Abdominal wall closure in bladder exstrophy complex repair by ...

African Journals Online (AJOL)

Background and Objectives: The Exstrophy Complex (EC) is a serious malformation of midline abdominal wall. Wide pubis prevents approximating the lateralized rectus muscle and leads to dehiscence and fi stula formation. Our aim was to recommend an easier method for abdominal wall closure in the Bladder Exstrophy ...

Ultrasonographic diagnosis of limb-body wall complex: a case report

Energy Technology Data Exchange (ETDEWEB)

Goo, Dong Erk; Yoo, Shi Joon; Cho, Kyoung Sik; Choi, Kee Young; Kim, Am [University of Ulsan College of Medicine, Asan Medical Center, Ulsan (Korea, Republic of)

1993-12-15

Limb-body wall complex (LBWC) is a rare congenital process believed to result from early rupture of the amnion, possibly as a consequence of vascular disruption. Characteristic fetal deformities include limb defects, scoliosis, thoracoschisis and/or abdominoschisis, and severe craniofacial anomalies. This complex should be distinguished from other body-wall defect including omphalocele and gastroschisis since the prognosis of LBWC is uniformly poor. We report a case of LBWC which was diagnosed by prenatal ultrasonography in 26 weeks of gestation. Prenatal ultrasonograms are correlated with the gross pathologic findings. The present case demonstrates the superb capability of modern ultrasonography in the diagnosis of complex fetal anomalies

Ultrasonographic diagnosis of limb-body wall complex: a case report

International Nuclear Information System (INIS)

Goo, Dong Erk; Yoo, Shi Joon; Cho, Kyoung Sik; Choi, Kee Young; Kim, Am

1993-01-01

Limb-body wall complex (LBWC) is a rare congenital process believed to result from early rupture of the amnion, possibly as a consequence of vascular disruption. Characteristic fetal deformities include limb defects, scoliosis, thoracoschisis and/or abdominoschisis, and severe craniofacial anomalies. This complex should be distinguished from other body-wall defect including omphalocele and gastroschisis since the prognosis of LBWC is uniformly poor. We report a case of LBWC which was diagnosed by prenatal ultrasonography in 26 weeks of gestation. Prenatal ultrasonograms are correlated with the gross pathologic findings. The present case demonstrates the superb capability of modern ultrasonography in the diagnosis of complex fetal anomalies

Limb-body wall complex: Prenatal sonographic findings versus autopsy findings

International Nuclear Information System (INIS)

Song, Mi Jin; Cho, Jeong Yeon; Lee, Young Ho

2001-01-01

To evaluate prenatal ultrasonographic findings of limb-body wall complex and to correlate them with autopsy findings. From October 1995 to June 2000, a retrospectively review of prenatal ultrasonography (US) of 11 patients with pathologically proven limb-body wall complex was done. US findings were then compared with autopsy findings. Prenatal ultrasonography revealed thoraco-abdominoschists (n=7.64%), kyphoscoliosis (n=7.64%), cranial defect (n=5.45%), limb defect (n=4.36%), facial defect (n=1.10%), amniotic band (n=5.45%), and umbilical cord anomaly (n=3.27%). Meanwhile, autopsy findings showed thoraco-abdominoschisis (n=8.72%), limb defect (n=7.64%), facial defect (n=7.64%), kyphoscoliosis (n=5.45%), cranial defect (n=5.45%), amniotic band (n=5.45%) and umbilical cord anomaly (n=4.36%). The most common ultrasonography features of limb-body wall complex were thoraco-abdominoschisis and kyphoscoliosis while the thoraco-abdominoschisis and limb defects were the most frequent findings at autopsy.

The role of the cell wall in plant immunity

DEFF Research Database (Denmark)

Malinovsky, Frederikke Gro; Fangel, Jonatan Ulrik; Willats, William George Tycho

2014-01-01

The battle between plants and microbes is evolutionarily ancient, highly complex, and often co-dependent. A primary challenge for microbes is to breach the physical barrier of host cell walls whilst avoiding detection by the plant's immune receptors. While some receptors sense conserved microbial...... features, others monitor physical changes caused by an infection attempt. Detection of microbes leads to activation of appropriate defense responses that then challenge the attack. Plant cell walls are formidable and dynamic barriers. They are constructed primarily of complex carbohydrates joined...... by numerous distinct connection types, and are subject to extensive post-synthetic modification to suit prevailing local requirements. Multiple changes can be triggered in cell walls in response to microbial attack. Some of these are well described, but many remain obscure. The study of the myriad of subtle...

Combined effect of synthetic enterocin CRL35 with cell wall, membrane-acting antibiotics and muranolytic enzymes against Listeria cells.

Science.gov (United States)

Salvucci, E; Hebert, E M; Sesma, F; Saavedra, L

2010-08-01

To evaluate the inhibition effectiveness of enterocin CRL35 in combination with cell wall, membrane-acting antibiotics and muranolytic enzymes against the foodborne pathogen Listeria. Synthetic enterocin CRL35 alone and in combination with monensin, bacitracin, gramicidin, mutanolysin and lysozyme were used in this study. Minimal inhibitory concentration (MIC) and fractional inhibitory concentration (FIC) index assays were performed using Listeria innocua 7 and Listeria monocytogenes FBUNT as sensitive strains. Antibiotics showed positive interactions with the bacteriocin in both strains tested. On the other hand, when mutanolysin and enterocin CRL35 were added to resting cells in a buffer system, the lytic effect of mutanolysin was enhanced. However, the addition of mutanolysin showed no effect on the growth of L. innocua 7 cells in a culture medium. Moreover, mutanolysin allowed the overgrowth of L. innocua 7 cells to an OD similar to control cells in the presence of inhibitory concentration of enterocin CRL35. In contrast, the combination of lysozyme and enterocin CRL35 resulted in a 50% inhibition of the L. innocua 7 growth. Based on our results, we conclude that the combination of synthetic enterocin CRL35 with some antibiotics is effective against L. innocua 7 and L. monocytogenes FBUNT cells, and more importantly the amount of these agents to be used was considerably reduced. The effectiveness of the combination of synthetic enterocin CRL35 with muramidases seems to depend on complex environments, and more detailed studies need to be performed to elucidate this issue. Enterocin CRL35 represents a promising agent that not only can ensure the quality and safety of food but it can also be combined with several antimicrobial agents important in the medical field.

Labile synthetic cadmium complexes are not bioavailable to Pseudokirchneriella subcapitata in resin buffered solutions

Energy Technology Data Exchange (ETDEWEB)

Verheyen, L., E-mail: Liesbeth.Verheyen@ees.kuleuven.be [Division of Soil and Water Management, K.U. Leuven, Kasteelpark Arenberg 20, Box 2459, 3001 Heverlee (Belgium); Merckx, R. [Division of Soil and Water Management, K.U.Leuven, Kasteelpark Arenberg 20, Box 2459, 3001 Heverlee (Belgium); Smolders, E., E-mail: Erik.Smolders@ees.kuleuven.be [Division of Soil and Water Management, K.U. Leuven, Kasteelpark Arenberg 20, Box 2459, 3001 Heverlee (Belgium)

2012-11-15

The Free Ion Activity Model (FIAM) predicts that cadmium (Cd) uptake by organisms is identical for solutions with the same free Cd{sup 2+} concentration and inorganic composition. Clear exceptions to the FIAM have been shown for Cd uptake by plant roots, periphyton and human cells where labile Cd complexes increase bioavailability and which has been attributed to their role in enhancing Cd diffusion towards the uptake cells. Here, we assessed the role of labile Cd complexes on Cd uptake by algae, for which diffusion limitations should be less pronounced due to their smaller size. Long-term (3 days) Cd uptake by the green algae Pseudokirchneriella subcapitata was measured in resin buffered solutions with or without synthetic ligands and at three Cd{sup 2+} ion activities (pCd 8.2-5.7). The free Cd{sup 2+} activity was maintained during the test using a metal-selective resin located in the algal bottles. Total dissolved Cd increased up to 35-fold by adding the synthetic ligands at constant Cd{sup 2+} activity. In contrast, Cd uptake by algae increased maximally 2.8 fold with increasing concentration of the synthetic ligands and the availability of the complexes were maximally 5.2% relative to Cd{sup 2+} for NTA and CDTA complexes. It is concluded that labile Cd complexes do not greatly enhance Cd bioavailability to the unicellular algae and calculations suggest that Cd transport from solution to these small cells is not rate limiting.

Labile synthetic cadmium complexes are not bioavailable to Pseudokirchneriella subcapitata in resin buffered solutions

International Nuclear Information System (INIS)

Verheyen, L.; Merckx, R.; Smolders, E.

2012-01-01

The Free Ion Activity Model (FIAM) predicts that cadmium (Cd) uptake by organisms is identical for solutions with the same free Cd 2+ concentration and inorganic composition. Clear exceptions to the FIAM have been shown for Cd uptake by plant roots, periphyton and human cells where labile Cd complexes increase bioavailability and which has been attributed to their role in enhancing Cd diffusion towards the uptake cells. Here, we assessed the role of labile Cd complexes on Cd uptake by algae, for which diffusion limitations should be less pronounced due to their smaller size. Long-term (3 days) Cd uptake by the green algae Pseudokirchneriella subcapitata was measured in resin buffered solutions with or without synthetic ligands and at three Cd 2+ ion activities (pCd 8.2–5.7). The free Cd 2+ activity was maintained during the test using a metal-selective resin located in the algal bottles. Total dissolved Cd increased up to 35-fold by adding the synthetic ligands at constant Cd 2+ activity. In contrast, Cd uptake by algae increased maximally 2.8 fold with increasing concentration of the synthetic ligands and the availability of the complexes were maximally 5.2% relative to Cd 2+ for NTA and CDTA complexes. It is concluded that labile Cd complexes do not greatly enhance Cd bioavailability to the unicellular algae and calculations suggest that Cd transport from solution to these small cells is not rate limiting.

Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

KAUST Repository

Jantke, Dominik; Marziale, Alexander N.; Reiner, Thomas; Kraus, Florian; Herdtweck, Eberhardt; Raba, Andreas; Eppinger, Jö rg

2013-01-01

Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

Synthetic strategies for efficient conjugation of organometallic complexes with pendant protein reactive markers

KAUST Repository

Jantke, Dominik

2013-11-01

Site-directed conjugation of metal centers to proteins is fundamental for biological and bioinorganic applications of transition metals. However, methods for the site-selective introduction of metal centers remain scarce. Herein, we present broadly applicable synthetic strategies for the conjugation of bioactive molecules with a range of organometallic complexes. Following three different synthetic strategies, we were able to synthesize a small library of metal conjugated protein markers featuring different types of protein reactive sites (epoxides, phenylphosphonates, fluorosulfonates and fluorophosphonate groups) as well as different late transition metals (iron, ruthenium, rhodium, palladium and platinum). The products were isolated in moderate to excellent yields and high purity. Furthermore, X-ray diffraction of the metalated protein markers corroborates structural integrity of the metal complex and the protein reactive site. © 2013 Elsevier B.V. All rights reserved.

INSOLUBLE HYDROPHOBIN COMPLEXES IN THE WALLS OF SCHIZOPHYLLUM-COMMUNE AND OTHER FILAMENTOUS FUNGI

NARCIS (Netherlands)

DEVRIES, OMH; FEKKES, MP; WOSTEN, HAB; WESSELS, JGH

Two closely related cysteine-rich hydrophobic proteins, Sc3p and Sc4p, of the basidiomycete Schizophyllum commune are developmentally regulated and associated with the walls of aerial hyphae and fruit-body hyphae. They are present in the walls as hot-SDS-insoluble complexes which can be extracted

Arabidopsis thaliana plants lacking the ARP2/3 complex show defects in cell wall assembly and auxin distribution.

Science.gov (United States)

Pratap Sahi, Vaidurya; Cifrová, Petra; García-González, Judith; Kotannal Baby, Innu; Mouillé, Gregory; Gineau, Emilie; Müller, Karel; Baluška, František; Soukup, Aleš; Petrášek, Jan; Schwarzerová, Katerina

2017-12-25

The cytoskeleton plays an important role in the synthesis of plant cell walls. Both microtubules and actin cytoskeleton are known to be involved in the morphogenesis of plant cells through their role in cell wall building. The role of ARP2/3-nucleated actin cytoskeleton in the morphogenesis of cotyledon pavement cells has been described before. Seedlings of Arabidopsis mutants lacking a functional ARP2/3 complex display specific cell wall-associated defects. In three independent Arabidopsis mutant lines lacking subunits of the ARP2/3 complex, phenotypes associated with the loss of the complex were analysed throughout plant development. Organ size and anatomy, cell wall composition, and auxin distribution were investigated. ARP2/3-related phenotype is associated with changes in cell wall composition, and the phenotype is manifested especially in mature tissues. Cell walls of mature plants contain less cellulose and a higher amount of homogalacturonan, and display changes in cell wall lignification. Vascular bundles of mutant inflorescence stems show a changed pattern of AUX1-YFP expression. Plants lacking a functional ARP2/3 complex have decreased basipetal auxin transport. The results suggest that the ARP2/3 complex has a morphogenetic function related to cell wall synthesis and auxin transport. © The Author(s) 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Pedicularis gracilis Wall. Ex Benth. (Scrophulariaceae Complex in the Himalayas – A Taxonomic Reinvestigation

Directory of Open Access Journals (Sweden)

Tariq Husain

2003-03-01

Full Text Available The paper highlights the complex nature of Pedicularis gracilis Wall. ex Benth. in the Himalayas and enumerates two subspecies and four varieties of this species. Morphological and distributional data have been appended to show that the subspecies – gracilis and brunoniana (Wall. ex Pennell Husain & Garg and varieties – gracilis and stricta (Wall. Husain & Garg (under subsp. gracilis and brunoniana and macrocarpa (Prain Husain & Garg (under subsp. brunoniana are distinct.

What is the evidence for the use of biologic or biosynthetic meshes in abdominal wall reconstruction?

Science.gov (United States)

Köckerling, F; Alam, N N; Antoniou, S A; Daniels, I R; Famiglietti, F; Fortelny, R H; Heiss, M M; Kallinowski, F; Kyle-Leinhase, I; Mayer, F; Miserez, M; Montgomery, A; Morales-Conde, S; Muysoms, F; Narang, S K; Petter-Puchner, A; Reinpold, W; Scheuerlein, H; Smietanski, M; Stechemesser, B; Strey, C; Woeste, G; Smart, N J

2018-04-01

Although many surgeons have adopted the use of biologic and biosynthetic meshes in complex abdominal wall hernia repair, others have questioned the use of these products. Criticism is addressed in several review articles on the poor standard of studies reporting on the use of biologic meshes for different abdominal wall repairs. The aim of this consensus review is to conduct an evidence-based analysis of the efficacy of biologic and biosynthetic meshes in predefined clinical situations. A European working group, "BioMesh Study Group", composed of invited surgeons with a special interest in surgical meshes, formulated key questions, and forwarded them for processing in subgroups. In January 2016, a workshop was held in Berlin where the findings were presented, discussed, and voted on for consensus. Findings were set out in writing by the subgroups followed by consensus being reached. For the review, 114 studies and background analyses were used. The cumulative data regarding biologic mesh under contaminated conditions do not support the claim that it is better than synthetic mesh. Biologic mesh use should be avoided when bridging is needed. In inguinal hernia repair biologic and biosynthetic meshes do not have a clear advantage over the synthetic meshes. For prevention of incisional or parastomal hernias, there is no evidence to support the use of biologic/biosynthetic meshes. In complex abdominal wall hernia repairs (incarcerated hernia, parastomal hernia, infected mesh, open abdomen, enterocutaneous fistula, and component separation technique), biologic and biosynthetic meshes do not provide a superior alternative to synthetic meshes. The routine use of biologic and biosynthetic meshes cannot be recommended.

Processive movement of MreB-associated cell wall biosynthetic complexes in bacteria.

Science.gov (United States)

Domínguez-Escobar, Julia; Chastanet, Arnaud; Crevenna, Alvaro H; Fromion, Vincent; Wedlich-Söldner, Roland; Carballido-López, Rut

2011-07-08

The peptidoglycan cell wall and the actin-like MreB cytoskeleton are major determinants of cell shape in rod-shaped bacteria. The prevailing model postulates that helical, membrane-associated MreB filaments organize elongation-specific peptidoglycan-synthesizing complexes along sidewalls. We used total internal reflection fluorescence microscopy to visualize the dynamic relation between MreB isoforms and cell wall synthesis in live Bacillus subtilis cells. During exponential growth, MreB proteins did not form helical structures. Instead, together with other morphogenetic factors, they assembled into discrete patches that moved processively along peripheral tracks perpendicular to the cell axis. Patch motility was largely powered by cell wall synthesis, and MreB polymers restricted diffusion of patch components in the membrane and oriented patch motion.

Synthetic biology, inspired by synthetic chemistry.

Science.gov (United States)

Malinova, V; Nallani, M; Meier, W P; Sinner, E K

2012-07-16

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Energy transfer from natural photosynthetic complexes to single-wall carbon nanotubes

Energy Technology Data Exchange (ETDEWEB)

Wiwatowski, Kamil [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland); Dużyńska, Anna; Świniarski, Michał [Faculty of Physics, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw (Poland); Szalkowski, Marcin [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland); Zdrojek, Mariusz; Judek, Jarosław [Faculty of Physics, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw (Poland); Mackowski, Sebastian, E-mail: mackowski@fizyka.umk.pl [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland); Wroclaw Research Center EIT+, Stablowicka 147, Wroclaw (Poland); Kaminska, Izabela [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland)

2016-02-15

Combination of fluorescence imaging and spectroscopy results indicates that single-walled carbon nanotubes are extremely efficient quenchers of fluorescence emission associated with chlorophylls embedded in a natural photosynthetic complex, peridinin-chlorophyll-protein. When deposited on a network of the carbon nanotubes forming a thin film, the emission of the photosynthetic complexes diminishes almost completely. This strong reduction of fluorescence intensity is accompanied with dramatic shortening of the fluorescence lifetime. Concluding, such thin films of carbon nanotubes can be extremely efficient energy acceptors in structures involving biologically functional complexes. - Highlights: • Fluorescence imaging of carbon nanotube - based hybrid structure. • Observation of efficient energy transfer from chlorophylls to carbon nanotubes.

Pea border cell maturation and release involve complex cell wall structural dynamics

DEFF Research Database (Denmark)

Mravec, Jozef; Guo, Xiaoyuan; Hansen, Aleksander Riise

2017-01-01

The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases though, plant cells are programmed to detach and root cap-derived border cells are examples of this....... Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we...... undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immuno-carbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy (FT-IR), quantitative RT-PCR of cell wall biosynthetic genes, analysis...

A synthetic NO reduction cycle on a bis(pyrazolato)-bridged dinuclear ruthenium complex including photo-induced transformation.

Science.gov (United States)

Arikawa, Yasuhiro; Hiura, Junko; Tsuchii, Chika; Kodama, Mika; Matsumoto, Naoki; Umakoshi, Keisuke

2018-05-17

A synthetic NO reduction cycle (2NO + 2H+ + 2e- → N2O + H2O) on a dinuclear platform {(TpRu)2(μ-pz)2} (Tp = HB(pyrazol-1-yl)3) was achieved, where an unusual N-N coupling complex was included. Moreover, an interesting photo-induced conversion of the N-N coupling complex to an oxido-bridged complex was revealed.

Understanding how the complex molecular architecture of mannan-degrading hydrolases contributes to plant cell wall degradation.

Science.gov (United States)

Zhang, Xiaoyang; Rogowski, Artur; Zhao, Lei; Hahn, Michael G; Avci, Utku; Knox, J Paul; Gilbert, Harry J

2014-01-24

Microbial degradation of plant cell walls is a central component of the carbon cycle and is of increasing importance in environmentally significant industries. Plant cell wall-degrading enzymes have a complex molecular architecture consisting of catalytic modules and, frequently, multiple non-catalytic carbohydrate binding modules (CBMs). It is currently unclear whether the specificities of the CBMs or the topology of the catalytic modules are the primary drivers for the specificity of these enzymes against plant cell walls. Here, we have evaluated the relationship between CBM specificity and their capacity to enhance the activity of GH5 and GH26 mannanases and CE2 esterases against intact plant cell walls. The data show that cellulose and mannan binding CBMs have the greatest impact on the removal of mannan from tobacco and Physcomitrella cell walls, respectively. Although the action of the GH5 mannanase was independent of the context of mannan in tobacco cell walls, a significant proportion of the polysaccharide was inaccessible to the GH26 enzyme. The recalcitrant mannan, however, was fully accessible to the GH26 mannanase appended to a cellulose binding CBM. Although CE2 esterases display similar specificities against acetylated substrates in vitro, only CjCE2C was active against acetylated mannan in Physcomitrella. Appending a mannan binding CBM27 to CjCE2C potentiated its activity against Physcomitrella walls, whereas a xylan binding CBM reduced the capacity of esterases to deacetylate xylan in tobacco walls. This work provides insight into the biological significance for the complex array of hydrolytic enzymes expressed by plant cell wall-degrading microorganisms.

Formation of wood secondary cell wall may involve two type cellulose synthase complexes in Populus.

Science.gov (United States)

Xi, Wang; Song, Dongliang; Sun, Jiayan; Shen, Junhui; Li, Laigeng

2017-03-01

Cellulose biosynthesis is mediated by cellulose synthases (CesAs), which constitute into rosette-like cellulose synthase complexe (CSC) on the plasma membrane. Two types of CSCs in Arabidopsis are believed to be involved in cellulose synthesis in the primary cell wall and secondary cell walls, respectively. In this work, we found that the two type CSCs participated cellulose biosynthesis in differentiating xylem cells undergoing secondary cell wall thickening in Populus. During the cell wall thickening process, expression of one type CSC genes increased while expression of the other type CSC genes decreased. Suppression of different type CSC genes both affected the wall-thickening and disrupted the multilaminar structure of the secondary cell walls. When CesA7A was suppressed, crystalline cellulose content was reduced, which, however, showed an increase when CesA3D was suppressed. The CesA suppression also affected cellulose digestibility of the wood cell walls. The results suggest that two type CSCs are involved in coordinating the cellulose biosynthesis in formation of the multilaminar structure in Populus wood secondary cell walls.

A Review of Double-Walled and Triple-Walled Carbon Nanotube Synthesis and Applications

Directory of Open Access Journals (Sweden)

Kazunori Fujisawa

2016-04-01

Full Text Available Double- and triple-walled carbon nanotubes (DWNTs and TWNTs consist of coaxially-nested two and three single-walled carbon nanotubes (SWNTs. They act as the geometrical bridge between SWNTs and multi-walled carbon nanotubes (MWNTs, providing an ideal model for studying the coupling interactions between different shells in MWNTs. Within this context, this article comprehensively reviews various synthetic routes of DWNTs’ and TWNTs’ production, such as arc discharge, catalytic chemical vapor deposition and thermal annealing of pea pods (i.e., SWNTs encapsulating fullerenes. Their structural features, as well as promising applications and future perspectives are also discussed.

