daino, Gian Luca; Tramontano, Enzo; Branch, Donald R; Mouland, Andrew J

2017-02-01

Stress granules (SGs) are dynamic cytoplasmic aggregates of translationally silenced mRNAs that assemble in response to environmental stress. SGs appear to play an important role in antiviral innate immunity and many viruses have evolved to block or subvert SGs components for their own benefit. Here, we demonstrate that intracellular Ebola virus (EBOV) replication and transcription-competent virus like particles (trVLP) infection does not lead to SG assembly but leads to a blockade to Arsenite-induced SG assembly. Moreover we show that EBOV VP35 represses the assembly of canonical and non-canonical SGs induced by a variety of pharmacological stresses. This SG blockade requires, at least in part, the C-terminal domain of VP35. Furthermore, results from our co-immunoprecipitation studies indicate that VP35 interacts with multiple SG components, including G3BP1, eIF3 and eEF2 through a stress- and RNA-independent mechanism. These data suggest a novel function for EBOV VP35 in the repression of SG assembly. Copyright © 2016 Elsevier Inc. All rights reserved.

Droplet microfluidics for synthetic biology

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

Gach, Philip Charles; Iwai, Kosuke; Kim, Peter Wonhee

Here, synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to mostmore » researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.« less

Droplet microfluidics for synthetic biology

DOE PAGES

Gach, Philip Charles; Iwai, Kosuke; Kim, Peter Wonhee; ...

2017-08-10

Here, synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to mostmore » researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.« less

Fabrication of complex structures or assemblies by Hot Isostatic Pressure (HIP) welding

NASA Technical Reports Server (NTRS)

Ashurst, A. N.; Goldstein, M.; Ryan, M. J.; Lessmann, G. G.; Bryant, W. A.

1974-01-01

HIP welding is effective method for fabricating complex structures or assemblies such as alternator rotors, regeneratively-cooled rocket-motor thrust chambers, and jet engine turbine blades. It can be applied to fabrication of many assemblies which require that component parts be welded together along complex interfaces.

49 CFR 572.113 - Neck assembly.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal centerline...

49 CFR 572.113 - Neck assembly.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal centerline...

49 CFR 572.113 - Neck assembly.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal centerline...

49 CFR 572.113 - Neck assembly.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal centerline...

49 CFR 572.113 - Neck assembly.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Using neck brackets 78051-303 and -307, mount the head/neck assembly to the part 572 pendulum test... to the plane of motion of the pendulum's longitudinal centerline (see § 572.33, Figure 20, except... (horizontal surface at the base of the skull) rotation with respect to the pendulum's longitudinal centerline...

Higher-order structures assembly of gold nanorods caused by captopril in high ionic strength solutions.

PubMed