Beam model for seismic analysis of complex shear wall structure based on the strain energy equivalence

International Nuclear Information System (INIS)

Reddy, G.R.; Mahajan, S.C.; Suzuki, Kohei

1997-01-01

A nuclear reactor building structure consists of shear walls with complex geometry, beams and columns. The complexity of the structure is explained in the section Introduction. Seismic analysis of the complex reactor building structure using the continuum mechanics approach may produce good results but this method is very difficult to apply. Hence, the finite element approach is found to be an useful technique for solving the dynamic equations of the reactor building structure. In this approach, the model which uses finite elements such as brick, plate and shell elements may produce accurate results. However, this model also poses some difficulties which are explained in the section Modeling Techniques. Therefore, seismic analysis of complex structures is generally carried out using a lumped mass beam model. This model is preferred because of its simplicity and economy. Nevertheless, mathematical modeling of a shear wall structure as a beam requires specialized skill and a thorough understanding of the structure. For accurate seismic analysis, it is necessary to model more realistically the stiffness, mass and damping. In linear seismic analysis, modeling of the mass and damping may pose few problems compared to modeling the stiffness. When used to represent a complex structure, the stiffness of the beam is directly related to the shear wall section properties such as area, shear area and moment of inertia. Various beam models which are classified based on the method of stiffness evaluation are also explained under the section Modeling Techniques. In the section Case Studies the accuracy and simplicity of the beam models are explained. Among various beam models, the one which evaluates the stiffness using strain energy equivalence proves to be the simplest and most accurate method for modeling the complex shear wall structure. (author)

Modelling complex draft-tube flows using near-wall turbulence closures

Energy Technology Data Exchange (ETDEWEB)

Ventikos, Y.; Sotiropoulos, F. [Georgia Institute of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering; Patel, V.C. [Univ. of Iowa, Iowa City, IA (United States). Iowa Institute of Hydraulic Research

1996-12-31

This paper presents a finite-volume method for simulating flows through complex hydroturbine draft-tube configurations using near-wall turbulence closures. The method employs the artificial-compressibility pressure-velocity coupling approach in conjunction with multigrid acceleration for fast convergence on very fine grids. Calculations are carried out for a draft tube with two downstream piers on a computational mesh consisting of 1.2x10{sup 6} nodes. Comparisons of the computed results with measurements demonstrate the ability of the method to capture most experimental trends with reasonable accuracy. Calculated three-dimensional particle traces reveal very complex flow features in the vicinity of the piers, including horse-shoe longitudinal vortices and and regions of flow reversal.

Spatio-temporal diversification of the cell wall matrix materials in the developing stomatal complexes of Zea mays.

Science.gov (United States)

Giannoutsou, E; Apostolakos, P; Galatis, B

2016-11-01

The matrix cell wall materials, in developing Zea mays stomatal complexes are asymmetrically distributed, a phenomenon appearing related to the local cell wall expansion and deformation, the establishment of cell polarity, and determination of the cell division plane. In cells of developing Zea mays stomatal complexes, definite cell wall regions expand determinately and become locally deformed. This differential cell wall behavior is obvious in the guard cell mother cells (GMCs) and the subsidiary cell mother cells (SMCs) that locally protrude towards the adjacent GMCs. The latter, emitting a morphogenetic stimulus, induce polarization/asymmetrical division in SMCs. Examination of immunolabeled specimens revealed that homogalacturonans (HGAs) with a high degree of de-esterification (2F4- and JIM5-HGA epitopes) and arabinogalactan proteins are selectively distributed in the extending and deformed cell wall regions, while their margins are enriched with rhamnogalacturonans (RGAs) containing highly branched arabinans (LM6-RGA epitope). In SMCs, the local cell wall matrix differentiation constitutes the first structural event, indicating the establishment of cell polarity. Moreover, in the premitotic GMCs and SMCs, non-esterified HGAs (2F4-HGA epitope) are preferentially localized in the cell wall areas outlining the cytoplasm where the preprophase band is formed. In these areas, the forthcoming cell plate fuses with the parent cell walls. These data suggest that the described heterogeneity in matrix cell wall materials is probably involved in: (a) local cell wall expansion and deformation, (b) the transduction of the inductive GMC stimulus, and (c) the determination of the division plane in GMCs and SMCs.

Survey and research of the latest works of LES about models near wall boundary and applications to complex flow path

International Nuclear Information System (INIS)

Sakai, Norio; Shimizu, Takeshi

2005-02-01

Since treatments for wall boundaries and flows around complex paths are issues in LES modeling, a literature research on the LES methods for wall boundaries and applications to flows at complex paths was conducted to investigate the latest trend. Publications of domestic or international societies, workshops, symposiums, and journals about for past 3 years (2001-2004) were searched and collected, from which 23 research papers were selected and investigated. For the investigation, the treatments for wall boundaries used in the literature were classified roughly into five methods, i.e. (1) no-slip condition, (2) algebraic wall model (wall function), (3) wall model based on boundary-layer approximations (differential equation wall model), (4) hybrid method, (5) immersed boundary method. No-slip conditions were widely applied in recent works. For algebraic wall models, new wall functions that considered the effect of the velocity component vertical to a wall or circulation regions were examined. There were also some researches that devised the process of calculating the wall-shear stress with a conventional wall function. The researches using differential equation wall models presented the dynamic modification of model coefficients, or the application of high-order turbulence model such as the k-e model to the solution of Navier-Stokes equation in the boundary layer. The researches of hybrid methods focused on the discontinuity of velocity and eddy viscosity at the LES/RANS interface. Several researches that adopted immersed boundary methods for Cartesian girds with curved wall boundaries introduced the investigation of the Poisson solvers and the numerical modification of pressure boundary conditions. Many of investigated researches used hybrid methods. Thus, it is expected that they will be mainly applied to large-scale and complex simulations if the standard treatment for the discontinuity at the interface is developed. (author)

Effects of reactive Mn(III)-oxalate complexes on structurally intact plant cell walls

Science.gov (United States)

Summering, J. A.; Keiluweit, M.; Goni, M. A.; Nico, P. S.; Kleber, M.

2011-12-01

Lignin components in the in plant litter are commonly assumed to have longer residence times in soil than many other compounds, which are supposedly, more easily degradable. The supposed resistance of lignin compounds to decomposition is generally attributed to the complex chain of biochemical steps required to create footholds in the non-porous structure of ligno-cellulose in cell walls. Interestingly, Mn(III) complexes have shown the ability to degrade ligno-cellulose. Mn(III) chelated by ligands such as oxalate are soluble oxidizers with a high affinity for lignin structures. Here we determined (i) the formation and decay kinetics of the Mn(III)-oxalate complexes in aqueous solution and (ii) the effects that these complexes have on intact ligno-cellulose. UV/vis spectroscopy and iodometric titrations confirmed the transient nature of Mn(III)-oxalate complexes with decay rates being in the order of hours. Zinnia elegans tracheary elements - a model ligno-cellulose substrate - were treated with Mn(III)-oxalate complexes in a newly developed flow-through reactor. Soluble decomposition products released during the treatment were analyzed by GC/MS and the degree of cell integrity was measured by cell counts, pre- and post-treatment counts indicate a decrease in intact Zinnia elegans as a result of Mn(III)-treatment. GC/MS results showed the release of a multitude of solubilized lignin breakdown products from plant cell walls. We conclude that Mn(III)-oxalate complexes have the ability to lyse intact plant cells and solubilize lignin. Lignin decomposition may thus be seen as resource dependent, with Mn(III) a powerful resource that should be abundant in terrestrial characterized by frequent redox fluctuations.

Diversity of total and functional microbiome of anammox reactors fed with complex and synthetic nitrogen-rich wastewaters

DEFF Research Database (Denmark)

Gülay, Arda; Pellicer i Nàcher, Carles; Mutlu, Ayten Gizem

diversity than the bioreactors treating synthetic wastewaters inferred from observed OTUs0.03, Chao1, Shannon index and Phylogenetic distance calculations. Differences in total microbial diversity agreed with the ecological theory concerning the positive correlation between substrate complexity...

Structural studies of complex carbohydrates of plant cell walls. Progress report, June 15, 1992--June 14, 1993

Energy Technology Data Exchange (ETDEWEB)

Darvill, A.G.

1994-10-01

This report contains the abstracts of fourteen papers published, in press, or in preparation reporting on research activities to investigate the structure, as well as the function of cell walls in plants. This document also contains research on methods to determine the structure of complex carbohydrates of the cell walls.

Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics.

Science.gov (United States)

Mravec, Jozef; Guo, Xiaoyuan; Hansen, Aleksander Riise; Schückel, Julia; Kračun, Stjepan Krešimir; Mikkelsen, Maria Dalgaard; Mouille, Grégory; Johansen, Ida Elisabeth; Ulvskov, Peter; Domozych, David S; Willats, William George Tycho

2017-06-01

The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases, though, plant cells are programmed to detach, and root cap-derived border cells are examples of this. Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we undertook a systematic, detailed analysis of pea ( Pisum sativum ) root tip cell walls. Our study included immunocarbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy, quantitative reverse transcription-PCR of cell wall biosynthetic genes, analysis of hydrolytic activities, transmission electron microscopy, and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our findings provide a new level of detail about border cell maturation and enable us to develop a model of the separation process. We propose that loss of adhesion by the dissolution of homogalacturonan in the middle lamellae is augmented by an active biophysical process of cell curvature driven by the polarized distribution of xyloglucan and extensin epitopes. © 2017 American Society of Plant Biologists. All Rights Reserved.

Positioning cell wall synthetic complexes by the bacterial morphogenetic proteins MreB and MreD.

Science.gov (United States)

White, Courtney L; Kitich, Aleksandar; Gober, James W

2010-05-01

In Caulobacter crescentus, intact cables of the actin homologue, MreB, are required for the proper spatial positioning of MurG which catalyses the final step in peptidoglycan precursor synthesis. Similarly, in the periplasm, MreC controls the spatial orientation of the penicillin binding proteins and a lytic transglycosylase. We have now found that MreB cables are required for the organization of several other cytosolic murein biosynthetic enzymes such as MraY, MurB, MurC, MurE and MurF. We also show these proteins adopt a subcellular pattern of localization comparable to MurG, suggesting the existence of cytoskeletal-dependent interactions. Through extensive two-hybrid analyses, we have now generated a comprehensive interaction map of components of the bacterial morphogenetic complex. In the cytosol, this complex contains both murein biosynthetic enzymes and morphogenetic proteins, including RodA, RodZ and MreD. We show that the integral membrane protein, MreD, is essential for lateral peptidoglycan synthesis, interacts with the precursor synthesizing enzymes MurG and MraY, and additionally, determines MreB localization. Our results suggest that the interdependent localization of MreB and MreD functions to spatially organize a complex of peptidoglycan precursor synthesis proteins, which is required for propagation of a uniform cell shape and catalytically efficient peptidoglycan synthesis.

Synthetic biology: programming cells for biomedical applications.

Science.gov (United States)

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

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

Papillae formation on trichome cell walls requires the function of the mediator complex subunit Med25.

Science.gov (United States)

Fornero, Christy; Suo, Bangxia; Zahde, Mais; Juveland, Katelyn; Kirik, Viktor

2017-11-01

Glassy Hair 1 (GLH1) gene that promotes papillae formation on trichome cell walls was identified as a subunit of the transcriptional mediator complex MED25. The MED25 gene is shown to be expressed in trichomes. The expression of the trichome development marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) is not affected in the glh1 mutant. Presented data suggest that Arabidopsis MED25 mediator component is likely involved in the transcription of genes promoting papillae deposition in trichomes. The plant cell wall plays an important role in communication, defense, organization and support. The importance of each of these functions varies by cell type. Specialized cells, such as Arabidopsis trichomes, exhibit distinct cell wall characteristics including papillae. To better understand the molecular processes important for papillae deposition on the cell wall surface, we identified the GLASSY HAIR 1 (GLH1) gene, which is necessary for papillae formation. We found that a splice-site mutation in the component of the transcriptional mediator complex MED25 gene is responsible for the near papillae-less phenotype of the glh1 mutant. The MED25 gene is expressed in trichomes. Reporters for trichome developmental marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) were not affected in the glh1 mutant. Collectively, the presented results show that MED25 is necessary for papillae formation on the cell wall surface of leaf trichomes and suggest that the Arabidopsis MED25 mediator component is likely involved in the transcription of a subset of genes that promote papillae deposition in trichomes.

Oxygen Sensing by the Hybrid Langmuir-Blodgett Films of Iridium(III Complexes and Synthetic Saponite on the Basis of Energy Transfer

Directory of Open Access Journals (Sweden)

Hisako Sato

2017-09-01

Full Text Available An ultra-thin hybrid film of amphiphilic iridium(III complexes and synthetic saponite was manipulated by means of the modified Langmuir-Blodgett method. In the film deposited onto a quartz substrate, the external mixed molecular layer of amphiphilic iridium(III complexes was reinforced by the inner layer of exfoliated synthetic saponite. As components of the molecular layer, two iridium(III complexes were used: [Ir(dfppy2(dc9bpy]+ (dfppyH = 2-(4′,6′-difluorophenyl pyridine; dc9bpy = 4,4′-dinonyl-2,2′-bipyridine (denoted as DFPPY and [Ir(piq2(dc9bpy]+ (piqH = 1-phenyisoquinoline denoted as PIQ. The emission spectra from the films changed from blue to red maxima with the decrease of a ratio of DFPPY/PIQ due to the energy transfer from excited DFPPY to PIQ. The intensity of red decreased with the increase of oxygen pressure through the quenching of excited iridium(III complexes, promising a possibility as an oxygen-sensing film.

Tissue Harmonic Synthetic Aperture Imaging

DEFF Research Database (Denmark)

Rasmussen, Joachim

The main purpose of this PhD project is to develop an ultrasonic method for tissue harmonic synthetic aperture imaging. The motivation is to advance the field of synthetic aperture imaging in ultrasound, which has shown great potentials in the clinic. Suggestions for synthetic aperture tissue...... system complexity compared to conventional synthetic aperture techniques. In this project, SASB is sought combined with a pulse inversion technique for 2nd harmonic tissue harmonic imaging. The advantages in tissue harmonic imaging (THI) are expected to further improve the image quality of SASB...

Structural Studies of Complex Carbohydrates of Plant Cell Walls

Energy Technology Data Exchange (ETDEWEB)

Darvill, Alan [Univ. of Georgia, Athens, GA (United States); Hahn, Michael G. [Univ. of Georgia, Athens, GA (United States); O' Neill, Malcolm A. [Univ. of Georgia, Athens, GA (United States); York, William S. [Univ. of Georgia, Athens, GA (United States)

2015-02-17

Most of the solar energy captured by land plants is converted into the polysaccharides (cellulose, hemicellulose, and pectin) that are the predominant components of the cell wall. These walls, which account for the bulk of plant biomass, have numerous roles in the growth and development of plants. Moreover, these walls have a major impact on human life as they are a renewable source of biomass, a source of diverse commercially useful polymers, a major component of wood, and a source of nutrition for humans and livestock. Thus, understanding the molecular mechanisms that lead to wall assembly and how cell walls and their component polysaccharides contribute to plant growth and development is essential to improve and extend the productivity and value of plant materials. The proposed research will develop and apply advanced analytical and immunological techniques to study specific changes in the structures and interactions of the hemicellulosic and pectic polysaccharides that occur during differentiation and in response to genetic modification and chemical treatments that affect wall biosynthesis. These new techniques will make it possible to accurately characterize minute amounts of cell wall polysaccharides so that subtle changes in structure that occur in individual cell types can be identified and correlated to the physiological or developmental state of the plant. Successful implementation of this research will reveal fundamental relationships between polysaccharide structure, cell wall architecture, and cell wall functions.

Properties of meshes used in hernia repair: a comprehensive review of synthetic and biologic meshes.

Science.gov (United States)

Ibrahim, Ahmed M S; Vargas, Christina R; Colakoglu, Salih; Nguyen, John T; Lin, Samuel J; Lee, Bernard T

2015-02-01

Data on the mechanical properties of the adult human abdominal wall have been difficult to obtain rendering manufacture of the ideal mesh for ventral hernia repair a challenge. An ideal mesh would need to exhibit greater biomechanical strength and elasticity than that of the abdominal wall. The aim of this study is to quantitatively compare the biomechanical properties of the most commonly used synthetic and biologic meshes in ventral hernia repair and presents a comprehensive literature review. A narrative review of the literature was performed using the PubMed database spanning articles from 1982 to 2012 including a review of company Web sites to identify all available information relating to the biomechanical properties of various synthetic and biologic meshes used in ventral hernia repair. There exist differences in the mechanical properties and the chemical nature of different meshes. In general, most synthetic materials have greater stiffness and elasticity than what is required for abdominal wall reconstruction; however, each exhibits unique properties that may be beneficial for clinical use. On the contrary, biologic meshes are more elastic but less stiff and with a lower tensile strength than their synthetic counterparts. The current standard of practice for the treatment of ventral hernias is the use of permanent synthetic mesh material. Recently, biologic meshes have become more frequently used. Most meshes exhibit biomechanical properties over the known abdominal wall thresholds. Augmenting strength requires increasing amounts of material contributing to more stiffness and foreign body reaction, which is not necessarily an advantage. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Synthetic Defects for Vibrothermography

Science.gov (United States)

Renshaw, Jeremy; Holland, Stephen D.; Thompson, R. Bruce; Eisenmann, David J.

2010-02-01

Synthetic defects are an important tool used for characterizing the performance of nondestructive evaluation techniques. Viscous material-filled synthetic defects were developed for use in vibrothermography (also known as sonic IR) as a tool to improve inspection accuracy and reliability. This paper describes how the heat-generation response of these VMF synthetic defects is similar to the response of real defects. It also shows how VMF defects can be applied to improve inspection accuracy for complex industrial parts and presents a study of their application in an aircraft engine stator vane.

Pea Border Cell Maturation and Release Involve Complex Cell Wall Structural Dynamics1[OPEN

Science.gov (United States)

2017-01-01

The adhesion of plant cells is vital for support and protection of the plant body and is maintained by a variety of molecular associations between cell wall components. In some specialized cases, though, plant cells are programmed to detach, and root cap-derived border cells are examples of this. Border cells (in some species known as border-like cells) provide an expendable barrier between roots and the environment. Their maturation and release is an important but poorly characterized cell separation event. To gain a deeper insight into the complex cellular dynamics underlying this process, we undertook a systematic, detailed analysis of pea (Pisum sativum) root tip cell walls. Our study included immunocarbohydrate microarray profiling, monosaccharide composition determination, Fourier-transformed infrared microspectroscopy, quantitative reverse transcription-PCR of cell wall biosynthetic genes, analysis of hydrolytic activities, transmission electron microscopy, and immunolocalization of cell wall components. Using this integrated glycobiology approach, we identified multiple novel modes of cell wall structural and compositional rearrangement during root cap growth and the release of border cells. Our findings provide a new level of detail about border cell maturation and enable us to develop a model of the separation process. We propose that loss of adhesion by the dissolution of homogalacturonan in the middle lamellae is augmented by an active biophysical process of cell curvature driven by the polarized distribution of xyloglucan and extensin epitopes. PMID:28400496

Robotic Transversus Abdominis Release (TAR: is it possible to offer minimally invasive surgery for abdominal wall complex defects?

Directory of Open Access Journals (Sweden)

MARIA VITÓRIA FRANÇA DO AMARAL

Full Text Available ABSTRACT We describe the preliminary national experience and the early results of the use of robotic surgery to perform the posterior separation of abdominal wall components by the Transversus Abdominis Release (TAR technique for the correction of complex defects of the abdominal wall. We performed the procedures between 04/2/2015 and 06/15/2015 and the follow-up time was up to six months, with a minimum of two months. The mean surgical time was five hours and 40 minutes. Two patients required laparoscopic re-intervention, since one developed hernia by peritoneal migration of the mesh and one had mesh extrusion. The procedure proved to be technically feasible, with a still long surgical time. Considering the potential advantages of robotic surgery and those related to TAR and the results obtained when these two techniques are associated, we conclude that they seem to be a good option for the correction of complex abdominal wall defects.

Lower abdominal wall reconstructions with pedicled rectus femoris flaps

International Nuclear Information System (INIS)

Arashiro, Ken; Nishizeki, Osamu; Ishida, Kunihiro

2003-01-01

During the past 10 years, seven pedicled rectus femoris muscle or musculocutaneous flaps were used to repair lower abdominal defects; three recalcitrant incisional hernias with previous radiotherapy, two long-standing wound infections after synthetic mesh reconstruction, one posttraumatic wall defect and one metastatic tumor. There were two flap complications, one skin paddle necrosis and one wound infection. There was no significant disability of the donor limb encountered. During the two-year and seven month average follow-up, there was no recurrence of the problems except for one minor fascial dehiscence in the patient with metastatic abdominal wall tumor. Easy approach, rapid harvest, relatively large and reliable overlying fascia lata, a single dominant neurovascular pedicle, easy primary closure of the donor site, and minimal donor site morbidity all make the rectus femoris flap a good alternative flap for lower abdominal wall reconstruction. It is especially useful in a condition where synthetic mesh would be unsuitable for defects with infection or recurrent incisional hernia after radiotherapy. (author)

Distributed detection of communities in complex networks using synthetic coordinates

International Nuclear Information System (INIS)

Papadakis, H; Fragopoulou, P; Panagiotakis, C

2014-01-01

Various applications like finding Web communities, detecting the structure of social networks, and even analyzing a graph’s structure to uncover Internet attacks are just some of the applications for which community detection is important. In this paper, we propose an algorithm that finds the entire community structure of a network, on the basis of local interactions between neighboring nodes and an unsupervised distributed hierarchical clustering algorithm. The novelty of the proposed approach, named SCCD (standing for synthetic coordinate community detection), lies in the fact that the algorithm is based on the use of Vivaldi synthetic network coordinates computed by a distributed algorithm. The current paper not only presents an efficient distributed community finding algorithm, but also demonstrates that synthetic network coordinates could be used to derive efficient solutions to a variety of problems. Experimental results and comparisons with other methods from the literature are presented for a variety of benchmark graphs with known community structure, derived from varying a number of graph parameters and real data set graphs. The experimental results and comparisons to existing methods with similar computation cost on real and synthetic data sets demonstrate the high performance and robustness of the proposed scheme. (paper)

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

Science.gov (United States)

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

Synthesis and Characterization of Hexahapto-Chromium Complexes of Single-Walled Carbon Nanotubes

KAUST Repository

Kalinina, Irina

2016-12-17

This chapter employs purified pristine single-walled carbon nanotubes (SWNTs) and octadecylaminefunctionalized-SWNTs. These SWNTs are employed for investigate the potential of the SWNT sidewall to function as a hexahapto ligand for chromium (Cr), with in-depth characterization of the products using some of the techniques, such as thermogravimetric analysis (TGA), transmission electron microscopy (TEM), x-ray photoelectron spectroscopy (XPS). Purified electric arc (EA)-produced SWNTs (P2-SWNT) and octadecylaminefunctionalized SWNTs were obtained from Carbon Solutions, Inc. The TEM images show the removal of the Cr particles from the outer surface of the SWNT bundles in the SWNT-Cr complexes after decomplexation; Cr attachment to the surface of the as-prepared complexes (η6-SWNT)Cr(CO)3 and (η6-SWNT-CONH(CH2)17CH3)Cr(CO)3 is clearly evident. The positions of the bands in the Raman spectra of SWNTs are sensitive to doping and thus the chapter examines the effect of complexation of the Cr(CO)3 and Cr(η6-benzene) units on the position of the G and 2D bands in the (η6-SWNT)Cr(CO)3 and (η6-SWNT)Cr(η6-benzene) complexes.

Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach

International Nuclear Information System (INIS)

Economou, Nicoleta J.; Zentner, Isaac J.; Lazo, Edwin; Jakoncic, Jean; Stojanoff, Vivian; Weeks, Stephen D.; Grasty, Kimberly C.; Cocklin, Simon; Loll, Patrick J.

2013-01-01

Using a carrier-protein strategy, the structure of teicoplanin bound to its bacterial cell-wall target has been determined. The structure reveals the molecular determinants of target recognition, flexibility in the antibiotic backbone and intrinsic radiation sensitivity of teicoplanin. Multidrug-resistant bacterial infections are commonly treated with glycopeptide antibiotics such as teicoplanin. This drug inhibits bacterial cell-wall biosynthesis by binding and sequestering a cell-wall precursor: a d-alanine-containing peptide. A carrier-protein strategy was used to crystallize the complex of teicoplanin and its target peptide by fusing the cell-wall peptide to either MBP or ubiquitin via native chemical ligation and subsequently crystallizing the protein–peptide–antibiotic complex. The 2.05 Å resolution MBP–peptide–teicoplanin structure shows that teicoplanin recognizes its ligand through a combination of five hydrogen bonds and multiple van der Waals interactions. Comparison of this teicoplanin structure with that of unliganded teicoplanin reveals a flexibility in the antibiotic peptide backbone that has significant implications for ligand recognition. Diffraction experiments revealed an X-ray-induced dechlorination of the sixth amino acid of the antibiotic; it is shown that teicoplanin is significantly more radiation-sensitive than other similar antibiotics and that ligand binding increases radiosensitivity. Insights derived from this new teicoplanin structure may contribute to the development of next-generation antibacterials designed to overcome bacterial resistance

Novel heterometallic metal–azido complex synthesized by “one-step” reaction: synthetic strategy and magnetic properties

International Nuclear Information System (INIS)

Jiao, Yong-Kun; Li, Xiu-Ping; Zhao, Cui; Wang, Hai-Chao; Xue, Min; Zhao, Jiong-Peng; Liu, Fu-Chen

2013-01-01

A novel heterometallic complex, [Ni 2 Mn(N 3 ) 2 (nic) 4 ·(H 2 O) 2 ] n (1) (nic=nicotinate), was obtained by assembling MnCl 2 ·4H 2 O, Ni(NO 3 ) 2 ·6H 2 O, NaN 3 and nicotinic acid with a “one step” synthetic strategy—hydrothermal reaction. The 3D structure of the complex can be described as end-on (EO) azido and syn,syn carboxylates mixed bridged by alternate Ni–Mn–Ni trimers linked by the nicotinate. Dominant ferromagnetic interactions were observed between the Ni II and Mn II ions in the trimer. - Graphical abstract: A novel heterometallic 3D complex [Ni 2 Mn(N 3 ) 2 (nic) 4 ·(H 2 O) 2 ] n (1) (nic=nicotinate) was synthesized by hydrothermal reaction. This complex exhibits interesting structural and magnetic properties. - Highlights: • It is difficult to construct simple coordination complexes with azide as “ligands” to obtain heterometallic metal–azido compounds. • A “one-step” method—hydrothermal reaction— was introduced to avoid the disadvantages of azide mentioned above. • The magnetic property is different with the isostructural homometal–azido complex due to the changed metal center

Attraction of Chrysoperla carnea complex and Chrysopa spp. lacewings (Neuroptera: Chrysopidae) to aphid sex pheromone components and a synthetic blend of floral compounds in Hungary.

Science.gov (United States)

Koczor, Sándor; Szentkirályi, Ferenc; Birkett, Michael A; Pickett, John A; Voigt, Erzsébet; Tóth, Miklós

2010-12-01

The deployment of synthetic attractants for the manipulation of lacewing populations as aphid predators is currently used in integrated pest management. This study investigates a synthetic bait comprising floral compounds previously found to attract the Chrysoperla carnea complex, and, for the first time, the aphid sex pheromone components (1R,4aS,7S,7aR)-nepetalactol and (4aS,7S,7aR)-nepetalactone, in field experiments in Hungary, for their ability to manipulate lacewing populations. The synthetic floral bait attracted both sexes of the Chrysoperla carnea complex, and Chrysopa formosa Brauer showed minimal attraction. The aphid sex pheromone compounds alone attracted males of C. formosa and C. pallens (Rambur). When the two baits were combined, Chrysopa catches were similar to those with aphid sex pheromone baits alone, but carnea complex catches decreased significantly (by 85-88%). As the floral bait alone attracted both sexes of the carnea complex, it showed potential to manipulate the location of larval density via altering the site of oviposition. Aphid sex pheromone compounds alone attracted predatory males of Chrysopa spp. and can potentially be used to enhance biological control of aphids. For the carnea complex, however, a combination of both baits is not advantageous because of the decrease in adults attracted. Assumptions of intraguild avoidance underlying this phenomenon are discussed. Copyright © 2010 Society of Chemical Industry.

Efficacy of bio and synthetic pesticides against the American ...

African Journals Online (AJOL)

Management for the bollworm complex in Uganda is largely synthetic chemical use with little or no biopesticide use which reduces natural enemies population and resistance development to continuous use of a single synthetic pesticide product. Therefore this study aimed at determining the efficacy of bio and synthetic ...

Mammalian synthetic biology: emerging medical applications.

Science.gov (United States)

Kis, Zoltán; Pereira, Hugo Sant'Ana; Homma, Takayuki; Pedrigi, Ryan M; Krams, Rob

2015-05-06

In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Mirror-Imaged Rapid Prototype Skull Model and Pre-Molded Synthetic Scaffold to Achieve Optimal Orbital Cavity Reconstruction.

Science.gov (United States)

Park, Sung Woo; Choi, Jong Woo; Koh, Kyung S; Oh, Tae Suk

2015-08-01

Reconstruction of traumatic orbital wall defects has evolved to restore the original complex anatomy with the rapidly growing use of computer-aided design and prototyping. This study evaluated a mirror-imaged rapid prototype skull model and a pre-molded synthetic scaffold for traumatic orbital wall reconstruction. A single-center retrospective review was performed of patients who underwent orbital wall reconstruction after trauma from 2012 to 2014. Patients were included by admission through the emergency department after facial trauma or by a tertiary referral for post-traumatic orbital deformity. Three-dimensional (3D) computed tomogram-based mirror-imaged reconstruction images of the orbit and an individually manufactured rapid prototype skull model by a 3D printing technique were obtained for each case. Synthetic scaffolds were anatomically pre-molded using the skull model as guide and inserted at the individual orbital defect. Postoperative complications were assessed and 3D volumetric measurements of the orbital cavity were performed. Paired samples t test was used for statistical analysis. One hundred four patients with immediate orbital defect reconstructions and 23 post-traumatic orbital deformity reconstructions were included in this study. All reconstructions were successful without immediate postoperative complications, although there were 10 cases with mild enophthalmos and 2 cases with persistent diplopia. Reoperations were performed for 2 cases of persistent diplopia and secondary touchup procedures were performed to contour soft tissue in 4 cases. Postoperative volumetric measurement of the orbital cavity showed nonsignificant volume differences between the damaged orbit and the reconstructed orbit (21.35 ± 1.93 vs 20.93 ± 2.07 cm(2); P = .98). This protocol was extended to severe cases in which more than 40% of the orbital frame was lost and combined with extensive soft tissue defects. Traumatic orbital reconstruction can be optimized and

Mechanical behaviour of synthetic surgical meshes: finite element simulation of the herniated abdominal wall.

Science.gov (United States)

Hernández-Gascón, B; Peña, E; Melero, H; Pascual, G; Doblaré, M; Ginebra, M P; Bellón, J M; Calvo, B

2011-11-01

The material properties of meshes used in hernia surgery contribute to the overall mechanical behaviour of the repaired abdominal wall. The mechanical response of a surgical mesh has to be defined since the haphazard orientation of an anisotropic mesh can lead to inconsistent surgical outcomes. This study was designed to characterize the mechanical behaviour of three surgical meshes (Surgipro®, Optilene® and Infinit®) and to describe a mechanical constitutive law that accurately reproduces the experimental results. Finally, through finite element simulation, the behaviour of the abdominal wall was modelled before and after surgical mesh implant. Uniaxial loading of mesh samples in two perpendicular directions revealed the isotropic response of Surgipro® and the anisotropic behaviour of Optilene® and Infinit®. A phenomenological constitutive law was used to reproduce the measured experimental curves. To analyze the mechanical effect of the meshes once implanted in the abdomen, finite element simulation of the healthy and partially herniated repaired rabbit abdominal wall served to reproduce wall behaviour before and after mesh implant. In all cases, maximal displacements were lower and maximal principal stresses higher in the implanted abdomen than the intact wall model. Despite the fact that no mesh showed a behaviour that perfectly matched that of abdominal muscle, the Infinit® mesh was able to best comply with the biomechanics of the abdominal wall. Copyright © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

[Progress in synthetic biology of "973 Funding Program" in China].

Science.gov (United States)

Chen, Guoqiang; Wang, Ying

2015-06-01

This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.

Perpendicularly magnetized CoFeB multilayers with tunable interlayer exchange for synthetic ferrimagnets

Energy Technology Data Exchange (ETDEWEB)

Pirro, P., E-mail: ppirro@physik.uni-kl.de [Institut Jean Lamour, Université de Lorraine, UMR 7198 CNRS, 54506 Vandoeuvre-lés-Nancy (France); Hamadeh, A.; Lavanant-Jambert, M. [Institut Jean Lamour, Université de Lorraine, UMR 7198 CNRS, 54506 Vandoeuvre-lés-Nancy (France); Meyer, T. [Fachbereich Physik and Landesforschungszentrum OPTIMAS, Technische Universität Kaiserslautern, 67663 Kaiserslautern (Germany); Tao, B.; Rosario, E.; Lu, Y.; Hehn, M.; Mangin, S.; Petit Watelot, S. [Institut Jean Lamour, Université de Lorraine, UMR 7198 CNRS, 54506 Vandoeuvre-lés-Nancy (France)

2017-06-15

Highlights: • MgO/CoFeB/Ta/CoFeB/MgO multilayers as synthetic ferrimagnets. • Comprehensive characterization by measurement of static and dynamic properties. • Different pinning for domain walls with different alignment of the individual layers. - Abstract: A study of the multilayer system MgO/CoFeB(1.1 nm)/Ta(t)/CoFeB(0.8 nm)/MgO is presented, where the two CoFeB layers are separated by a Ta interlayer of varying thickness t. The magnetization properties deduced from complementary techniques such as superconducting quantum interference magnetometry, ferromagnetic resonance frequency measurements and Brillouin light scattering spectroscopy can be tuned by changing the Ta thickness between t = 0.25 nm, 0.5 nm and 0.75 nm. For t = 0.5 nm, a ferromagnetic coupling is observed, whereas for t = 0.75 nm, the antiferromagnetic coupling needed to construct a synthetic ferrimagnet is realized. In the latter case, the shape of magnetic domain walls between two ferrimagnetic alignments or between a ferro- and a ferrimagnetic alignment is very different. This behavior can be interpreted as a result of the change in dipolar as well as interlayer exchange energy and domain wall pinning, which is an important conclusion for the realization of data storage devices based on synthetic ferri- and antiferromagnets.

Evidence for replacement of an infected synthetic by a biological mesh in abdominal wall hernia repair

Directory of Open Access Journals (Sweden)

Agneta eMontgomery

2016-01-01

Full Text Available The incidence of deep infection using a synthetic mesh in inguinal hernia repair is low and reported to be well below 1%. This is in contrast to incisional hernia surgery where the reported incidence is 3% respective 13% comparing laparoscopic to open mesh repair reported in a Cochrane review. Main risk factors were long operation time, surgical site contamination and early wound complications. An infected mesh can be preserved using conservative treatment were negative pressure wound therapy (VAC® could play an important role. If strategy fails, the mesh needs to be removed. This review aims to look at evidence for situations were a biological mesh would work as a replacement of a removed infected synthetic mesh. Material and MethodsA literature search of the Medline database was performed using the PubMed search engine. Twenty publications were found relevant for this review.ResultsFor studies reviewed three options are presented: removal of the infected synthetic mesh alone, replacement with either a new synthetic or a new biological mesh. Operations were all performed at specialist centers. Removal of the mesh alone was an option limited to inguinal hernias. In ventral/incisional hernias the use of a biological mesh for replacement resulted in a very high recurrence rate, if bridging was required. Either a synthetic or a biological mesh seems to work as a replacement when fascial closure can be achieved. Evidence is though very low. ConclusionWhen required, either a synthetic or a biological meshes seems to work as a replacement for an infected synthetic mesh if the defect can be closed. It is however not recommended to use a biological mesh for bridging. Mesh replacement surgery is demanding and is recommended to be performed in a specialist center.

[New materia medica project: synthetic biology based bioactive metabolites research in medicinal plant].

Science.gov (United States)

Wang, Yong

2017-03-25

In the last decade, synthetic biology research has been gradually transited from monocellular parts or devices toward more complex multicellular systems. The emerging plant synthetic biology is regarded as the "next chapter" of synthetic biology. The complex and diverse plant metabolism as the entry point, plant synthetic biology research not only helps us understand how real life is working, but also facilitates us to learn how to design and construct more complex artificial life. Bioactive compounds innovation and large-scale production are expected to be breakthrough with the redesigned plant metabolism as well. In this review, we discuss the research progress in plant synthetic biology and propose the new materia medica project to lift the level of traditional Chinese herbal medicine research.

Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo.

Science.gov (United States)

Sharma, Sunil V; Tong, Xiaoxue; Pubill-Ulldemolins, Cristina; Cartmell, Christopher; Bogosyan, Emma J A; Rackham, Emma J; Marelli, Enrico; Hamed, Refaat B; Goss, Rebecca J M

2017-08-09

Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C-Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living cultures.Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.

Wall shear stress measurement of near-wall flow over inclined and curved boundaries by stereo interfacial particle image velocimetry

International Nuclear Information System (INIS)

Nguyen, Thien Duy; Wells, John Craig; Nguyen, Chuong Vinh

2010-01-01

In investigations of laminar or turbulent flows, wall shear is often important. Nevertheless, conventional particle image velocimetry (PIV) is difficult in near-wall regions. A near-wall measurement technique, named interfacial PIV (IPIV) [Nguyen, C., Nguyen, T., Wells, J., Nakayama, A., 2008. Proposals for PIV of near-wall flow over curved boundaries. In: Proceedings of 14th International Symposium on Applications of Laser Technique to Fluid Mechanics], handles curved boundaries by means of conformal transformation, directly measures the wall gradient, and yields the near-wall tangential velocity profile at one-pixel resolution. In this paper, we show the feasibility of extending IPIV to measure wall gradients by stereo reconstruction. First, we perform a test on synthetic images generated from a direct numerical simulation (DNS) snapshot of turbulent flow over sinusoidal bed. Comparative assessment of wall gradients derived by IPIV, stereo-IPIV and particle image distortion (PID) [Huang, H.T., Fiedler, H.E., Wang, J.J., 1993. Limitation and improvement of PIV. Experiments in Fluids 15(4), 263-273] is evaluated with DNS data. Also, the sensitivity of IPIV and stereo-IPIV results to the uncertainty of identified wall position is examined. As a practical application of IPIV and stereo-IPIV to experimental images, results from turbulent open channel flow over a backward-facing step are discussed in detail.

Novel heterometallic metal–azido complex synthesized by “one-step” reaction: synthetic strategy and magnetic properties

Energy Technology Data Exchange (ETDEWEB)

Jiao, Yong-Kun [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Li, Xiu-Ping [Technical center for safety of industrial products of Tianjin entry-exit inspection and quarantine bureau, Tianjin 300201 (China); Zhao, Cui; Wang, Hai-Chao; Xue, Min [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Zhao, Jiong-Peng, E-mail: horryzhao@yahoo.com [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Liu, Fu-Chen, E-mail: fuchenliutj@yahoo.com [School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384 (China); Lanzhou Petrochemical College of Vocational Technology, Lanzhou 730060 (China)

2013-06-15

A novel heterometallic complex, [Ni{sub 2}Mn(N{sub 3}){sub 2}(nic){sub 4}·(H{sub 2}O){sub 2}]{sub n} (1) (nic=nicotinate), was obtained by assembling MnCl{sub 2}·4H{sub 2}O, Ni(NO{sub 3}){sub 2}·6H{sub 2}O, NaN{sub 3} and nicotinic acid with a “one step” synthetic strategy—hydrothermal reaction. The 3D structure of the complex can be described as end-on (EO) azido and syn,syn carboxylates mixed bridged by alternate Ni–Mn–Ni trimers linked by the nicotinate. Dominant ferromagnetic interactions were observed between the Ni{sup II} and Mn{sup II} ions in the trimer. - Graphical abstract: A novel heterometallic 3D complex [Ni{sub 2}Mn(N{sub 3}){sub 2}(nic){sub 4}·(H{sub 2}O){sub 2}]{sub n} (1) (nic=nicotinate) was synthesized by hydrothermal reaction. This complex exhibits interesting structural and magnetic properties. - Highlights: • It is difficult to construct simple coordination complexes with azide as “ligands” to obtain heterometallic metal–azido compounds. • A “one-step” method—hydrothermal reaction— was introduced to avoid the disadvantages of azide mentioned above. • The magnetic property is different with the isostructural homometal–azido complex due to the changed metal center.

The Pagoda Sequence: a Ramble through Linear Complexity, Number Walls, D0L Sequences, Finite State Automata, and Aperiodic Tilings

Directory of Open Access Journals (Sweden)

Fred Lunnon

2009-06-01

Full Text Available We review the concept of the number wall as an alternative to the traditional linear complexity profile (LCP, and sketch the relationship to other topics such as linear feedback shift-register (LFSR and context-free Lindenmayer (D0L sequences. A remarkable ternary analogue of the Thue-Morse sequence is introduced having deficiency 2 modulo 3, and this property verified via the re-interpretation of the number wall as an aperiodic plane tiling.

Cleaved thioredoxin fusion protein enables the crystallization of poorly soluble ERα in complex with synthetic ligands

International Nuclear Information System (INIS)

Cura, Vincent; Gangloff, Monique; Eiler, Sylvia; Moras, Dino; Ruff, Marc

2007-01-01

A new crystallization strategy: the presence of cleaved thioredoxin fusion is critical for crystallization of the estrogen nuclear receptor ligand binding domain in complex with synthetic ligands. This novel technique should be regarded as an interesting alternative for crystallization of difficult proteins. The ligand-binding domain (LBD) of human oestrogen receptor α was produced in Escherichia coli as a cleavable thioredoxin (Trx) fusion in order to improve solubility. Crystallization trials with either cleaved and purified LBD or with the purified fusion protein both failed to produce crystals. In another attempt, Trx was not removed from the LBD after endoproteolytic cleavage and its presence promoted nucleation and subsequent crystal growth, which allowed the structure determination of two different LBD–ligand–coactivator peptide complexes at 2.3 Å resolution. This technique is likely to be applicable to other low-solubility proteins

A Variable Stiffness Analysis Model for Large Complex Thin-Walled Guide Rail

Directory of Open Access Journals (Sweden)

Wang Xiaolong

2016-01-01

Full Text Available Large complex thin-walled guide rail has complicated structure and no uniform low rigidity. The traditional cutting simulations are time consuming due to huge computation especially in large workpiece. To solve these problems, a more efficient variable stiffness analysis model has been propose, which can obtain quantitative stiffness value of the machining surface. Applying simulate cutting force in sampling points using finite element analysis software ABAQUS, the single direction variable stiffness rule can be obtained. The variable stiffness matrix has been propose by analyzing multi-directions coupling variable stiffness rule. Combining with the three direction cutting force value, the reasonability of existing processing parameters can be verified and the optimized cutting parameters can be designed.

Philosophy of Systems and Synthetic Biology

DEFF Research Database (Denmark)

Green, Sara

2017-01-01

This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

Synthetic analog computation in living cells.

Science.gov (United States)

Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

2013-05-30

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

Method of constructing shielding wall

International Nuclear Information System (INIS)

Nagao, Tetsuya.

1990-01-01

For instance, surfaces of lead particles each formed into a sphere of about 0.5 to 0.3 mm grain size are coated with a coating material of a synthetic resin comprising a polymeric material such as teflon. Subsequently, the floated lead particle are kneaded with concrete materials and then poured into a molding die by way of a hose. After coagulation, the molding die is removed to complete shielding walls in which lead particles are scattered substantially at an equal distance. In this way, since the lead particles are mixed into the shielding walls, shielding effects can be improved by so much as the lead particles are mixed, thereby enabling to reduce the thickness of the shielding walls. Further, since the lead particles are coated with the coating material, the lead particles are insulated from the concrete materials, thereby enabling to prevent the corrosion of the lead particles. Furthermore, since the lead particles and the concrete materials can be transported with ease, operation labors can be reduced. (T.M.)

Control theory meets synthetic biology.

Science.gov (United States)

Del Vecchio, Domitilla; Dy, Aaron J; Qian, Yili

2016-07-01

The past several years have witnessed an increased presence of control theoretic concepts in synthetic biology. This review presents an organized summary of how these control design concepts have been applied to tackle a variety of problems faced when building synthetic biomolecular circuits in living cells. In particular, we describe success stories that demonstrate how simple or more elaborate control design methods can be used to make the behaviour of synthetic genetic circuits within a single cell or across a cell population more reliable, predictable and robust to perturbations. The description especially highlights technical challenges that uniquely arise from the need to implement control designs within a new hardware setting, along with implemented or proposed solutions. Some engineering solutions employing complex feedback control schemes are also described, which, however, still require a deeper theoretical analysis of stability, performance and robustness properties. Overall, this paper should help synthetic biologists become familiar with feedback control concepts as they can be used in their application area. At the same time, it should provide some domain knowledge to control theorists who wish to enter the rising and exciting field of synthetic biology. © 2016 The Author(s).

Characterization of the Sclerotinia sclerotiorum cell wall proteome.

Science.gov (United States)

Liu, Longzhou; Free, Stephen J

2016-08-01

We used a proteomic analysis to identify cell wall proteins released from Sclerotinia sclerotiorum hyphal and sclerotial cell walls via a trifluoromethanesulfonic acid (TFMS) digestion. Cell walls from hyphae grown in Vogel's glucose medium (a synthetic medium lacking plant materials), from hyphae grown in potato dextrose broth and from sclerotia produced on potato dextrose agar were used in the analysis. Under the conditions used, TFMS digests the glycosidic linkages in the cell walls to release intact cell wall proteins. The analysis identified 24 glycosylphosphatidylinositol (GPI)-anchored cell wall proteins and 30 non-GPI-anchored cell wall proteins. We found that the cell walls contained an array of cell wall biosynthetic enzymes similar to those found in the cell walls of other fungi. When comparing the proteins in hyphal cell walls grown in potato dextrose broth with those in hyphal cell walls grown in the absence of plant material, it was found that a core group of cell wall biosynthetic proteins and some proteins associated with pathogenicity (secreted cellulases, pectin lyases, glucosidases and proteases) were expressed in both types of hyphae. The hyphae grown in potato dextrose broth contained a number of additional proteins (laccases, oxalate decarboxylase, peroxidase, polysaccharide deacetylase and several proteins unique to Sclerotinia and Botrytis) that might facilitate growth on a plant host. A comparison of the proteins in the sclerotial cell wall with the proteins in the hyphal cell wall demonstrated that sclerotia formation is not marked by a major shift in the composition of cell wall protein. We found that the S. sclerotiorum cell walls contained 11 cell wall proteins that were encoded only in Sclerotinia and Botrytis genomes. © 2015 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.

Synthetic biology analysed tools for discussion and evaluation

CERN Document Server

2016-01-01

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

Wall Shear Stress, Wall Pressure and Near Wall Velocity Field Relationships in a Whirling Annular Seal

Science.gov (United States)

Morrison, Gerald L.; Winslow, Robert B.; Thames, H. Davis, III

1996-01-01

The mean and phase averaged pressure and wall shear stress distributions were measured on the stator wall of a 50% eccentric annular seal which was whirling in a circular orbit at the same speed as the shaft rotation. The shear stresses were measured using flush mounted hot-film probes. Four different operating conditions were considered consisting of Reynolds numbers of 12,000 and 24,000 and Taylor numbers of 3,300 and 6,600. At each of the operating conditions the axial distribution (from Z/L = -0.2 to 1.2) of the mean pressure, shear stress magnitude, and shear stress direction on the stator wall were measured. Also measured were the phase averaged pressure and shear stress. These data were combined to calculate the force distributions along the seal length. Integration of the force distributions result in the net forces and moments generated by the pressure and shear stresses. The flow field inside the seal operating at a Reynolds number of 24,000 and a Taylor number of 6,600 has been measured using a 3-D laser Doppler anemometer system. Phase averaged wall pressure and wall shear stress are presented along with phase averaged mean velocity and turbulence kinetic energy distributions located 0.16c from the stator wall where c is the seal clearance. The relationships between the velocity, turbulence, wall pressure and wall shear stress are very complex and do not follow simple bulk flow predictions.

Developments in the Tools and Methodologies of Synthetic Biology

Science.gov (United States)

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

2014-01-01

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

Developments in the tools and methodologies of synthetic biology

Directory of Open Access Journals (Sweden)

Richard eKelwick

2014-11-01

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

Indirect complexometric determination of mercury(II in synthetic alloys and complexes using ethanethiol as a selective masking agent

Directory of Open Access Journals (Sweden)

J. KARTHIKEYAN

2006-03-01

Full Text Available Acomplexometric method for the determination of mercury(II in presence of other metal ions, based on the selective masking action of ethanethiol towards mercury(II is described. Mercury(II present in a given sample solution is first complexed with an excess of EDTAand the unreacted EDTAis titrated against zinc sulphate solution at pH 5–6 (hexamine buffer using xylenol orange as the indicator. An excess of a 0.3 % solution of ethanethiol is then added to displace EDTA from the Hg(II–EDTA complex. The released EDTAis titrated with a standard zinc sulphate solution. Reproducible and accurate results are obtained for 4–85 mg of mercury(II with a relative error of less than ± 0.46 % and coefficient of variation of not more than 0.47 %. The effects of the presence of various ions were studied. The method can be used for the analysis of mercury in its synthetic alloy mixtures and also in complexes.

Carbon Nanotube-Based Synthetic Gecko Tapes

Science.gov (United States)

Dhinojwala, Ali

2008-03-01

Wall-climbing geckos have unique ability to attach to different surfaces without the use of any viscoelastic glues. On coming in contact with any surface, the micron-size gecko foot-hairs deform, enabling molecular contact over large areas, thus translating weak van der Waals (vdW) interactions into enormous shear forces. We will present our recent results on the development of synthetic gecko tape using aligned carbon nanotubes to mimic the keratin hairs found on gecko feet. The patterned carbon nanotube-based gecko tape can support a shear stress (36 N/cm^2) nearly four times higher than the gecko foot and sticks to a variety of surfaces, including Teflon. Both the micron-size setae (replicated by nanotube bundles) and nanometer-size spatulas (individual nanotubes) are necessary to achieve macroscopic shear adhesion and to translate the weak vdW interactions into high shear forces. The carbon nanotube based tape offers an excellent synthetic option as a dry conductive reversible adhesive in microelectronics, robotics and space applications. The mechanism behind these large shear forces and self-cleaning properties of these carbon nanotube based synthetic gecko tapes will be discussed. This work was performed in collaboration with graduate students Liehui Ge, and Sunny Sethi, and collaborators from RPI; Lijie Ci and Professor Pulickel Ajayan.

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Using synthetic biology to make cells tomorrow's test tubes.

Science.gov (United States)

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Synthetic biology and its promises

Directory of Open Access Journals (Sweden)

José Manuel De Cózar Escalante

2016-12-01

Full Text Available Synthetic biology is a new science and emerging technology, or rather a technoscience, which converges with others such as nanotechnology, information technology, robotics, artificial intelligence and neuroscience. All have common features that could have highly concerning social and environmental impacts. With its ambitious goals of controlling complexity, redesigning and creating new living entities, synthetic biology perfectly exemplifies the new bioeconomic reality. This requires expanding the focus of the discussion beyond the limited comparative analysis of risks and benefits, to address uncertainties, reassign responsibilities and initiate a thorough social assessment of what is at stake.

The structure-property relationship of oxovanadium(IV) complexes in the wall framework of PMOs and their catalytic applications

Energy Technology Data Exchange (ETDEWEB)

Zhou, Shijian [State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009 (China); Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 210009 Jiangsu (China); Wang, Bangbang; Gao, Shuying; Ding, Yun [State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009 (China); Kong, Yan, E-mail: kongy36@njtech.edu.cn [State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, Nanjing 210009 (China)

2017-03-01

Graphical abstract: In this work, oxovanadium(IV) species have been successfully incorporated into the wall framework of PMOs materials by the co-condensation of the silica source with oxovanadium organic complexes. The oxovanadium(IV) species are existed as the tetrahedral coordination and also be stable and well-dispersed in the framework of the PMOs materials. These as-prepared functional catalysts are proved to be effective in the oxidation of styrene, and high catalytic stabilities are obtained. - Highlights: • The oxovanadium complexes were directly incorporated into the wall framework of PMOs instead of the pore channels by one-step synthesis process, partly avoiding the destruction of the mesoporous channels. • The vanadium species in the framework of PMOs are highly stable as pseudotetrahedral monovanadate. • These as-prepared V-PMO catalysts display high catalytic activity and stability in the styrene oxidation reaction. - Abstract: Oxovanadium(IV) species could be considered as effective active sites in the catalytic oxidation reactions, but in the traditional vanadium-containing catalysts, the unstable and undispersible status of these active sites cause great limitation in their application. In this study, we present a novel approach to utilize the co-condensation of the silica source with oxovanadium organic complexes through the liquid-crystal templating (LCT) process introducing the vanadium species into the framework of periodically meosporous organosilicas (PMOs). Oxovanadium organic complexes are successfully obtained by the coordination effect between vanadium species and organic complexes. Thus the vanadium-containing PMOs catalysts are accordingly synthesized; the model structure of as-prepared catalysts is proposed and further verified by different characterization measurements. These vanadium-containing PMOs catalysts display the extremely stable and well-dispersed oxovanadium(IV) species in the framework, and due to this advanced

Synthetic Brainbows

KAUST Repository

Wan, Y.

2013-06-01

Brainbow is a genetic engineering technique that randomly colorizes cells. Biological samples processed with this technique and imaged with confocal microscopy have distinctive colors for individual cells. Complex cellular structures can then be easily visualized. However, the complexity of the Brainbow technique limits its applications. In practice, most confocal microscopy scans use different florescence staining with typically at most three distinct cellular structures. These structures are often packed and obscure each other in rendered images making analysis difficult. In this paper, we leverage a process known as GPU framebuffer feedback loops to synthesize Brainbow-like images. In addition, we incorporate ID shuffing and Monte-Carlo sampling into our technique, so that it can be applied to single-channel confocal microscopy data. The synthesized Brainbow images are presented to domain experts with positive feedback. A user survey demonstrates that our synthetic Brainbow technique improves visualizations of volume data with complex structures for biologists.

Manipulation of Turbulent Boundary Layers Using Synthetic Jets

Science.gov (United States)

Berger, Zachary; Gomit, Guillaume; Lavoie, Philippe; Ganapathisubramani, Bharath

2015-11-01

This work focuses on the application of active flow control, in the form of synthetic jet actuators, of turbulent boundary layers. An array of 2 synthetic jets are oriented in the spanwise direction and located approximately 2.7 meters downstream from the leading edge of a flat plate. Actuation is applied perpendicular to the surface of the flat plate with varying blowing ratios and reduced frequencies (open-loop). Two-component large window particle image velocimetry (PIV) was performed at the University of Southampton, in the streamwise-wall-normal plane. Complementary stereo PIV measurements were performed at the University of Toronto Institute for Aerospace Studies (UTIAS), in the spanwise-wall-normal plane. The freestream Reynolds number is 3x104, based on the boundary layer thickness. The skin friction Reynolds number is 1,200 based on the skin friction velocity. The experiments at Southampton allow for the observation of the control effects as the flow propagates downstream. The experiments at UTIAS allow for the observation of the streamwise vorticity induced from the actuation. Overall the two experiments provide a 3D representation of the flow field with respect to actuation effects. The current work focuses on the comparison of the two experiments, as well as the effects of varying blowing ratios and reduced frequencies on the turbulent boundary layer. Funded Supported by Airbus.

Domain wall networks on solitons

International Nuclear Information System (INIS)

Sutcliffe, Paul

2003-01-01

Domain wall networks on the surface of a soliton are studied in a simple theory. It consists of two complex scalar fields, in 3+1 dimensions, with a global U(1)xZ n symmetry, where n>2. Solutions are computed numerically in which one of the fields forms a Q ball and the other field forms a network of domain walls localized on the surface of the Q ball. Examples are presented in which the domain walls lie along the edges of a spherical polyhedron, forming junctions at its vertices. It is explained why only a small restricted class of polyhedra can arise as domain wall networks

An economic parametric analysis of the synthetic fuel produced by a fusion-fission complex

International Nuclear Information System (INIS)

Tai, A.S.; Krakowski, R.A.

1980-01-01

A simple analytic model is used to examine economic constraints of a fusion-fission complex in which a portion of a thermal energy is used for producing synthetic fuel (synfuel). Since the values of many quantities are not well-known, a parametric analysis has been carried out for testing the sensitivity of the synfuel production cost in relation to crucial economic and technological quantities (investment costs of hybrid and synfuel plants, energy multiplication of the fission blanket, recirculating power fraction of the fusion driver, etc.). In addition, a minimum synfuel selling price has been evaluated, from which the fission-fusion-synfuel complex brings about a higher economic benefit than does the fusion-fission hybrid entirely devoted to fissile-fuel and electricity generation. This paper describes the energy flow diagram of fusion-fission synfuel concept, express the revenue-to-cost formulation and the breakeven synfuel selling price. The synfuel production cost given by the model is evaluated within a range of values of crucial parameters. Assuming an electric cost of 2.7 cents/kWh, an annual investment cost per energy unit of 4.2 to 6 $/FJ for the fusion-fission complex and 1.5 to 3 $/GJ for the synfuel plant, the synfuel production cost lies between 6.5 and 8.5 $/GJ. These production costs can compete with those evaluated for other processes. The study points out a potential use of the fusion-fission hybrid reactor for other than fissile-fuel and electricity generation. (orig.) [de

New phenotypic aspects of the decidual spiral artery wall during early post-implantation mouse pregnancy

International Nuclear Information System (INIS)

Elia, Artemis; Charalambous, Fotini; Georgiades, Pantelis

2011-01-01

Highlights: ► Spiral artery (SA) wall remodeling (SAR) is ill-defined and clinically important. ► SA muscular phenotype prior to and during SAR in mice is underexplored. ► SA muscular wall consists of contractile and non-contractile components. ► SA wall non-contractile component may be synthetic smooth muscle. ► Timing and extent of SA wall contractile component loss is revealed. -- Abstract: During pregnancy the walls of decidual spiral arteries (SAs) undergo clinically important structural modifications crucial for embryo survival/growth and maternal health. However, the mechanisms of SA remodeling (SAR) are poorly understood. Although an important prerequisite to this understanding is knowledge about the phenotype of SA muscular wall prior to and during the beginning of mouse SAR, this remains largely unexplored and was the main aim of this work. Using histological and immunohistochemical techniques, this study shows for the first time that during early mouse gestation, from embryonic day 7.5 (E7.5) to E10.5, the decidual SA muscular coat is not a homogeneous structure, but consists of two concentric layers. The first is a largely one cell-thick sub-endothelial layer of contractile mural cells (positive for α-smooth muscle actin, calponin and SM22α) with pericyte characteristics (NG2 positive). The second layer is thicker, and evidence is presented that it may be of the synthetic/proliferative smooth muscle phenotype, based on absence (α-smooth muscle actin and calponin) or weak (SM22α) expression of contractile mural cell markers, and presence of synthetic smooth muscle characteristics (expression of non-muscle Myosin heavy chain-IIA and of the cell proliferation marker PCNA). Importantly, immunohistochemistry and morphometrics showed that the contractile mural cell layer although prominent at E7.5–E8.5, becomes drastically reduced by E10.5 and is undetectable by E12.5. In conclusion, this study reveals novel aspects of the decidual SA muscular

Designing tough and fracture resistant polypropylene/multi wall carbon nanotubes nanocomposites by controlling stereo-complexity and dispersion morphology

International Nuclear Information System (INIS)

Das, Dibyendu; Satapathy, Bhabani K.

2014-01-01

Highlights: • New pathway to improve dispersion and toughness by tacticity modification. • >330% toughness enhancement in PP/MWCNT nanocomposites with stereo-complex PP. • Prominent dispersion and distribution morphology due to matrix stereocomplexity. • Tacticity induced “Semi-ductile-to-tough-to-quasi-brittle” transitions in the PP/MWCNT. • Two-fold reduced steady state CTOD rate in i-PP+s-PP/ MWCNT nanocomposites. - Abstract: A remarkable toughness enhancement (>330%) of multi wall carbon nanotubes (MWCNT) filled stereo-complex polypropylene (PP) matrix i.e. blend of isotactic-PP and syndiotactic-PP (70:30) with differences in stereo-regularity has been observed. The enhancement has been correlated to quantifiable morphological parameters such as free-space lengths concerning dispersion and relatively greater reduction in crystallite size/lamellar thickness. Systematic analysis of glass transition data and estimation of multi wall carbon nanotubes induced reduction in interfacial polymer chain immobilization reiterates susceptibility of polymer segments to ready-mobility. The extent of toughening has quantitatively been analyzed by fracture-energy partitioning, essential work of fracture (EWF), approach enabling the detection of a “semi-ductile-to-tough-to-quasi-brittle” transition in the MWCNT filled stereo-complex polypropylene. Real-time fracture kinetics analysis revealed toughening mechanism to be primarily blunting-assisted; an aspect also corroborated by extensive plastic flow without much energy dissipation in the inner fracture process zone. Thus the study establishes a new pathway of tacticity-defined matrix modification to toughen nanocomposites

Green Walls as an Approach in Grey Water Treatment

Science.gov (United States)

Rysulova, Martina; Kaposztasova, Daniela; Vranayova, Zuzana

2017-10-01

Grey water contributes significantly to waste water parameters such as biochemical oxygen demand (BOD), chemical oxygen demand (COD), total suspended solids (TSS), total phosphorus (Ptotal), total nitrogen (Ntotal), ammonium, boron, metals, salts, surfactants, synthetic chemicals, oils and greases, xenobiotic substances and microorganisms. Concentration of these pollutants and the water quality highlights the importance of treatment process in grey water systems. Treatment technologies operating under low energy and maintenance are usually preferred, since they are more cost effective for users. Treatment technologies based on natural processes represent an example of such technology including vegetated wall. Main aim of this paper is to introduce the proposal of vegetated wall managing grey water and brief characteristic of proposed system. Is expected that prepared experiment will establish the purifying ability and the potential of green wall application as an efficient treatment technology.

Advanced technologies for plant cell wall evolution and diversity

DEFF Research Database (Denmark)

Fangel, Jonatan Ulrik

Plant cell walls consist of polysaccharides, glycoproteins and phenolic polymers interlinked together in a highly complex network. The detailed analysis of cell walls is challenging because of their inherent complexity and heterogeneity. Also, complex carbohydrates, unlike proteins and nucleotides...... cannot really be synthesised or sequenced. The work described in this thesis is focused to a large extent on the development of a microarray-based high-throughput method for cell wall analysis known as Comprehensive microarray polymer profiling or CoMPP. The procedure uses highly specific molecular...... probes (monoclonal antibodies mAbs and carbohydrate binding modules, CBMs) to rapidly profile polysaccharides across a sample set. During my PhD I have further developed the CoMPP technique and used it for cell wall analysis within the context of a variety of applied and fundamental projects. The data...

Paper-based synthetic gene networks.

Science.gov (United States)

Pardee, Keith; Green, Alexander A; Ferrante, Tom; Cameron, D Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J

2014-11-06

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.

Paper-based Synthetic Gene Networks

Science.gov (United States)

Pardee, Keith; Green, Alexander A.; Ferrante, Tom; Cameron, D. Ewen; DaleyKeyser, Ajay; Yin, Peng; Collins, James J.

2014-01-01

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides a new venue for synthetic biologists to operate, and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze-dried onto paper, enabling the inexpensive, sterile and abiotic distribution of synthetic biology-based technologies for the clinic, global health, industry, research and education. For field use, we create circuits with colorimetric outputs for detection by eye, and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors. PMID:25417167

Microfluidics with fluid walls.

Science.gov (United States)

Walsh, Edmond J; Feuerborn, Alexander; Wheeler, James H R; Tan, Ann Na; Durham, William M; Foster, Kevin R; Cook, Peter R

2017-10-10

Microfluidics has great potential, but the complexity of fabricating and operating devices has limited its use. Here we describe a method - Freestyle Fluidics - that overcomes many key limitations. In this method, liquids are confined by fluid (not solid) walls. Aqueous circuits with any 2D shape are printed in seconds on plastic or glass Petri dishes; then, interfacial forces pin liquids to substrates, and overlaying an immiscible liquid prevents evaporation. Confining fluid walls are pliant and resilient; they self-heal when liquids are pipetted through them. We drive flow through a wide range of circuits passively by manipulating surface tension and hydrostatic pressure, and actively using external pumps. Finally, we validate the technology with two challenging applications - triggering an inflammatory response in human cells and chemotaxis in bacterial biofilms. This approach provides a powerful and versatile alternative to traditional microfluidics.The complexity of fabricating and operating microfluidic devices limits their use. Walsh et al. describe a method in which circuits are printed as quickly and simply as writing with a pen, and liquids in them are confined by fluid instead of solid walls.

Complex regional pain syndrome with associated chest wall dystonia: a case report

Directory of Open Access Journals (Sweden)

Schwartzman Robert J

2011-09-01

Full Text Available Abstract Patients with complex regional pain syndrome (CRPS often suffer from an array of associated movement disorders, including dystonia of an affected limb. We present a case of a patient with long standing CRPS after a brachial plexus injury, who after displaying several features of the movement disorder previously, developed painful dystonia of chest wall musculature. Detailed neurologic examination found palpable sustained contractions of the pectoral and intercostal muscles in addition to surface allodynia. Needle electromyography of the intercostal and paraspinal muscles supported the diagnosis of dystonia. In addition, pulmonary function testing showed both restrictive and obstructive features in the absence of a clear cardiopulmonary etiology. Treatment was initiated with intrathecal baclofen and the patient had symptomatic relief and improvement of dystonia. This case illustrates a novel form of the movement disorder associated with CRPS with response to intrathecal baclofen treatment.

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Synthetic Aperture Beamformation using the GPU

DEFF Research Database (Denmark)

Hansen, Jens Munk; Schaa, Dana; Jensen, Jørgen Arendt

2011-01-01

A synthetic aperture ultrasound beamformer is implemented for a GPU using the OpenCL framework. The implementation supports beamformation of either RF signals or complex baseband signals. Transmit and receive apodization can be either parametric or dynamic using a fixed F-number, a reference...

Evaluation of a Group A Streptococcus synthetic oligosaccharide as vaccine candidate.

Science.gov (United States)

Kabanova, Anna; Margarit, Immaculada; Berti, Francesco; Romano, Maria R; Grandi, Guido; Bensi, Giuliano; Chiarot, Emiliano; Proietti, Daniela; Swennen, Erwin; Cappelletti, Emilia; Fontani, Paola; Casini, Daniele; Adamo, Roberto; Pinto, Vittoria; Skibinski, David; Capo, Sabrina; Buffi, Giada; Gallotta, Marilena; Christ, William J; Campbell, A Stewart; Pena, John; Seeberger, Peter H; Rappuoli, Rino; Costantino, Paolo

2010-12-10

Bacterial infections caused by Group A Streptococcus (GAS) are a serious health care concern that currently cannot be prevented by vaccination. The GAS cell-wall polysaccharide (GAS-PS) is an attractive vaccine candidate due to its constant expression pattern on different bacterial strains and protective properties of anti-GAS-PS antibodies. Here we report for the first time the immunoprotective efficacy of glycoconjugates with synthetic GAS oligosaccharides as compared to those containing the native GAS-PS. A series of hexa- and dodecasaccharides based on the GAS-PS structure were prepared by chemical synthesis and conjugated to CRM(197). When tested in mice, the conjugates containing the synthetic oligosaccharides conferred levels of immunoprotection comparable to those elicited by the native conjugate. Antisera from immunized rabbits promoted phagocytosis of encapsulated GAS strains. Furthermore we discuss variables that might correlate with glycoconjugate immunogenicity and demonstrate the potential of the synthetic approach that benefits from increased antigen purity and facilitated manufacturing. Copyright © 2010 Elsevier Ltd. All rights reserved.

Plant cell wall extensibility: connecting plant cell growth with cell wall structure, mechanics, and the action of wall-modifying enzymes

Energy Technology Data Exchange (ETDEWEB)

Cosgrove, Daniel J.

2015-11-25

The advent of user-friendly instruments for measuring force/deflection curves of plant surfaces at high spatial resolution has resulted in a recent outpouring of reports of the ‘Young's modulus’ of plant cell walls. The stimulus for these mechanical measurements comes from biomechanical models of morphogenesis of meristems and other tissues, as well as single cells, in which cell wall stress feeds back to regulate microtubule organization, auxin transport, cellulose deposition, and future growth directionality. In this article I review the differences between elastic modulus and wall extensibility in the context of cell growth. Some of the inherent complexities, assumptions, and potential pitfalls in the interpretation of indentation force/deflection curves are discussed. Reported values of elastic moduli from surface indentation measurements appear to be 10- to >1000-fold smaller than realistic tensile elastic moduli in the plane of plant cell walls. Potential reasons for this disparity are discussed, but further work is needed to make sense of the huge range in reported values. The significance of wall stress relaxation for growth is reviewed and connected to recent advances and remaining enigmas in our concepts of how cellulose, hemicellulose, and pectins are assembled to make an extensible cell wall. A comparison of the loosening action of α-expansin and Cel12A endoglucanase is used to illustrate two different ways in which cell walls may be made more extensible and the divergent effects on wall mechanics.

Synthetic vision display evaluation studies

Science.gov (United States)

Regal, David M.; Whittington, David H.

1994-01-01

The goal of this research was to help us understand the display requirements for a synthetic vision system for the High Speed Civil Transport (HSCT). Four experiments were conducted to examine the effects of different levels of perceptual cue complexity in displays used by pilots in a flare and landing task. Increased levels of texture mapping of terrain and runway produced mixed results, including harder but shorter landings and a lower flare initiation altitude. Under higher workload conditions, increased texture resulted in an improvement in performance. An increase in familiar size cues did not result in improved performance. Only a small difference was found between displays using two patterns of high resolution texture mapping. The effects of increased perceptual cue complexity on performance was not as strong as would be predicted from the pilot's subjective reports or from related literature. A description of the role of a synthetic vision system in the High Speed Civil Transport is provide along with a literature review covering applied research related to perceptual cue usage in aircraft displays.

Assembly and enlargement of the primary cell wall in plants

Science.gov (United States)

Cosgrove, D. J.

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

Spalling of concrete walls under blast load

International Nuclear Information System (INIS)

Kot, C.A.

1977-01-01

A common effect of the detonation of explosives in close proximity of concrete shield walls is the spalling (scabbing) of the back face of the wall. Spalling is caused by the free surface reflection of the shock wave induced in the wall by high pressure air blast and occurs whenever the dynamic tensile rupture strength is exceeded. While a complex process, reasonable analytical spall estimates can be obtained for brittle materials with low tensile strengths, such as concrete, by assuming elastic material behavior and instantaneous spall formation. Specifically, the spall thicknesses and velocities for both normal and oblique incidence of the shock wave on the back face of the wall are calculated. The complex exponential decay wave forms of the air blast are locally approximated by simple power law expressions. Variations of blast wave strength with distance to the wall, charge weight and angle of incidence are taken into consideration. The shock wave decay in the wall is also accounted for by assuming elastic wave propagation. For explosions close-in to the wall, where the reflected blast wave pressures are sufficiently high, multiple spall layers are formed. Successive spall layers are of increasing thickness, at the same time the spall velocities decrease. The spall predictions based on elastic theory are in overall agreement with experimntal results and provide a rapid means of estimating spalling trends of concrete walls subjected to air blast. (Auth.)

Setting up and validating a complex model for a simple homogeneous wall

DEFF Research Database (Denmark)

Naveros, I.; Bacher, Peder; Ruiz, D. P.

2014-01-01

the regression averages method for estimation of parameters which describe the thermal behaviour of the wall. Solar irradiance and long-wave radiation balance terms are added in the heat balance equation besides modelling of wind speed effect to achieve a complete description of the relevant phenomena which......The present paper describes modelling of the thermal dynamics of a real wall tested in dynamic outdoor weather conditions, to identify all the parameters needed for its characterisation. Specifically, the U value, absorptance and effective heat capacity are estimated for the wall using grey......-box modelling based on statistical methods and known physical dynamic energy balance equations, related to the heat flux density through a simple and homogeneous wall. The experimental test was carried out in a hot-temperature climate for nine months. This study aims at proposing a dynamic method improving...

RNA and RNP as Building Blocks for Nanotechnology and Synthetic Biology.

Science.gov (United States)

Ohno, Hirohisa; Saito, Hirohide

2016-01-01

Recent technologies that aimed to elucidate cellular function have revealed essential roles for RNA molecules in living systems. Our knowledge concerning functional and structural information of naturally occurring RNA and RNA-protein (RNP) complexes is increasing rapidly. RNA and RNP interaction motifs are structural units that function as building blocks to constitute variety of complex structures. RNA-central synthetic biology and nanotechnology are constructive approaches that employ the accumulated information and build synthetic RNA (RNP)-based circuits and nanostructures. Here, we describe how to design and construct synthetic RNA (RNP)-based devices and structures at the nanometer-scale for biological and future therapeutic applications. RNA/RNP nanostructures can also be utilized as the molecular scaffold to control the localization or interactions of target molecule(s). Moreover, RNA motifs recognized by RNA-binding proteins can be applied to make protein-responsive translational "switches" that can turn gene expression "on" or "off" depending on the intracellular environment. This "synthetic RNA and RNP world" will expand tools for nanotechnology and synthetic biology. In addition, these reconstructive approaches would lead to a greater understanding of building principle in naturally occurring RNA/RNP molecules and systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthetic Biomaterials to Rival Nature's Complexity-a Path Forward with Combinatorics, High-Throughput Discovery, and High-Content Analysis.

Science.gov (United States)

Zhang, Douglas; Lee, Junmin; Kilian, Kristopher A

2017-10-01

Cells in tissue receive a host of soluble and insoluble signals in a context-dependent fashion, where integration of these cues through a complex network of signal transduction cascades will define a particular outcome. Biomaterials scientists and engineers are tasked with designing materials that can at least partially recreate this complex signaling milieu towards new materials for biomedical applications. In this progress report, recent advances in high throughput techniques and high content imaging approaches that are facilitating the discovery of efficacious biomaterials are described. From microarrays of synthetic polymers, peptides and full-length proteins, to designer cell culture systems that present multiple biophysical and biochemical cues in tandem, it is discussed how the integration of combinatorics with high content imaging and analysis is essential to extracting biologically meaningful information from large scale cellular screens to inform the design of next generation biomaterials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New phenotypic aspects of the decidual spiral artery wall during early post-implantation mouse pregnancy

Energy Technology Data Exchange (ETDEWEB)

Elia, Artemis; Charalambous, Fotini [Department of Biological Sciences, University of Cyprus, University Campus, P.O. Box 20537, 1678 Nicosia (Cyprus); Georgiades, Pantelis, E-mail: pgeor@ucy.ac.cy [Department of Biological Sciences, University of Cyprus, University Campus, P.O. Box 20537, 1678 Nicosia (Cyprus)

2011-12-09

Highlights: Black-Right-Pointing-Pointer Spiral artery (SA) wall remodeling (SAR) is ill-defined and clinically important. Black-Right-Pointing-Pointer SA muscular phenotype prior to and during SAR in mice is underexplored. Black-Right-Pointing-Pointer SA muscular wall consists of contractile and non-contractile components. Black-Right-Pointing-Pointer SA wall non-contractile component may be synthetic smooth muscle. Black-Right-Pointing-Pointer Timing and extent of SA wall contractile component loss is revealed. -- Abstract: During pregnancy the walls of decidual spiral arteries (SAs) undergo clinically important structural modifications crucial for embryo survival/growth and maternal health. However, the mechanisms of SA remodeling (SAR) are poorly understood. Although an important prerequisite to this understanding is knowledge about the phenotype of SA muscular wall prior to and during the beginning of mouse SAR, this remains largely unexplored and was the main aim of this work. Using histological and immunohistochemical techniques, this study shows for the first time that during early mouse gestation, from embryonic day 7.5 (E7.5) to E10.5, the decidual SA muscular coat is not a homogeneous structure, but consists of two concentric layers. The first is a largely one cell-thick sub-endothelial layer of contractile mural cells (positive for {alpha}-smooth muscle actin, calponin and SM22{alpha}) with pericyte characteristics (NG2 positive). The second layer is thicker, and evidence is presented that it may be of the synthetic/proliferative smooth muscle phenotype, based on absence ({alpha}-smooth muscle actin and calponin) or weak (SM22{alpha}) expression of contractile mural cell markers, and presence of synthetic smooth muscle characteristics (expression of non-muscle Myosin heavy chain-IIA and of the cell proliferation marker PCNA). Importantly, immunohistochemistry and morphometrics showed that the contractile mural cell layer although prominent at E7.5-E8

Economics of abdominal wall reconstruction.

Science.gov (United States)

Bower, Curtis; Roth, J Scott

2013-10-01

The economic aspects of abdominal wall reconstruction are frequently overlooked, although understandings of the financial implications are essential in providing cost-efficient health care. Ventral hernia repairs are frequently performed surgical procedures with significant economic ramifications for employers, insurers, providers, and patients because of the volume of procedures, complication rates, the significant rate of recurrence, and escalating costs. Because biological mesh materials add significant expense to the costs of treating complex abdominal wall hernias, the role of such costly materials needs to be better defined to ensure the most cost-efficient and effective treatments for ventral abdominal wall hernias. Copyright © 2013 Elsevier Inc. All rights reserved.

Agent-based modelling in synthetic biology.

Science.gov (United States)

Gorochowski, Thomas E

2016-11-30

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

Synthetic Aperture Sequential Beamformation applied to medical imaging

DEFF Research Database (Denmark)

Hemmsen, Martin Christian; Hansen, Jens Munk; Jensen, Jørgen Arendt

2012-01-01

Synthetic Aperture Sequential Beamforming (SASB) is applied to medical ultrasound imaging using a multi element convex array transducer. The main motivation for SASB is to apply synthetic aperture techniques without the need for storing RF-data for a number of elements and hereby devise a system...... with a reduced system complexity. Using a 192 element, 3.5 MHz, λ-pitch transducer, it is demonstrated using tissue-phantom and wire-phantom measurements, how the speckle size and the detail resolution is improved compared to conventional imaging....

Yeast synthetic biology for high-value metabolites.

Science.gov (United States)

Dai, Zhubo; Liu, Yi; Guo, Juan; Huang, Luqi; Zhang, Xueli

2015-02-01

Traditionally, high-value metabolites have been produced through direct extraction from natural biological sources which are inefficient, given the low abundance of these compounds. On the other hand, these high-value metabolites are usually difficult to be synthesized chemically, due to their complex structures. In the last few years, the discovery of genes involved in the synthetic pathways of these metabolites, combined with advances in synthetic biology tools, has allowed the construction of increasing numbers of yeast cell factories for production of these metabolites from renewable biomass. This review summarizes recent advances in synthetic biology in terms of the use of yeasts as microbial hosts for the identification of the pathways involved in the synthesis, as well as for the production of high-value metabolites. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Natural - synthetic - artificial!

DEFF Research Database (Denmark)

Nielsen, Peter E

2010-01-01

The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life.......The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life....

PREFACE: Domain wall dynamics in nanostructures Domain wall dynamics in nanostructures

Science.gov (United States)

Marrows, C. H.; Meier, G.

2012-01-01

Domain structures in magnetic materials are ubiquitous and have been studied for decades. The walls that separate them are topological defects in the magnetic order parameter and have a wide variety of complex forms. In general, their investigation is difficult in bulk materials since only the domain structure on the surface of a specimen is visible. Cutting the sample to reveal the interior causes a rearrangement of the domains into a new form. As with many other areas of magnetism, the study of domain wall physics has been revitalised by the advent of nanotechnology. The ability to fabricate nanoscale structures has permitted the formation of simplified and controlled domain patterns; the development of advanced microscopy methods has permitted them to be imaged and then modelled; subjecting them to ultrashort field and current pulses has permitted their dynamics to be explored. The latest results from all of these advances are described in this special issue. Not only has this led to results of great scientific beauty, but also to concepts of great applicability to future information technologies. In this issue the reader will find the latest results for these domain wall dynamics and the high-speed processes of topological structures such as domain walls and magnetic vortices. These dynamics can be driven by the application of magnetic fields, or by flowing currents through spintronic devices using the novel physics of spin-transfer torque. This complexity has been studied using a wide variety of experimental techniques at the edge of the spatial and temporal resolution currently available, and can be described using sophisticated analytical theory and computational modelling. As a result, the dynamics can be engineered to give rise to finely controlled memory and logic devices with new functionality. Moreover, the field is moving to study not only the conventional transition metal ferromagnets, but also complex heterostructures, novel magnets and even other

Strategy revealing phenotypic differences among synthetic oscillator designs.

Science.gov (United States)

Lomnitz, Jason G; Savageau, Michael A

2014-09-19

Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested.

A preclinical evaluation of alternative synthetic biomaterials for fascial defect repair using a rat abdominal hernia model.

Directory of Open Access Journals (Sweden)

Daniela Ulrich

Full Text Available Fascial defects are a common problem in the abdominal wall and in the vagina leading to hernia or pelvic organ prolapse that requires mesh enhancement to reduce operation failure. However, the long-term outcome of synthetic mesh surgery may be unsatisfactory due to post-surgical complications. We hypothesized that mesh fabricated from alternative synthetic polymers may evoke a different tissue response, and provide more appropriate mechanical properties for hernia repair. Our aim was to compare the in vivo biocompatibility of new synthetic meshes with a commercial mesh.We have fabricated 3 new warp-knitted synthetic meshes from different polymers with different tensile properties polyetheretherketone (PEEK, polyamide (PA and a composite, gelatin coated PA (PA+G. The rat abdominal hernia model was used to implant the meshes (25 × 35 mm, n = 24/ group. After 7, 30, 60, 90 days tissues were explanted for immunohistochemical assessment of foreign body reaction and tissue integration, using CD31, CD45, CD68, alpha-SMA antibodies. The images were analysed using an image analysis software program. Biomechanical properties were uniaxially evaluated using an Instron Tensile® Tester.This study showed that the new meshes induced complex differences in the type of foreign body reaction over the time course of implantation. The PA, and particularly the composite PA+G meshes, evoked a milder early inflammatory response, and macrophages were apparent throughout the time course. Our meshes led to better tissue integration and new collagen deposition, particularly with the PA+G meshes, as well as greater and sustained neovascularisation compared with the PP meshes.PA, PA+G and PEEK appear to be well tolerated and are biocompatible, evoking an overlapping and different host tissue response with time that might convey mechanical variations in the healing tissue. These new meshes comprising different polymers may provide an alternative option for future treatment

Molecular regulation of plant cell wall extensibility

Science.gov (United States)

Cosgrove, D. J.

1998-01-01

Gravity responses in plants often involve spatial and temporal changes in cell growth, which is regulated primarily by controlling the ability of the cell wall to extend. The wall is thought to be a cellulose-hemicellulose network embedded in a hydrated matrix of complex polysaccharides and a small amount of structural protein. The wall extends by a form of polymer creep, which is mediated by expansins, a novel group of wall-loosening proteins. Expansins were discovered during a molecular dissection of the "acid growth" behavior of cell walls. Expansin alters the rheology of plant walls in profound ways, yet its molecular mechanism of action is still uncertain. It lacks detectable hydrolytic activity against the major components of the wall, but it is able to disrupt noncovalent adhesion between wall polysaccharides. The discovery of a second family of expansins (beta-expansins) sheds light on the biological role of a major group of pollen allergens and implies that expansins have evolved for diverse developmental functions. Finally, the contribution of other processes to wall extensibility is briefly summarized.

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

Science.gov (United States)

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

2016-04-18

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

Rheological characteristics of synthetic road binders

Energy Technology Data Exchange (ETDEWEB)

Gordon D. Airey; Musarrat H. Mohammed; Caroline Fichter [University of Nottingham, Nottingham (United Kingdom)

2008-08-15

This paper deals with the synthesis of polymer binders from monomers that could in future be derived from renewable resources. These binders consist of polyethyl acrylate (PEA) of different molecular weight, polymethyl acrylate (PMA) and polybutyl acrylate (PBA), which were synthesised from ethyl acrylate, methyl acrylate and butyl acrylate, respectively, by atom transfer radical polymerization (ATRP). The fundamental rheological properties of these binders were determined by means of a dynamic shear rheometer (DSR) using a combination of temperature and frequency sweeps. The results indicate that PEA has rheological properties similar to that of 100/150 penetration grade bitumen, PMA similar rheological properties to that of 10/20 penetration grade bitumen, while PBA, due to its highly viscous nature and low complex modulus, cannot be used on its own as an asphalt binder. The synthetic binders were also combined with conventional penetration grade bitumen to produce a range of bitumen-synthetic polymer binder blends. These blends were batched by mass in the ratio of 1:1 or 3:1 and subjected to the same DSR rheological testing as the synthetic binders. The blends consisting of a softer bitumen (70/100 pen or 100/150 pen) with a hard synthetic binder (PMA) tended to be more compatible and therefore stable and produced rheological properties that combined the properties of the two components. The synthetic binders and particularly the extended bitumen samples (blends) produced rheological properties that showed similar characteristics to elastomeric SBS PMBs. 30 refs., 12 figs., 2 tabs.

Varieties of noise: analogical reasoning in synthetic biology.

Science.gov (United States)

Knuuttila, Tarja; Loettgers, Andrea

2014-12-01

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

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

Directory of Open Access Journals (Sweden)

Zhenyu Shi

2016-12-01

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

Tools to Understand Structural Property Relationships for Wood Cell Walls

Science.gov (United States)

Joseph E. Jakes; Daniel J. Yelle; Charles R. Frihart

2011-01-01

Understanding structure-property relationships for wood cell walls has been hindered by the complex polymeric structures comprising these cell walls and the difficulty in assessing meaningful mechanical property measurements of individual cell walls. To help overcome these hindrances, we have developed two experimental methods: 1) two-dimensional solution state nuclear...

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

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

2017-01-02

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

Computational synthetic geometry

CERN Document Server

Bokowski, Jürgen

1989-01-01

Computational synthetic geometry deals with methods for realizing abstract geometric objects in concrete vector spaces. This research monograph considers a large class of problems from convexity and discrete geometry including constructing convex polytopes from simplicial complexes, vector geometries from incidence structures and hyperplane arrangements from oriented matroids. It turns out that algorithms for these constructions exist if and only if arbitrary polynomial equations are decidable with respect to the underlying field. Besides such complexity theorems a variety of symbolic algorithms are discussed, and the methods are applied to obtain new mathematical results on convex polytopes, projective configurations and the combinatorics of Grassmann varieties. Finally algebraic varieties characterizing matroids and oriented matroids are introduced providing a new basis for applying computer algebra methods in this field. The necessary background knowledge is reviewed briefly. The text is accessible to stud...

Effects of local high-frequency perturbation on a turbulent boundary layer by synthetic jet injection

International Nuclear Information System (INIS)

Guo, Hao; Huang, Qian-Min; Liu, Pei-qing; Qu, Qiu-Lin

2015-01-01

An experimental study is performed to investigate the local high-frequency perturbation effects of a synthetic jet injection on a flat-plate turbulent boundary layer. Parameters of the synthetic jet are designed to force a high-frequency perturbation from a thin spanwise slot in the wall. In the test locations downstream of the slot, it is found that skin-friction is reduced by the perturbation, which is languishingly evolved downstream of the slot with corresponding influence on the near-wall regeneration mechanism of turbulent structures. The downstream slot region is divided into two regions due to the influence strength of the movement of spanwise vortices generated by the high-frequency perturbation. Interestingly, the variable interval time average technique is found to be disturbed by the existence of the spanwise vortices’ motion, especially in the region close to the slot. Similar results are obtained from the analysis of the probability density functions of the velocity fluctuation time derivatives, which is another indirect technique for detecting the enhancement or attenuation of streamwise vortices. However, both methods have shown consistent results with the skin-friction reduction mechanism in the far-away slot region. The main purpose of this paper is to remind researchers to be aware of the probable influence of spanwise vortices’ motion in wall-bounded turbulence control. (paper)

Application of improved PSO-RBF neural network in the synthetic ammonia decarbonization

Directory of Open Access Journals (Sweden)

Yongwei LI

2017-12-01

Full Text Available The synthetic ammonia decarbonization is a typical complex industrial process, which has the characteristics of time variation, nonlinearity and uncertainty, and the on-line control model is difficult to be established. An improved PSO-RBF neural network control algorithm is proposed to solve the problems of low precision and poor robustness in the complex process of the synthetic ammonia decarbonization. The particle swarm optimization algorithm and RBF neural network are combined. The improved particle swarm algorithm is used to optimize the RBF neural network's hidden layer primary function center, width and the output layer's connection value to construct the RBF neural network model optimized by the improved PSO algorithm. The improved PSO-RBF neural network control model is applied to the key carbonization process and compared with the traditional fuzzy neural network. The simulation results show that the improved PSO-RBF neural network control method used in the synthetic ammonia decarbonization process has higher control accuracy and system robustness, which provides an effective way to solve the modeling and optimization control of a complex industrial process.

Assessment of synthetic image fidelity

Science.gov (United States)

Mitchell, Kevin D.; Moorhead, Ian R.; Gilmore, Marilyn A.; Watson, Graham H.; Thomson, Mitch; Yates, T.; Troscianko, Tomasz; Tolhurst, David J.

2000-07-01

Computer generated imagery is increasingly used for a wide variety of purposes ranging from computer games to flight simulators to camouflage and sensor assessment. The fidelity required for this imagery is dependent on the anticipated use - for example when used for camouflage design it must be physically correct spectrally and spatially. The rendering techniques used will also depend upon the waveband being simulated, spatial resolution of the sensor and the required frame rate. Rendering of natural outdoor scenes is particularly demanding, because of the statistical variation in materials and illumination, atmospheric effects and the complex geometric structures of objects such as trees. The accuracy of the simulated imagery has tended to be assessed subjectively in the past. First and second order statistics do not capture many of the essential characteristics of natural scenes. Direct pixel comparison would impose an unachievable demand on the synthetic imagery. For many applications, such as camouflage design, it is important that nay metrics used will work in both visible and infrared wavebands. We are investigating a variety of different methods of comparing real and synthetic imagery and comparing synthetic imagery rendered to different levels of fidelity. These techniques will include neural networks (ICA), higher order statistics and models of human contrast perception. This paper will present an overview of the analyses we have carried out and some initial results along with some preliminary conclusions regarding the fidelity of synthetic imagery.

Plant synthetic biology.

Science.gov (United States)

Liu, Wusheng; Stewart, C Neal

2015-05-01

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

Regeneration of near-wall turbulence structures

Science.gov (United States)

Hamilton, James M.; Kim, John J.; Waleffe, Fabian A.

1993-01-01

An examination of the regeneration mechanisms of near-wall turbulence and an attempt to investigate the critical Reynolds number conjecture of Waleffe & Kim is presented. The basis is an extension of the 'minimal channel' approach of Jimenez and Moin which emphasizes the near-wall region and further reduces the complexity of the turbulent flow. Reduction of the flow Reynolds number to the minimum value which will allow turbulence to be sustained has the effect of reducing the ratio of the largest scales to the smallest scales or, equivalently, of causing the near-wall region to fill more of the area between the channel walls. In addition, since each wall may have an active near-wall region, half of the channel is always somewhat redundant. If a plane Couette flow is instead chosen as the base flow, this redundancy is eliminated: the mean shear of a plane Couette flow has a single sign, and at low Reynolds numbers, the two wall regions share a single set of structures. A minimal flow with these modifications possesses, by construction, the strongest constraints which allow sustained turbulence, producing a greatly simplified flow in which the regeneration process can be examined.

Modeling of Two-Phase Flow in Rough-Walled Fracture Using Level Set Method

Directory of Open Access Journals (Sweden)

Yunfeng Dai

2017-01-01

Full Text Available To describe accurately the flow characteristic of fracture scale displacements of immiscible fluids, an incompressible two-phase (crude oil and water flow model incorporating interfacial forces and nonzero contact angles is developed. The roughness of the two-dimensional synthetic rough-walled fractures is controlled with different fractal dimension parameters. Described by the Navier–Stokes equations, the moving interface between crude oil and water is tracked using level set method. The method accounts for differences in densities and viscosities of crude oil and water and includes the effect of interfacial force. The wettability of the rough fracture wall is taken into account by defining the contact angle and slip length. The curve of the invasion pressure-water volume fraction is generated by modeling two-phase flow during a sudden drainage. The volume fraction of water restricted in the rough-walled fracture is calculated by integrating the water volume and dividing by the total cavity volume of the fracture while the two-phase flow is quasistatic. The effect of invasion pressure of crude oil, roughness of fracture wall, and wettability of the wall on two-phase flow in rough-walled fracture is evaluated.

Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes

International Nuclear Information System (INIS)

Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih; Leong, Susanna Su Jan; Chang, Matthew Wook

2014-01-01

Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.

Production of Fatty Acid-Derived Valuable Chemicals in Synthetic Microbes

Energy Technology Data Exchange (ETDEWEB)

Yu, Ai-Qun; Pratomo Juwono, Nina Kurniasih [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore); Leong, Susanna Su Jan [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore); Singapore Institute of Technology, Singapore (Singapore); Chang, Matthew Wook, E-mail: bchcmw@nus.edu.sg [Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore (Singapore); Synthetic Biology Research Program, National University of Singapore, Singapore (Singapore)

2014-12-23

Fatty acid derivatives, such as hydroxy fatty acids, fatty alcohols, fatty acid methyl/ethyl esters, and fatty alka(e)nes, have a wide range of industrial applications including plastics, lubricants, and fuels. Currently, these chemicals are obtained mainly through chemical synthesis, which is complex and costly, and their availability from natural biological sources is extremely limited. Metabolic engineering of microorganisms has provided a platform for effective production of these valuable biochemicals. Notably, synthetic biology-based metabolic engineering strategies have been extensively applied to refactor microorganisms for improved biochemical production. Here, we reviewed: (i) the current status of metabolic engineering of microbes that produce fatty acid-derived valuable chemicals, and (ii) the recent progress of synthetic biology approaches that assist metabolic engineering, such as mRNA secondary structure engineering, sensor-regulator system, regulatable expression system, ultrasensitive input/output control system, and computer science-based design of complex gene circuits. Furthermore, key challenges and strategies were discussed. Finally, we concluded that synthetic biology provides useful metabolic engineering strategies for economically viable production of fatty acid-derived valuable chemicals in engineered microbes.

Boundary Conditions and SGS Models for LES of Wall-Bounded Separated Flows: An Application to Engine-Like Geometries

Directory of Open Access Journals (Sweden)

Piscaglia F.

2013-11-01

Full Text Available The implementation and the combination of advanced boundary conditions and subgrid scale models for Large Eddy Simulations are presented. The goal is to perform reliable cold flow LES simulations in complex geometries, such as in the cylinders of internal combustion engines. The implementation of an inlet boundary condition for synthetic turbulence generation and of two subgrid scale models, the local Dynamic Smagorinsky and the Wall-Adapting Local Eddy-viscosity SGS model ( WALE is described. The WALE model is based on the square of the velocity gradient tensor and it accounts for the effects of both the strain and the rotation rate of the smallest resolved turbulent fluctuations and it recovers the proper y3 near-wall scaling for the eddy viscosity without requiring dynamic pressure; hence, it is supposed to be a very reliable model for ICE simulation. Model validation has been performed separately on two steady state flow benches: a backward facing step geometry and a simple IC engine geometry with one axed central valve. A discussion on the completeness of the LES simulation (i.e. LES simulation quality is given.

Ubiquinol-cytochrome c reductase (Complex III) electrochemistry at multi-walled carbon nanotubes/Nafion modified glassy carbon electrodes

International Nuclear Information System (INIS)

Pelster, Lindsey N.; Minteer, Shelley D.

2012-01-01

Highlights: ► The electron transport chain is important to the understanding of metabolism in the living cell. ► Ubiquinol-cytochrome c reductase is a membrane bound complex of the electron transport chain (Complex III). ► The paper details the first bioelectrochemical characterization of ubiquinol-cytochrome c reductase at an electrode. - Abstract: Electron transport chain complexes are critical to metabolism in living cells. Ubiquinol-cytochrome c reductase (Complex III) is responsible for carrying electrons from ubiquinol to cytochrome c, but the complex has not been evaluated electrochemically. This work details the bioelectrochemistry of ubiquinol-cytochrome c reductase of the electron transport chain of tuber mitochondria. The characterization of the electrochemistry of this enzyme is investigated in carboxylated multi-walled carbon nanotube/tetrabutyl ammonium bromide-modified Nafion ® modified glassy carbon electrodes by cyclic voltammetry. Increasing concentrations of cytochrome c result in a catalytic response from the active enzyme in the nanotube sandwich. The experiments show that the enzyme followed Michaelis–Menten kinetics with a K m for the immobilized enzyme of 2.97 (±0.11) × 10 −6 M and a V max of 6.31 (±0.82) × 10 −3 μmol min −1 at the electrode, but the K m and V max values decreased compared to the free enzyme in solution, which is expected for immobilized redox proteins. This is the first evidence of ubiquinol-cytochrome c reductase bioelectrocatalysis.

An emerging role of pectic rhamnogalacturonanII for cell wall integrity

OpenAIRE

Reboul, Rebecca; Tenhaken, Raimund

2012-01-01

The plant cell wall is a complex network of different polysaccharides and glycoproteins, showing high diversity in nature. The essential components, tethering cell wall are under debate, as novel mutants challenge established models. The mutant ugd2,3 with a reduced supply of the important wall precursor UDP-glucuronic acid reveals the critical role of the pectic compound rhamnogalacturonanII for cell wall stability. This polymer seems to be more important for cell wall integrity than the pre...

Using Piezoelectric Devices to Transmit Power through Walls

Science.gov (United States)

Sherrit, Stewart; Bar-Cohen, Yoseph; Bao, Xiaoqi

2008-01-01

A method denoted wireless acoustic-electric feed-through (WAEF) has been conceived for transmitting power and/or data signals through walls or other solid objects made of a variety of elastic materials that could be electrically conductive or nonconductive. WAEF would make it unnecessary to use wires, optical fibers, tubes, or other discrete wall-penetrating signal-transmitting components, thereby eliminating the potential for structural weakening or leakage at such penetrations. Avoidance of such penetrations could be essential in some applications in which maintenance of pressure, vacuum, or chemical or biological isolation is required. In a basic WAEF setup, a transmitting piezoelectric transducer on one side of a wall would be driven at resonance to excite ultrasonic vibrations in the wall. A receiving piezoelectric transducer on the opposite side of the wall would convert the vibrations back to an ultrasonic AC electric signal, which would then be detected and otherwise processed in a manner that would depend on the modulation (if any) applied to the signal and whether the signal was used to transmit power, data, or both. An electromechanical-network model has been derived as a computationally efficient means of analyzing and designing a WAEF system. This model is a variant of a prior model, known in the piezoelectric-transducer art as Mason's equivalent-circuit model, in which the electrical and mechanical dynamics, including electromechanical couplings, are expressed as electrical circuit elements that can include inductors, capacitors, and lumped-parameter complex impedances. The real parts of the complex impedances are used to account for dielectric, mechanical, and coupling losses in all components (including all piezoelectric-transducer, wall, and intermediate material layers). In an application to a three-layer piezoelectric structure, this model was shown to yield the same results as do solutions of the wave equations of piezoelectricity and acoustic

Conceptual design of the INTOR first-wall system

International Nuclear Information System (INIS)

Smith, D.L.; Majumdar, S.; Mattas, R.F.; Turner, L.; Jung, J.; Abdou, M.A.; Bowers, D.; Trachsel, C.; Merrill, B.

1981-10-01

The design concept and performance characteristics of the first-wall design for the phase-1 INTOR (International Tokamak Reactor) study is described. The reference design consists of a water-cooled stainless steel panel. The major uncertainty regarding the performance of the bare stainless steel wall relates to the response of a thin-melt layer predicted to form on limited regions during a plasma disruption. A more-complex backup design, which incorporates radiatively cooled graphite tiles on the inboard wall, is briefly described

Synthetic Cannabinoids

Directory of Open Access Journals (Sweden)

Aslihan Okan Ibiloglu

2017-09-01

Full Text Available Synthetic cannabinoids which is a subgroup of cannabinoids are commonly used for recreational drug use throughout the whole world. Although both marijuana and synthetic cannabinoids stimulate the same receptors, cannabinoid receptor 1 (CB1 and cannabinoid receptor 2 (CB2, studies have shown that synthetic cannabinoids are much more potent than marijuana. The longer use of synthetic cannabinoids can cause severe physical and psychological symptoms that might even result in death, similar to many known illicit drugs. Main treatment options mostly involve symptom management and supportive care. The aim of this article is to discuss clinical and pharmacological properties of the increasingly used synthetic cannabinoids. [Psikiyatride Guncel Yaklasimlar - Current Approaches in Psychiatry 2017; 9(3.000: 317-328

Studying behavior of multilayer materials: A 1-D model correlated to magnetic domain walls through complex permeability

International Nuclear Information System (INIS)

Ahmadi, B.; Chazal, H.; Waeckerle, T.; Roudet, J.

2008-01-01

Multilayer cores are suitable for integrated planar magnetic components. We proposed here to investigate the frequency behavior of multilayer nanocrystalline cores in the frame of a one-dimensional (1-D) electromagnetic propagation model. Electromagnetic wave equations are considered to explain the phenomena from the macroscopic point of view. A domain wall description is considered to take into account non-homogeneity of magnetic media. This mesoscopic model is correlated to macroscopic model through complex permeability. The scope of validity of the model is determined by means of indirect permeability measurement. Finally, the behavior of the multilayer core is predicted by using an equivalent electrical circuit and will interest component designers

Plant cell wall polysaccharide analysis during cell elongation

DEFF Research Database (Denmark)

Guo, Xiaoyuan

Plant cell walls are complex structures whose composition and architecture are important to various cellular activities. Plant cell elongation requires a high level of rearrangement of the cell wall polymers to enable cell expansion. However, the cell wall polysaccharides dynamics during plant cell...... elongation is poorly understood. This PhD project aims to elucidate the cell wall compositional and structural change during cell elongation by using Comprehensive Microarray Polymer Profiling (CoMPP), microscopic techniques and molecular modifications of cell wall polysaccharide. Developing cotton fibre......, pea and Arabidopsis thaliana were selected as research models to investigate different types of cell elongation, developmental elongation and tropism elongation. A set of comprehensive analysis covering 4 cotton species and 11 time points suggests that non-cellulosic polysaccharides contribute...

Synthetic glycopeptides and glycoproteins with applications in biological research

Directory of Open Access Journals (Sweden)

Ulrika Westerlind

2012-05-01

Full Text Available Over the past few years, synthetic methods for the preparation of complex glycopeptides have been drastically improved. The need for homogenous glycopeptides and glycoproteins with defined chemical structures to study diverse biological phenomena further enhances the development of methodologies. Selected recent advances in synthesis and applications, in which glycopeptides or glycoproteins serve as tools for biological studies, are reviewed. The importance of specific antibodies directed to the glycan part, as well as the peptide backbone has been realized during the development of synthetic glycopeptide-based anti-tumor vaccines. The fine-tuning of native chemical ligation (NCL, expressed protein ligation (EPL, and chemoenzymatic glycosylation techniques have all together enabled the synthesis of functional glycoproteins. The synthesis of structurally defined, complex glycopeptides or glyco-clusters presented on natural peptide backbones, or mimics thereof, offer further possibilities to study protein-binding events.

Formation of covalent complexes between human O sup 6 -alkylguanine-DNA alkyltransferase and BCNU-treated defined length synthetic oligodeoxynucleotides

Energy Technology Data Exchange (ETDEWEB)

Brent, T.P.; Remack, J.S. (St. Jude Children' s Research Hospital, Memphis, TN (USA))

1988-07-25

Repair of chloroethylnitrosourea (CENU)-induced precursors of DNA interstrand cross-links by O{sup 6}-alkylguanine-DNA alkyltransferase (GAT or GATase) appears to be a factor in tumor resistance to therapy with this class of antineoplastic drugs. Since human GAT is highly specific for O{sup 6}-guanine, yet the probably cross-link structure is N{prime}-Guanine N{sup 3}cytosine ethane, rearrangement of the initial O{sup 6}-guanine adduct via O{sup 6},N{sup 1}ethanoguanine has been proposed. The authors suggested that GAT reaction with this intermediate would produce DNA covalently linked to protein through an ethane link from N{sup 1}-guanine to the alkylacceptor site on GAT. In preliminary studies they demonstrated a covalent complex between GAT and carmustine (BCNU)-treated DNA by a precipitation assay method. They have now developed a method for isolating the reaction product of BCNU-treated synthetic 14-mer ({sup 32}P)-labeled oligodeoxynucleotide and GAT using polyacrylamide gel electrophoresis. This approach can be used to characterize the adducts induced by CENUs that lead to complex formation with GAT.

Webs of domain walls in supersymmetric gauge theories

International Nuclear Information System (INIS)

Eto, Minoru; Isozumi, Youichi; Nitta, Muneto; Ohashi, Keisuke; Sakai, Norisuke

2005-01-01

Webs of domain walls are constructed as 1/4 Bogomol'nyi-Prasad-Sommerfield (BPS) states in d=4, N=2 supersymmetric U(N C ) gauge theories with N F hypermultiplets in the fundamental representation. Webs of walls can contain any numbers of external legs and loops like (p,q) string/5-brane webs. We find the moduli space M of a 1/4 BPS equation for wall webs to be the complex Grassmann manifold. When moduli spaces of 1/2 BPS states (parallel walls) and the vacua are removed from M, the noncompact moduli space of genuine 1/4 BPS wall webs is obtained. All the solutions are obtained explicitly and exactly in the strong gauge coupling limit. In the case of Abelian gauge theory, we work out the correspondence between configurations of wall web and the moduli space CP N F -1

Synthetic biology to access and expand nature’s chemical diversity

Science.gov (United States)

Smanski, Michael J.; Zhou, Hui; Claesen, Jan; Shen, Ben; Fischbach, Michael; Voigt, Christopher A.

2016-01-01

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Economically accessing the potential encoded within sequenced genomes promises to reinvigorate waning drug discovery pipelines and provide novel routes to intricate chemicals. This is a tremendous undertaking, as the pathways often comprise dozens of genes spanning as much as 100+ kiliobases of DNA, are controlled by complex regulatory networks, and the most interesting molecules are made by non-model organisms. Advances in synthetic biology address these issues, including DNA construction technologies, genetic parts for precision expression control, synthetic regulatory circuits, computer aided design, and multiplexed genome engineering. Collectively, these technologies are moving towards an era when chemicals can be accessed en mass based on sequence information alone. This will enable the harnessing of metagenomic data and massive strain banks for high-throughput molecular discovery and, ultimately, the ability to forward design pathways to complex chemicals not found in nature. PMID:26876034

Yeast cell wall chitin reduces wine haze formation.

Science.gov (United States)

Ndlovu, Thulile; Divol, Benoit; Bauer, Florian F

2018-04-27

Protein haze formation in bottled wines is a significant concern for the global wine industry and wine clarification before bottling is therefore a common but expensive practice. Previous studies have shown that wine yeast strains can reduce haze formation through the secretion of certain mannoproteins, but it has been suggested that other yeast-dependent haze protective mechanisms exist. On the other hand, addition of chitin has been shown to reduce haze formation, likely because grape chitinases have been shown to be the major contributors to haze. In this study, Chardonnay grape must fermented by various yeast strains resulted in wines with different protein haze levels indicating differences in haze protective capacities of the strains. The cell wall chitin levels of these strains were determined, and a strong correlation between cell wall chitin levels and haze protection capability was observed. To further evaluate the mechanism of haze protection, Escherichia coli -produced GFP-tagged grape chitinase was shown to bind efficiently to yeast cell walls in a cell wall chitin concentration-dependent manner, while commercial chitinase was removed from synthetic wine in quantities also correlated with the cell wall chitin levels of the strains. Our findings suggest a new mechanism of reducing wine haze, and propose a strategy for optimizing wine yeast strains to improve wine clarification. Importance In this study, we establish a new mechanism by which wine yeast strains can impact on the protein haze formation of wines, and demonstrate that yeast cell wall chitin binds grape chitinase in a chitin-concentration dependent manner. We also show that yeast can remove this haze-forming protein from wine. Chitin has in the past been shown to efficiently reduce wine haze formation when added to the wine in high concentration as a clarifying agent. Our data suggest that the selection of yeast strains with high levels of cell wall chitin can reduce protein haze. We also

[Application of microelectronics CAD tools to synthetic biology].

Science.gov (United States)

Madec, Morgan; Haiech, Jacques; Rosati, Élise; Rezgui, Abir; Gendrault, Yves; Lallement, Christophe

2017-02-01

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process. Nevertheless, with the increasing complexity of biological circuits, this is no longer the case and a large number of computer aided design softwares have been developed in the past few years. These tools include languages for the behavioral description and the mathematical modelling of biological systems, simulators at different levels of abstraction, libraries of biological devices and circuit design automation algorithms. All of these tools already exist in other fields of engineering sciences, particularly in microelectronics. This is the approach that is put forward in this paper. © 2017 médecine/sciences – Inserm.

Synthesis of plant cell wall oligosaccharides

DEFF Research Database (Denmark)

Clausen, Mads Hartvig

Plant cell walls are structurally complex and contain a large number of diverse carbohydrate polymers. These plant fibers are a highly valuable bio-resource and the focus of food, energy and health research. We are interested in studying the interplay of plant cell wall carbohydrates with proteins...... for characterizing protein-carbohydrate binding. The presentation will highlight chemical syntheses of plant cell wall oligosaccharides from the group and provide examples from studies of their interactions with proteins....... such as enzymes, cell surface lectins, and antibodies. However, detailed molecular level investigations of such interactions are hampered by the heterogeneity and diversity of the polymers of interest. To circumvent this, we target well-defined oligosaccharides with representative structures that can be used...

Plant cell wall signalling and receptor-like kinases.

Science.gov (United States)

Wolf, Sebastian

2017-02-15

Communication between the extracellular matrix and the cell interior is essential for all organisms as intrinsic and extrinsic cues have to be integrated to co-ordinate development, growth, and behaviour. This applies in particular to plants, the growth and shape of which is governed by deposition and remodelling of the cell wall, a rigid, yet dynamic, extracellular network. It is thus generally assumed that cell wall surveillance pathways exist to monitor the state of the wall and, if needed, elicit compensatory responses such as altered expression of cell wall remodelling and biosynthesis genes. Here, I highlight recent advances in the field of cell wall signalling in plants, with emphasis on the role of plasma membrane receptor-like kinase complexes. In addition, possible roles for cell wall-mediated signalling beyond the maintenance of cell wall integrity are discussed. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

[From synthetic biology to synthetic humankind].

Science.gov (United States)

Nouvel, Pascal

2015-01-01

In this paper, we propose an historical survey of the expression "synthetic biology" in order to identify its main philosophical components. The result of the analysis is then used to investigate the meaning of the notion of "synthetic man". It is shown that both notions share a common philosophical background that can be summed up by the short but meaningful assertion: "biology is technology". The analysis allows us to distinguish two notions that are often confused in transhumanist literature: the notion of synthetic man and the notion of renewed man. The consequences of this crucial distinction are discussed. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Structure measurements in a synthetic turbulent boundary layer

Science.gov (United States)

Arakeri, Jaywant H.

1987-09-01

Extensive hot-wire measurements have been made to determine the structure of the large eddy in a synthejc turbulent boundary layer on a flat-plate model. The experiments were carried out in a wind tunnel at a nominal free-stream velocity of 12 m/s. The synthetic turbulent boundary layer had a hexagonal pattern of eddies and a ratio of streamwise scale to spanwise scale of 3.2:1. The measured celerity of the large eddy was 84.2 percent of the free-stream velocity. There was some loss of coherence, but very little distortion, as the eddies moved downstream. Several mean properties of the synthetic boundary layer were found to agree quite well with the mean properties of a natural turbulent boundary layer at the same Reynolds number. The large eddy is composed of a pair of primary counter-rotating vortices about five [...] long in the streamwise direction and about one [...] apart in the spanwise direction, where [...] is the mean boundary-layer thickness. The sense of the primary pair is such as to pump fluid away from the wall in the region between the vortices. A secondary pair of counter-rotating streamwise vortices, having a sense opposite to that of the primary pair, is observed outside of and slightly downstream from the primary vortices. Both pairs of vortices extend across the full thickness of the boundary layer and are inclined at a shallow angle to the surface of the flat plate. The data show that the mean vorticity vectors are not tangential to the large-eddy vortices. In fact, the streamwise and normal vorticity components that signal the presence of the eddy are of the same order of magnitude. Definite signatures are obtained in terms of the mean skin-friction coefficient and the mean wake parameter averaged at constant phase. Velocities induced by the vortices are partly responsible for entrainment of irrotational fluid, for transport of momentum, for generation of Reynolds stresses, and for maintenance of streamwise and normal vorticity in the outer

Coloring of synthetic fluorite

International Nuclear Information System (INIS)

Birsoy, R.

1980-01-01

A synthetic fluorite of the Harshaw Chemical Company is analyzed for rare earth elements, yttrium, and sodium. Samples of this fluorite are irradiated with X-rays, γ-rays, neutrons, electrons, protons, and α-particles at different energies, and their absorption spectra are analyzed. Analyzing the thermal bleaching of these radiation-coloured fluorites shows that both, impurities and radiation play a part in the coloration of synthetic fluorite. However, the main contribution comes from the radiation induced lattice defects. In the visible region spectra, the colour centre of the 5800 to 5900 A absorption band is probably mainly related with large aggregates of F-centres. The 5450 and the 5300 A absorption bands are mainly related to monovalent and divalent ion impurities and their association with lattice defects. The 3800 A absorption band seems to be related with F-centre aggregates. However, the contribution from the rare earth elements related complex color centres also plays some part for the production of this absorption band. These results indicate that the color centres of different origin can absorb light at the same wavelength. (author)

A novel non-enzymatic hydrogen peroxide sensor based on single walled carbon nanotubes-manganese complex modified glassy carbon electrode

International Nuclear Information System (INIS)

Salimi, Abdollah; Mahdioun, Monierosadat; Noorbakhsh, Abdollah; Abdolmaleki, Amir; Ghavami, Raoof

2011-01-01

A simple procedure was developed to prepare a glassy carbon (GC) electrode modified with single wall carbon nanotubes (SWCNTs) and phenazine derivative of Mn-complex. With immersing the GC/CNTs modified electrode into Mn-complex solution for a short period of time 20-100 s, a stable thin layer of the complex was immobilized onto electrode surface. Modified electrode showed a well defined redox couples at wide pH range (1-12). The surface coverages and heterogeneous electron transfer rate constants (k s ) of immobilized Mn-complex were approximately 1.58 x 10 -10 mole cm -2 and 48.84 s -1 . The modified electrode showed excellent electrocatalytic activity toward H 2 O 2 reduction. Detection limit, sensitivity, linear concentration range and k cat for H 2 O 2 were, 0.2 μM and 692 nA μM -1 cm -2 , 1 μM to 1.5 mM and 7.96(±0.2) x 10 3 M -1 s -1 , respectively. Compared to other modified electrodes, this electrode has many advantageous such as remarkable catalytic activity, good reproducibility, simple preparation procedure and long term stability.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

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

A Unifying Mathematical Framework for Genetic Robustness, Environmental Robustness, Network Robustness and their Trade-offs on Phenotype Robustness in Biological Networks. Part III: Synthetic Gene Networks in Synthetic Biology

Science.gov (United States)

Chen, Bor-Sen; Lin, Ying-Po

2013-01-01

Robust stabilization and environmental disturbance attenuation are ubiquitous systematic properties that are observed in biological systems at many different levels. The underlying principles for robust stabilization and environmental disturbance attenuation are universal to both complex biological systems and sophisticated engineering systems. In many biological networks, network robustness should be large enough to confer: intrinsic robustness for tolerating intrinsic parameter fluctuations; genetic robustness for buffering genetic variations; and environmental robustness for resisting environmental disturbances. Network robustness is needed so phenotype stability of biological network can be maintained, guaranteeing phenotype robustness. Synthetic biology is foreseen to have important applications in biotechnology and medicine; it is expected to contribute significantly to a better understanding of functioning of complex biological systems. This paper presents a unifying mathematical framework for investigating the principles of both robust stabilization and environmental disturbance attenuation for synthetic gene networks in synthetic biology. Further, from the unifying mathematical framework, we found that the phenotype robustness criterion for synthetic gene networks is the following: if intrinsic robustness + genetic robustness + environmental robustness ≦ network robustness, then the phenotype robustness can be maintained in spite of intrinsic parameter fluctuations, genetic variations, and environmental disturbances. Therefore, the trade-offs between intrinsic robustness, genetic robustness, environmental robustness, and network robustness in synthetic biology can also be investigated through corresponding phenotype robustness criteria from the systematic point of view. Finally, a robust synthetic design that involves network evolution algorithms with desired behavior under intrinsic parameter fluctuations, genetic variations, and environmental

[New polymer-drug systems based on natural and synthetic polymers].

Science.gov (United States)

Racoviţă, Stefania; Vasiliu, Silvia; Foia, Liliana

2010-01-01

The great versatility of polymers makes them very useful in the biomedical and pharmaceutical fields. The combination of natural and synthetic polymers leads to new materials with tailored functional properties. The aim of this work consists in the preparation of new drug delivery system based on chitosan (natural polymer) and polybetaines (synthetic polymers), by a simple process, well known in the literature as complex coacervation methods. Also, the adsorption and release studies of two antibiotics as well as the preservation of their bactericidal capacities were performed.

DNA recognition by synthetic constructs.

Science.gov (United States)

Pazos, Elena; Mosquera, Jesús; Vázquez, M Eugenio; Mascareñas, José L

2011-09-05

The interaction of transcription factors with specific DNA sites is key for the regulation of gene expression. Despite the availability of a large body of structural data on protein-DNA complexes, we are still far from fully understanding the molecular and biophysical bases underlying such interactions. Therefore, the development of non-natural agents that can reproduce the DNA-recognition properties of natural transcription factors remains a major and challenging goal in chemical biology. In this review we summarize the basics of double-stranded DNA recognition by transcription factors, and describe recent developments in the design and preparation of synthetic DNA binders. We mainly focus on synthetic peptides that have been designed by following the DNA interaction of natural proteins, and we discuss how the tools of organic synthesis can be used to make artificial constructs equipped with functionalities that introduce additional properties to the recognition process, such as sensing and controllability. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthetic Nano-Low Density Lipoprotein as Targeted Drug DeliveryVehicle for Glioblastoma Multiforme

Energy Technology Data Exchange (ETDEWEB)

Nikanjam, Mina; Blakely, Eleanor A.; Bjornstad, Kathleen A.; Shu,Xiao; Budinger, Thomas F.; Forte, Trudy M.

2006-06-14

This paper discribes a synthetic low density lipoprotein(LDL) made by complexing a 29 amino acid that consists of a lipid bindingdomain and the LDL receptor binding domain with a lipid microemulsion.The nano-LDL particles were intermdiate in size between LDL and HDL andbound to LDL receptors on GBM brain tumor cells. Synthetic nano-LDLuptake by GBM cells was LDL receptor specific and dependent on cellreceptor number. It is suggested that these synthetic particles can serveas a delivery vehicle for hydophobic anti-tumor drugs by targeting theLDL receptor.

Architecture and Biosynthesis of the Saccharomyces cerevisiae Cell Wall

Science.gov (United States)

Orlean, Peter

2012-01-01

The wall gives a Saccharomyces cerevisiae cell its osmotic integrity; defines cell shape during budding growth, mating, sporulation, and pseudohypha formation; and presents adhesive glycoproteins to other yeast cells. The wall consists of β1,3- and β1,6-glucans, a small amount of chitin, and many different proteins that may bear N- and O-linked glycans and a glycolipid anchor. These components become cross-linked in various ways to form higher-order complexes. Wall composition and degree of cross-linking vary during growth and development and change in response to cell wall stress. This article reviews wall biogenesis in vegetative cells, covering the structure of wall components and how they are cross-linked; the biosynthesis of N- and O-linked glycans, glycosylphosphatidylinositol membrane anchors, β1,3- and β1,6-linked glucans, and chitin; the reactions that cross-link wall components; and the possible functions of enzymatic and nonenzymatic cell wall proteins. PMID:23135325

The Cell Wall Teichuronic Acid Synthetase (TUAS Is an Enzyme Complex Located in the Cytoplasmic Membrane of Micrococcus luteus

Directory of Open Access Journals (Sweden)

Lingyi Lynn Deng

2010-01-01

composed of disaccharide repeating units [-4-β-D-ManNAcAp-(1→6α-D-Glcp−1-]n, which is covalently anchored to the peptidoglycan on the inner cell wall and extended to the outer surface of the cell envelope. An enzyme complex responsible for the TUA chain biosynthesis was purified and characterized. The 440 kDa enzyme complex, named teichuronic acid synthetase (TUAS, is an octomer composed of two kinds of glycosyltransferases, Glucosyltransferase, and ManNAcA-transferase, which is capable of catalyzing the transfer of disaccharide glycosyl residues containing both glucose and the N-acetylmannosaminuronic acid residues. TUAS displays hydrophobic properties and is found primarily associated with the cytoplasmic membrane. The purified TUAS contains carotinoids and lipids. TUAS activity is diminished by phospholipase digestion. We propose that TUAS serves as a multitasking polysaccharide assembling station on the bacterial membrane.

A new synthetic approach to the science of complexity: the MISSION project at NIFS

International Nuclear Information System (INIS)

Tetsuya Sato

1999-01-01

The present day stage of computer simulation has entered into the third phase. The age of computer simulation in plasma physics dawned in the late 1950's when Oscar Buneman and John Dawson developed the sheet particle model. In 1960's and the early part of 1970's, one devoted oneself to refine the particle model and to develop, more practically, fluid magnetic hydrodynamic models so that the feasibility of the computer simulation methodology could be tested. This age can be called 'dawning of computer simulation'. The so-called supercomputer appeared in the late 1970's and the computer simulation entered the second phase where individual nonlinear phenomena have become possible to be attacked. At present when a supercomputer with the ability of higher than 100 GFlops speed and lager than 10GBytes common memory is available, almost any individual nonlinear phenomenon, whatever it may look complex, can be solved. This age may well be called 'the age of nonlinear solver'. However, as far as the authors are satisfied with using a supercomputer for simply solving an individual nonlinear problem, the computer simulation plays only a passive role in science and would never cause a catastrophic transition to it. Then, the modern science of the 20th century based on reductionism would continue in the coming 21st century, thus the 21st century's science would stay boring and tedious. It must be the computer simulation that can refresh this boring state. At NIFS an extensive effort has been made to establish a new paradigm of science in the 21st century by developing a new synthetic methodology of computer simulation, which the authors call the MISSION Project. The authors present this MISSION Project and propose a working hypothesis of the science of complexity in this talk

Cell-free synthetic biology: thinking outside the cell.

Science.gov (United States)

Hodgman, C Eric; Jewett, Michael C

2012-05-01

Cell-free synthetic biology is emerging as a powerful approach aimed to understand, harness, and expand the capabilities of natural biological systems without using intact cells. Cell-free systems bypass cell walls and remove genetic regulation to enable direct access to the inner workings of the cell. The unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the rapid development of engineering foundations for cell-free systems in recent years. These efforts have led to programmed circuits, spatially organized pathways, co-activated catalytic ensembles, rational optimization of synthetic multi-enzyme pathways, and linear scalability from the micro-liter to the 100-liter scale. It is now clear that cell-free systems offer a versatile test-bed for understanding why nature's designs work the way they do and also for enabling biosynthetic routes to novel chemicals, sustainable fuels, and new classes of tunable materials. While challenges remain, the emergence of cell-free systems is poised to open the way to novel products that until now have been impractical, if not impossible, to produce by other means. Copyright © 2011 Elsevier Inc. All rights reserved.

Experience with synthetic fluorinated fluid lubricants

Science.gov (United States)

Conley, Peter L.; Bohner, John J.

1990-01-01

Since the late 1970's, the wet lubricant of choice for space mechanisms has been one of the family of synthetic perfluoro polyalkylether (PFPE) compounds, namely Fomblin Z-25 (Bray-815Z) or DuPont's Krytox 143xx series. While offering the advantages of extremely low vapor pressures and wide temperature ranges, these oils and derived greases have a complex chemistry compared to the more familiar natural and synthetic hydrocarbons. Many aerospace companies have conducted test programs to characterize the behavior of these compounds in a space environment, resulting in a large body of hard knowledge as well as considerable space lore concerning the suitability of the lubricants for particular applications and techniques for successful application. The facts are summarized and a few myths about the compounds are dispelled, and some performance guidelines for the mechanism design engineer are provided.

Hybrid protein-synthetic polymer nanoparticles for drug delivery.

Science.gov (United States)

Koseva, Neli S; Rydz, Joanna; Stoyanova, Ekaterina V; Mitova, Violeta A

2015-01-01

Among the most common nanoparticulate systems, the polymeric nanocarriers have a number of key benefits, which give a great choice of delivery platforms. Nevertheless, polymeric nanoparticles possess some limitations that include use of toxic solvents in the production process, polymer degradation, drug leakage outside the diseased tissue, and polymer cytotoxicity. The combination of polymers of biological and synthetic origin is an appealing modern strategy for the production of novel nanocarriers with unprecedented properties. Proteins' interface can play an important role in determining bioactivity and toxicity and gives perspective for future development of the polymer-based nanoparticles. The design of hybrid constructs composed of synthetic polymer and biological molecules such as proteins can be considered as a straightforward tool to integrate a broad spectrum of properties and biofunctions into a single device. This review discusses hybrid protein-synthetic polymer nanoparticles with different structures and levels in complexity and functionality, in view of their applications as drug delivery systems. © 2015 Elsevier Inc. All rights reserved.

Plasma-wall interaction and plasma facing materials

International Nuclear Information System (INIS)

Tanabe, Tetsuo; Miyahara, Akira.

1990-01-01

The recognition that plasma-wall interaction plays the essential role from both standpoints of energy balance and particle balance for realizing nuclear fusion reactors has become to prevail. However, on how each elementary process acts and what competitive effect the synthetic action brings about, the stage of doing the qualitative discussion has just come, and the quantitative investigation is the problem for the future. In this paper, the plasma-wall interaction as seen from the research field of plasma-facing materials is discussed centering around graphite materials which have been mostly used at present, and the present status of the research and development on the problems of impurities, hydrogen recycling and heat resistance and radiation resistance is mentioned. Moreover, the problems are pointed out, and the course for the future is looked for. The recent experiment with large tokamaks adopted graphite or carbon as the plasma-facing materials, and the reduction of metallic impurities in plasma showed the clear improvement of plasma confinement characteristics. However, for the next device which requires forced cooling, the usability of graphite is doubtful. (K.I.) 51 refs

Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy.

Directory of Open Access Journals (Sweden)

Michael Volpers

Full Text Available The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force. The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase-pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly

Targeting Synthetic Lethal Interactions between Myc and the eIF4F Complex Impedes Tumorigenesis

Directory of Open Access Journals (Sweden)

Chen-Ju Lin

2012-04-01

Full Text Available The energetically demanding process of translation is linked to multiple signaling events through mTOR-mediated regulation of eukaryotic initiation factor (eIF4F complex assembly. Disrupting mTOR constraints on eIF4F activity can be oncogenic and alter chemotherapy response, making eIF4F an attractive antineoplastic target. Here, we combine a newly developed inducible RNAi platform and pharmacological targeting of eIF4F activity to define a critical role for endogenous eIF4F in Myc-dependent tumor initiation. We find elevated Myc levels are associated with deregulated eIF4F activity in the prelymphomatous stage of the Eμ-Myc lymphoma model. Inhibition of eIF4F is synthetic lethal with elevated Myc in premalignant pre-B/B cells resulting in reduced numbers of cycling pre-B/B cells and delayed tumor onset. At the organismal level, eIF4F suppression affected a subset of normal regenerating cells, but this was well tolerated and rapidly and completely reversible. Therefore, eIF4F is a key Myc client that represents a tumor-specific vulnerability.

Physical Characterization of Synthetic Phosphatidylinositol Dimannosides and Analogues in Binary Systems with Phosphatidylcholine

DEFF Research Database (Denmark)

Hubert, Madlen; Larsen, David S; Hayman, Colin M

2014-01-01

Native phosphatidylinositol mannosides (PIMs) from the cell wall of Mycobacterium bovis (M. bovis) and synthetic analogues have been identified to exert immunostimulatory activities. These activities have been investigated using particulate delivery systems containing native mannosylated lipids...... the design of liposome-based delivery systems. In mixed films the phosphoglycolipids were found to be miscible with PC based on evaluation of collapse pressures and deviations of experimental molecular areas from calculated ideal values. Concanavalin A (ConA) agglutination confirmed the presence...

The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field.

Science.gov (United States)

Adams, Bryn L

2016-12-16

Escherichia coli (E. coli) has played a pivotal role in the development of genetics and molecular biology as scientific fields. It is therefore not surprising that synthetic biology (SB) was built upon E. coli and continues to dominate the field. However, scientific capabilities have advanced from simple gene mutations to the insertion of rationally designed, complex synthetic circuits and creation of entirely synthetic genomes. The point is rapidly approaching where E. coli is no longer an adequate host for the increasingly sophisticated genetic designs of SB. It is time to develop the next generation of SB chassis; robust organisms that can provide the advanced physiology novel synthetic circuits will require to move SB from the laboratory into fieldable technologies. This can be accomplished by developing chassis-specific genetic toolkits that are as extensive as those for E. coli. However, the holy grail of SB would be the development of a universal toolkit that can be ported into any chassis. This viewpoint article underscores the need for new bacterial chassis, as well as discusses some of the important considerations in their selection. It also highlights a few examples of robust, tractable bacterial species that can meet the demands of tomorrow's state-of-the-art in SB. Significant advances have been made in the first 15 years since this field has emerged. However, the advances over the next 15 years will occur not in laboratory organisms, but in fieldable species where the potential of SB can be fully realized in game changing technology.

Cell Wall Diversity in Forage Maize

NARCIS (Netherlands)

Torres, A.F.; Noordam-Boot, C.M.M.; Dolstra, Oene; Weijde, van der Tim; Combes, Eliette; Dufour, Philippe; Vlaswinkel, Louis; Visser, R.G.F.; Trindade, L.M.

2015-01-01

Genetic studies are ideal platforms for assessing the extent of genetic diversity, inferring the genetic architecture, and evaluating complex trait interrelations for cell wall compositional and bioconversion traits relevant to bioenergy applications. Through the characterization of a forage

The development of deep learning in synthetic aperture radar imagery

CSIR Research Space (South Africa)

Schwegmann, Colin P

2017-05-01

Full Text Available sensing techniques but comes at the price of additional complexities. To adequately cope with these, researchers have begun to employ advanced machine learning techniques known as deep learning to Synthetic Aperture Radar data. Deep learning represents...

First wall response to energy disposition in conceptual laser fusion reactors

International Nuclear Information System (INIS)

Hovingh, J.

1976-02-01

Discussed are energy depositions in the first wall of various proposed laser-fusion reactors and the effect of pulse time on the stress and temperature in the first wall. Simple models can be used to estimate the temperature and stress rise from x-rays and neutrons. More complex analysis is needed to estimate the response of the first wall to reflected laser light and the pellet debris

Changes in cell wall properties coincide with overexpression of extensin fusion proteins in suspension cultured tobacco cells.

Science.gov (United States)

Tan, Li; Pu, Yunqiao; Pattathil, Sivakumar; Avci, Utku; Qian, Jin; Arter, Allison; Chen, Liwei; Hahn, Michael G; Ragauskas, Arthur J; Kieliszewski, Marcia J

2014-01-01

Extensins are one subfamily of the cell wall hydroxyproline-rich glycoproteins, containing characteristic SerHyp4 glycosylation motifs and intermolecular cross-linking motifs such as the TyrXaaTyr sequence. Extensins are believed to form a cross-linked network in the plant cell wall through the tyrosine-derivatives isodityrosine, pulcherosine, and di-isodityrosine. Overexpression of three synthetic genes encoding different elastin-arabinogalactan protein-extensin hybrids in tobacco suspension cultured cells yielded novel cross-linking glycoproteins that shared features of the extensins, arabinogalactan proteins and elastin. The cell wall properties of the three transgenic cell lines were all changed, but in different ways. One transgenic cell line showed decreased cellulose crystallinity and increased wall xyloglucan content; the second transgenic cell line contained dramatically increased hydration capacity and notably increased cell wall biomass, increased di-isodityrosine, and increased protein content; the third transgenic cell line displayed wall phenotypes similar to wild type cells, except changed xyloglucan epitope extractability. These data indicate that overexpression of modified extensins may be a route to engineer plants for bioenergy and biomaterial production.

A novel non-enzymatic hydrogen peroxide sensor based on single walled carbon nanotubes-manganese complex modified glassy carbon electrode

Energy Technology Data Exchange (ETDEWEB)

Salimi, Abdollah, E-mail: absalimi@uok.ac.i [Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj (Iran, Islamic Republic of); Research Center for Nanotechnology, University of Kurdistan, P.O. Box 416, Sanandaj (Iran, Islamic Republic of); Mahdioun, Monierosadat; Noorbakhsh, Abdollah [Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj (Iran, Islamic Republic of); Abdolmaleki, Amir [Department of Chemistry, Isfahan University of Technology, Isfahan, 84156/83111 (Iran, Islamic Republic of); Ghavami, Raoof [Department of Chemistry, University of Kurdistan, P.O. Box 416, Sanandaj (Iran, Islamic Republic of)

2011-03-30

A simple procedure was developed to prepare a glassy carbon (GC) electrode modified with single wall carbon nanotubes (SWCNTs) and phenazine derivative of Mn-complex. With immersing the GC/CNTs modified electrode into Mn-complex solution for a short period of time 20-100 s, a stable thin layer of the complex was immobilized onto electrode surface. Modified electrode showed a well defined redox couples at wide pH range (1-12). The surface coverages and heterogeneous electron transfer rate constants (k{sub s}) of immobilized Mn-complex were approximately 1.58 x 10{sup -10} mole cm{sup -2} and 48.84 s{sup -1}. The modified electrode showed excellent electrocatalytic activity toward H{sub 2}O{sub 2} reduction. Detection limit, sensitivity, linear concentration range and k{sub cat} for H{sub 2}O{sub 2} were, 0.2 {mu}M and 692 nA {mu}M{sup -1} cm{sup -2}, 1 {mu}M to 1.5 mM and 7.96({+-}0.2) x 10{sup 3} M{sup -1} s{sup -1}, respectively. Compared to other modified electrodes, this electrode has many advantageous such as remarkable catalytic activity, good reproducibility, simple preparation procedure and long term stability.

Synthetic cation-selective nanotube: permeant cations chaperoned by anions.

Science.gov (United States)

Hilder, Tamsyn A; Gordon, Dan; Chung, Shin-Ho

2011-01-28

The ability to design ion-selective, synthetic nanotubes which mimic biological ion channels may have significant implications for the future treatment of bacteria, diseases, and as ultrasensitive biosensors. We present the design of a synthetic nanotube made from carbon atoms that selectively allows monovalent cations to move across and rejects all anions. The cation-selective nanotube mimics some of the salient properties of biological ion channels. Before practical nanodevices are successfully fabricated it is vital that proof-of-concept computational studies are performed. With this in mind we use molecular and stochastic dynamics simulations to characterize the dynamics of ion permeation across a single-walled (10, 10), 36 Å long, carbon nanotube terminated with carboxylic acid with an effective radius of 5.08 Å. Although cations encounter a high energy barrier of 7 kT, its height is drastically reduced by a chloride ion in the nanotube. The presence of a chloride ion near the pore entrance thus enables a cation to enter the pore and, once in the pore, it is chaperoned by the resident counterion across the narrow pore. The moment the chaperoned cation transits the pore, the counterion moves back to the entrance to ferry another ion. The synthetic nanotube has a high sodium conductance of 124 pS and shows linear current-voltage and current-concentration profiles. The cation-anion selectivity ratio ranges from 8 to 25, depending on the ionic concentrations in the reservoirs.

Cell-free synthetic biology for environmental sensing and remediation.

Science.gov (United States)

Karig, David K

2017-06-01

The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

Secondary cell wall formation in Cryptococcus neoformans as a rescue mechanism against acid-induced autolysis.

Science.gov (United States)

Farkas, Vladimír; Takeo, Kanji; Maceková, Danka; Ohkusu, Misako; Yoshida, Soichi; Sipiczki, Matthias

2009-03-01

Growth of the opportunistic yeast pathogen Cryptococcus neoformans in a synthetic medium containing yeast nitrogen base and 1.0-3.0% glucose is accompanied by spontaneous acidification of the medium, with its pH decreasing from the initial 5.5 to around 2.5 in the stationary phase. During the transition from the late exponential to the stationary phase of growth, many cells died as a consequence of autolytic erosion of their cell walls. Simultaneously, there was an increase in an ecto-glucanase active towards beta-1,3-glucan and having a pH optimum between pH 3.0 and 3.5. As a response to cell wall degradation, some cells developed an unusual survival strategy by forming 'secondary' cell walls underneath the original ones. Electron microscopy revealed that the secondary cell walls were thicker than the primary ones, exposing bundles of polysaccharide microfibrils only partially masked by an amorphous cell wall matrix on their surfaces. The cells bearing secondary cell walls had a three to five times higher content of the alkali-insoluble cell wall polysaccharides glucan and chitin, and their chitin/glucan ratio was about twofold higher than in cells from the logarithmic phase of growth. The cell lysis and the formation of the secondary cell walls could be suppressed by buffering the growth medium between pH 4.5 and 6.5.

Sunspot Light Walls Suppressed by Nearby Brightenings

Energy Technology Data Exchange (ETDEWEB)

Yang, Shuhong; Zhang, Jun; Hou, Yijun; Li, Xiaohong [CAS Key Laboratory of Solar Activity, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Erdélyi, Robertus [Solar Physics and Space Plasma Research Centre, School of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH (United Kingdom); Yan, Limei, E-mail: shuhongyang@nao.cas.cn [Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing 100029 (China)

2017-07-01

Light walls, as ensembles of oscillating bright structures rooted in sunspot light bridges, have not been well studied, although they are important for understanding sunspot properties. Using the Interface Region Imaging Spectrograph and Solar Dynamics Observatory observations, here we study the evolution of two oscillating light walls each within its own active region (AR). The emission of each light wall decays greatly after the appearance of adjacent brightenings. For the first light wall, rooted within AR 12565, the average height, amplitude, and oscillation period significantly decrease from 3.5 Mm, 1.7 Mm, and 8.5 minutes to 1.6 Mm, 0.4 Mm, and 3.0 minutes, respectively. For the second light wall, rooted within AR 12597, the mean height, amplitude, and oscillation period of the light wall decrease from 2.1 Mm, 0.5 Mm, and 3.0 minutes to 1.5 Mm, 0.2 Mm, and 2.1 minutes, respectively. Particularly, a part of the second light wall even becomes invisible after the influence of a nearby brightening. These results reveal that the light walls are suppressed by nearby brightenings. Considering the complex magnetic topology in light bridges, we conjecture that the fading of light walls may be caused by a drop in the magnetic pressure, where the flux is canceled by magnetic reconnection at the site of the nearby brightening. Another hypothesis is that the wall fading is due to the suppression of driver source ( p -mode oscillation), resulting from the nearby avalanche of downward particles along reconnected brightening loops.

The control effect in a detached laminar boundary layer of an array of normal synthetic jets

Science.gov (United States)

Valenzuela Calva, Fernando; Avila Rodriguez, Ruben

2016-11-01

In this work, 3D numerical simulations of an array of three normal circular synthetic jets embedded in an attached laminar boundary layer that separates under the influence of an inclined flap are performed for flow separation control. At the beginning of the present study, three cases are used to validate the numerical simulation with data obtained from experiments. The experimental data is chosen based on the cases which presented higher repeatability and reliability. Simulations showed reasonable agreement when compared with experiments. The simulations are undertaken at three synthetic jet operating conditions, i.e. Case A: L = 2, VR = 0.32; Case B: L = 4, VR = 0.64 and Case C: L = 6, VR = 0.96. The vortical structures produced for each synthetic jet operating condition are hairpin vortices for Case A and tilted vortices for Case B and C, respectively. By examining the spatial wall shear stress variations, the effect on the boundary layer prior to separation of the middle synthetic jet is evaluated. For effective flow control, produced at a relatively low the finding from this study suggests that hairpin vortical structures are more desirable structures. Universidad Nacional Autonoma de Mexico.

Synthetic Aperture Vector Flow Imaging

DEFF Research Database (Denmark)

Villagómez Hoyos, Carlos Armando

The main objective of this project was to continue the development of a synthetic aperture vector flow estimator. This type of estimator is capable of overcoming two of the major limitations in conventional ultrasound systems: 1) the inability to scan large region of interest with high temporal......, this thesis showed that novel information can be obtained with vector velocity methods providing quantitative estimates of blood flow and insight into the complexity of the hemodynamics dynamics. This could give the clinician a new tool in assessment and treatment of a broad range of diseases....

Hydroxycinnamate Conjugates as Potential Monolignol Replacements: In vitro Lignification and Cell Wall Studies with Rosmarinic Acid

Energy Technology Data Exchange (ETDEWEB)

Yuki, Tobimatsu; Sasikumar, Elumalai; Grabber, John H.; Davidson, Christy L.; Xuejun, Pan; John, Ralph

2012-04-01

The plasticity of lignin biosynthesis should permit the inclusion of new compatible phenolic monomers, such as rosmarinic acid (RA) and analogous catechol derivatives, into cell-wall lignins that are consequently less recalcitrant to biomass processing. In vitro lignin polymerization experiments revealed that RA readily underwent peroxidase-catalyzed copolymerization with monolignols and lignin oligomers to form polymers with new benzodioxane inter-unit linkages. Incorporation of RA permitted extensive depolymerization of synthetic lignins by mild alkaline hydrolysis, presumably by cleavage of ester intra-unit linkages within RA. Copolymerization of RA with monolignols into maize cell walls by in situ peroxidases significantly enhanced alkaline lignin extractability and promoted subsequent cell wall saccharification by fungal enzymes. Incorporating RA also improved cell wall saccharification by fungal enzymes and by rumen microflora even without alkaline pretreatments, possibly by modulating lignin hydrophobicity and/or limiting cell wall cross-linking. Consequently, we anticipate that bioengineering approaches for partial monolignol substitution with RA and analogous plant hydroxycinnamates would permit more efficient utilization of plant fiber for biofuels or livestock production.

Synthetic approaches to lanthanide complexes with tetrapyrrole type ligands

International Nuclear Information System (INIS)

Pushkarev, V E; Tomilova, L G; Tomilov, Yu V

2008-01-01

Approaches to the synthesis of single-, double- and triple-decker complexes of lanthanides with phthalocyanines and their analogues known to date are considered. Examples of preparation of sandwich-type complexes based on other metals of the Periodic system are given.

Designing synthetic biology.

Science.gov (United States)

Agapakis, Christina M

2014-03-21

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

Tracking developmentally regulated post-synthetic processing of homogalacturonan and chitin using reciprocal oligosaccharide probes

DEFF Research Database (Denmark)

Mravec, Jozef; Kračun, Stjepan K.; Rydahl, Maja G.

2014-01-01

Polysaccharides are major components of extracellular matrices and are often extensively modified post-synthetically to suit local requirements and developmental programmes. However, our current understanding of the spatiotemporal dynamics and functional significance of these modifications is lim...... and animal systems. We demonstrated their potential for providing new biological insights by using them to study homogalacturonan processing during Arabidopsis thaliana root cap development and by analyzing sites of chitosan deposition in fungal cell walls and arthropod exoskeletons....

Morphologic study of three collagen materials for body wall repair.

Science.gov (United States)

Soiderer, Emily E; Lantz, Gary C; Kazacos, Evelyn A; Hodde, Jason P; Wiegand, Ryan E

2004-05-15

The search for ideal prostheses for body wall repair continues. Synthetic materials such as polypropylene mesh (PPM) are associated with healing complications. A porcine-derived collagen-based material (CBM), small intestinal submucosa (SIS), has been studied for body wall repair. Renal capsule matrix (RCM) and urinary bladder submucosa (UBS) are CBMs not previously evaluated in this application. This is the first implant study using RCM. Full-thickness muscle/fascia ventral abdominal wall defects were repaired with SIS, RCM, UBS, and PPM in rats with omentum and omentectomy. A random complete block design was used to allot implant type to each of 96 rats. Healing was evaluated at 4 and 8 weeks. Adhesion tenacity and surface area were scored. Implant site dimensions were measured at implantation and necropsy. Inflammation, vascularization, and fibrosis were histopathologically scored. Data were compared by analysis of variance (P response in contrast to the organized healing of CBM implants. CBM mean scores were lower than PPM scores for adhesion tenacity, surface area, and inflammation at each follow-up time for rats with omentums (P fibrotic response to PPM was unique and more intense compared to CBMs. These CBM implants appear morphologically acceptable and warrant continued investigation.

Propensity of a single-walled carbon nanotube-peptide to mimic a KK10 peptide in an HLA-TCR complex

Science.gov (United States)

Feng, Mei; Bell, David R.; Zhou, Ruhong

2017-12-01

The application of nanotechnology to improve disease diagnosis, treatment, monitoring, and prevention is the goal of nanomedicine. We report here a theoretical study of a functionalized single-walled carbon nanotube (CNT) mimic binding to a human leukocyte antigen-T cell receptor (HLA-TCR) immune complex as a first attempt of a potential nanomedicine for human immunodeficiency virus (HIV) vaccine development. The carbon nanotube was coated with three arginine residues to imitate the HIV type 1 immunodominant viral peptide KK10 (gag 263-272: KRWIILGLNK), named CNT-peptide hereafter. Through molecular dynamics simulations, we explore the CNT-peptide and KK10 binding to an important HLA-TCR complex. Our results suggest that the CNT-peptide and KK10 bind comparably to the HLA-TCR complex, but the CNT-peptide forms stronger interactions with the TCR. Desorption simulations highlight the innate flexibility of KK10 over the CNT-peptide, resulting in a slightly higher desorption energy required for KK10 over the CNT-peptide. Our findings indicate that the designed CNT-peptide mimic has favorable propensity to activate TCR pathways and should be further explored to understand therapeutic potential.

Pectic arabinan side chains are essential for pollen cell wall integrity during pollen development

DEFF Research Database (Denmark)

Cankar, Katarina; Kortstee, Anne; Toonen, Marcel A.J.

2014-01-01

Pectin is a complex polysaccharide and an integral part of the primary plant cell wall and middle lamella, contributing to cell wall mechanical strength and cell adhesion. To understand the structure-function relationships of pectin in the cell wall, a set of transgenic potato lines with altered...

Synthetic biology: a challenge to mechanical explanations in biology?

Science.gov (United States)

Morange, Michel

2012-01-01

In their plans to modify organisms, synthetic biologists have contrasted engineering and tinkering. By drawing this contrast between their endeavors and what has happened during the evolution of organisms by natural selection, they underline the novelty of their projects and justify their ambitions. Synthetic biologists are at odds with a long tradition that has considered organisms as "perfect machines." This tradition had already been questioned by Stephen Jay Gould in the 1970s and received a major blow with the comparison made by François Jacob between organisms and the results of "bricolage" (tinkering). These contrasts between engineering and tinkering, synthetic biology and evolution, have no raison d'être. Machines built by humans are increasingly inspired by observations made on organisms. This is not a simple reversal of the previous trend-the mechanical conception of organisms-in which the characteristics of the latter were explained by comparison with human-built machines. Relations between organisms and machines have always been complex and ambiguous.

Domain walls in single-chain magnets

Science.gov (United States)

Pianet, Vivien; Urdampilleta, Matias; Colin, Thierry; Clérac, Rodolphe; Coulon, Claude

2017-12-01

The topology and creation energy of domain walls in different magnetic chains (called Single-Chain Magnets or SCMs) are discussed. As these domain walls, that can be seen as "defects", are known to control both static and dynamic properties of these one-dimensional systems, their study and understanding are necessary first steps before a deeper discussion of the SCM properties at finite temperature. The starting point of the paper is the simple regular ferromagnetic chain for which the characteristics of the domain walls are well known. Then two cases will be discussed (i) the "mixed chains" in which isotropic and anisotropic classical spins alternate, and (ii) the so-called "canted chains" where two different easy axis directions are present. In particular, we show that "strictly narrow" domain walls no longer exist in these more complex cases, while a cascade of phase transitions is found for canted chains as the canting angle approaches 45∘. The consequence for thermodynamic properties is briefly discussed in the last part of the paper.

Enzymatic Modification of Plant Cell Wall Polysaccharides

DEFF Research Database (Denmark)

Øbro, Jens; Hayashi, Takahisa; Mikkelsen, Jørn Dalgaard

2011-01-01

Plant cell walls are intricate structures with remarkable properties, widely used in almost every aspect of our life. Cell walls consist largely of complex polysaccharides and there is often a need for chemical and biochemical processing before industrial use. There is an increasing demand...... for sustainable processes that replace chemical treatments with white biotechnology. Plants can contribute significantly to this sustainable process by producing plant or microbialenzymes in planta that are necessary for plant cell wall modification or total degradation. This will give rise to superior food...... fibres, hydrocolloids, paper,textile, animal feeds or biofuels. Classical microbial-based fermentation systems could in the future face serious competition from plant-based expression systems for enzyme production. Plant expressed enzymes can either be targeted to specific cellular compartments...

A synthetic computational environment: To control the spread of respiratory infections in a virtual university

Science.gov (United States)

Ge, Yuanzheng; Chen, Bin; liu, Liang; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2018-02-01

Individual-based computational environment provides an effective solution to study complex social events by reconstructing scenarios. Challenges remain in reconstructing the virtual scenarios and reproducing the complex evolution. In this paper, we propose a framework to reconstruct a synthetic computational environment, reproduce the epidemic outbreak, and evaluate management interventions in a virtual university. The reconstructed computational environment includes 4 fundamental components: the synthetic population, behavior algorithms, multiple social networks, and geographic campus environment. In the virtual university, influenza H1N1 transmission experiments are conducted, and gradually enhanced interventions are evaluated and compared quantitatively. The experiment results indicate that the reconstructed virtual environment provides a solution to reproduce complex emergencies and evaluate policies to be executed in the real world.

Study on the Microwave Permittivity of Single-Walled Carbon Nanotube

Science.gov (United States)

Liu, Xiaolai; Zhao, Donglin

2009-01-01

In this article, we studied the microwave permittivity of the complex of the single-walled carbon nanotube and paraffin in 2-18GHz. In the range, the dielectric loss of single-walled carbon nanotube is higher, and the real part and the imaginary part of the dielectric constant decrease with the increase of frequency, and the dielectric constant…

Targeted and non-targeted effects in cell wall polysaccharides from transgenetically modified potato tubers

NARCIS (Netherlands)

Huang, J.H.

2016-01-01

The plant cell wall is a chemically complex network composed mainly of polysaccharides. Cell wall polysaccharides surround and protect plant cells and are responsible for the stability and rigidity of plant tissue. Pectin is a major component of primary cell wall and the middle lamella of plants.

Materials for heat flux components of the first wall in fusion reactors

International Nuclear Information System (INIS)

Hoven, H.; Koizlik, K.; Linke, J.; Nickel, H.; Wallura, E.

1985-08-01

Materials of the First Wall in near-fusion plasma machines are subjected to a complex load system resulting from the plasma-wall interaction. The materials for their part also influence the plasma. Suitable materials must be available in order to ensure that the wall components achieve a sufficiently long dwell time and that their effects on the plasma remain small and controllable. The present report discusses relations between the plasma-wall interaction, the reactions of the materials and testing and examination methods for specific problems in developing and selecting suitable materials for highly stressed components on the First Wall of fusion reactors. (orig.)

In vitro storage of synthetic seeds: Effect of different storage ...

African Journals Online (AJOL)

GREGORY

2010-08-30

Aug 30, 2010 ... comparative regrowth and conversion capacity of synthetic seeds. Cold stored .... solution for 35 min. After complexation, the hardened alginate ... difference (LSD) test at 5% probability level (Steel et al., 1997). RESULTS AND ..... dure already proposed by Roussos and Pontikis (2002) that simplified the ...

Crust growth and gas retention in synthetic Hanford waste

International Nuclear Information System (INIS)

Bryan, S.A.; Pederson, L.R.; Scheele, R.D.

1992-03-01

The focus of the work described here is to examine the principal contributing factors leading to slurry growth and gas retention within waste from a particular high-level waste tanks on the Hanford Site. Laboratory studies of aged synthetic waste have shown that the waste retains gases in the form of bubble attachment to solid particles. This attachment phenomenon is related to the presence of organic constituents (HEDTA, EDTA, and citrate) added to the waste matrix. The mechanism for bubble attachment is related to the hydrophobic surface produced by the organic complexant. The formation of a stable gas bubble/solid interaction is believed to be responsible for crust flotation and gas retention in the synthetic waste used here

Antibiotics from bacillus subtilis AECL69 8. isolation and purification of a complex of antibacterial antibiotics x

International Nuclear Information System (INIS)

Ahmad, M.S.; Malik, M.A.; Shaukat, G.A.

1996-01-01

A bacterial strain bacillus subtilis AECL69 produces two anti bacterial antibiotics in a specified complex or synthetic medium. One of the antibiotics is characteristically active against Xanthomonas citri. Procedures have been described to isolate and purify a complex of xanthmonas antibiotics from the fermented complex broths, and from the fermented synthetic medium as well. Paper chromatography coupled with bioautography has shown that the complex of xanthomonas antibiotics has at least three components. The three components were indicated irrespective of the fact whether it was isolated from the fermented complex or synthetic broth. (author)

INTERACTION OF ALBUMIN AND IMMUNOGLOBULIN G WITH SYNTHETIC HYDROXYAPATITE

Directory of Open Access Journals (Sweden)

E. Pylypchuk

2012-12-01

Full Text Available It was shown by X-ray phase analysis, IR spectra analysis and MALDI-ToF mass spectrometry methods that interaction of synthetic hydroxyapatite with a solution of immunoglobulin G leads to its partial dissolution due to leaching from the surface of calcium triphosphate which, in our opinion, forms complexes with immunoglobulin G.

Biochemical Characterisation of Phage Pseudomurein Endoisopeptidases PeiW and PeiP Using Synthetic Peptides

OpenAIRE

Schofield, Linley R.; Beattie, Amy K.; Tootill, Catherine M.; Dey, Debjit; Ronimus, Ron S.

2015-01-01

Pseudomurein endoisopeptidases cause lysis of the cell walls of methanogens by cleaving the isopeptide bond Ala-ε-Lys in the peptide chain of pseudomurein. PeiW and PeiP are two thermostable pseudomurein endoisopeptidases encoded by phage ΨM100 of Methanothermobacter wolfei and phages ΨM1 and ΨM2 of Methanothermobacter marburgensis, respectively. A continuous assay using synthetic peptide substrates was developed and used in the biochemical characterisation of recombinant PeiW and PeiP. The a...

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Science.gov (United States)

Huynh, Linh; Kececioglu, John; Köppe, Matthias; Tagkopoulos, Ilias

2012-01-01

Automatic design of synthetic gene circuits poses a significant challenge to synthetic biology, primarily due to the complexity of biological systems, and the lack of rigorous optimization methods that can cope with the combinatorial explosion as the number of biological parts increases. Current optimization methods for synthetic gene design rely on heuristic algorithms that are usually not deterministic, deliver sub-optimal solutions, and provide no guaranties on convergence or error bounds. Here, we introduce an optimization framework for the problem of part selection in synthetic gene circuits that is based on mixed integer non-linear programming (MINLP), which is a deterministic method that finds the globally optimal solution and guarantees convergence in finite time. Given a synthetic gene circuit, a library of characterized parts, and user-defined constraints, our method can find the optimal selection of parts that satisfy the constraints and best approximates the objective function given by the user. We evaluated the proposed method in the design of three synthetic circuits (a toggle switch, a transcriptional cascade, and a band detector), with both experimentally constructed and synthetic promoter libraries. Scalability and robustness analysis shows that the proposed framework scales well with the library size and the solution space. The work described here is a step towards a unifying, realistic framework for the automated design of biological circuits. PMID:22536398

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

OpenAIRE

Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

2015-01-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

Characterization of Thermal Stability of Synthetic and Semi-Synthetic Engine Oils

Directory of Open Access Journals (Sweden)

Anand Kumar Tripathi

2015-03-01

Full Text Available Engine oils undergo oxidative degradation and wears out during service. Hence it is important to characterize ageing of engine oils at different simulated conditions to evaluate the performance of existing oils and also design new formulations. This work focuses on characterizing the thermo-oxidative degradation of synthetic and semi-synthetic engine oils aged at 120, 149 and 200 °C. Apparent activation energy of decomposition of aged oils evaluated using the isoconversional Kissinger-Akahira-Sunose technique was used as a thermal stability marker. The temporal variation of stability at different ageing temperatures was corroborated with kinematic viscosity, oxidation, sulfation and nitration indices, total base number, antiwear additive content and molecular structure of the organic species present in the oils. At the lowest temperature employed, synthetic oil underwent higher rate of oxidation, while semi-synthetic oil was stable for longer time periods. At higher temperatures, the initial rate of change of average apparent activation energy of synthetic oil correlated well with a similar variation in oxidation number. A mixture of long chain linear, branched, and cyclic hydrocarbons were observed when semi-synthetic oil was degraded at higher temperatures.

Synthetic multielement standards used for instrumental neutron activation analysis as rock imitations

International Nuclear Information System (INIS)

Leypunskaya, D.I.; Drynkin, V.I.; Belenky, B.V.; Kolomijtsev, M.A.; Dundera, V.Yu.; Pachulia, N.V.

1975-01-01

Complex (multielemental) standards representing microelement composition of standard rocks such as trap ST-1 (USSR), gabbrodiorite SGD-1 (USSR), albitized granite SG-1 (USSR), basalt BCR-1 (USA) and granodiorite GSP-1 (USA) have been synthesized. It has been shown that the concentration of each microelement in the synthetic standards can be given with a high precision. Comparative investigation has been carried out of the synthetic imitations and the above natural standard rocks. It has been found that the result of the instrumental neutron activation analysis using the synthetic standards is as good as in the case when natural standard rocks are used. The results obtained have been also used for substantiation of the versatility of the method used for standard preparation, i.e. a generalization has been made of a possibility of using this method for the preparation of synthetic standards representing the microelement composition of any natural rocks with various compositions and concentrations of microelements. (T.G.)

antimicrobial properties of some natural and synthetic fabrics modified by radiation treatments

International Nuclear Information System (INIS)

Mohamed, R.M.A.

2008-01-01

natural and synthetic fabrics have been treated with different antimicrobial metal complexes under the effect of gamma radiation . in this regard, cotton, cotton/PET blend and PET were grafted with acrylic acid by gamma radiation and this grafted fabrics were complexed with Cu(ll),Ni(ll)and Co(ll) metal ions . the antimicrobial properties were evaluated by the measurement of tensile strength of fabrics after burring in a soil for one and two weeks as well as the effect of this treatment on the growth of certain bacteria and fungi incubated on a culture for 48 hours. the results showed that the highest protection to cotton, cotton/PET blend and PET fabrics by using Cu(ll) ion in the complexation process, where the order of protection by metals is Cu(ll) > Co(ll)> Ni(ll), moreover, the more grafted fabrics the more complexed fabrics with metal ions and is higher protection against microorganisms . the treatment with the metal ions has nearly no effect on the chemical and physical properties of the natural or the synthetic fabrics as indicated from the analysis by TGA, sem, ion exchange testing and wettability testing.

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

Science.gov (United States)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

Secondary Emission From Synthetic Opal Infiltrated by Colloidal Gold and Glycine

International Nuclear Information System (INIS)

Dovbeshko, G.I.; Fesenko, O.M.; Boyko, V.V.; Romanyuk, V.R.; Gorelik, V.S.; Moiseyenko, V.N.; Sobolev, V.B.; Shvalagin, V.V.

2012-01-01

A comparison of the secondary emission (photoluminescence) and Bragg reflection spectra of photonic crystals (PC), namely, synthetic opals, opals infiltrated by colloidal gold, glycine, and a complex of colloidal gold with glycine is performed. The infiltration of colloidal gold and a complex of colloidal gold with glycine into the pores of PC causes a short-wavelength shift (about 5-15 nm) of the Bragg reflection and increases the intensity of this band by 1.5-3 times. In photoluminescence, the infiltration of PC by colloidal gold and colloidal gold with glycine suppresses the PC emission band near 375-450 nm and enhances the shoulder of the stop-zone band of PC in the region of 470-510 nm. The shape of the observed PC emission band connected with defects in synthetic opal is determined by the type of infiltrates and the excitation wavelength. Possible mechanisms of the effects are discussed.

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

Science.gov (United States)

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.

State stiffness parameters of the vascular wall in hypertensive patients complex therapy cytoprotector and sartans

Directory of Open Access Journals (Sweden)

V. P. Mikhin

2015-01-01

Full Text Available A randomized study of the state of stiffness parameters arteries wall (CAVI — cardio-ankle vascular index, AI (augmentation index PEP (duration of the voltage of the left ventricle using «VaSera-1000» («Fukuda Denshi», Japan in primary hypertension patients (80 not treated with systemic antihypertensive therapy. The effect of long-term (3 months was be marketed. Losartan combined with Mexicor 300mg/day or mildronate 1000 mg/day for the specified parameters. It sets the initial reduction the properties of the arterial wall in patients with hypertension, in contrast to healthy individuals. Mexicor or mildronat accompanied by improvement east-cal properties of the arterial wall, reducing CAVI and AI in 3 months on 9.4% and 8.9%, 14.9% and 15.4%, respectively. In the control group-term change CAVI and AI no. Mexicor led to a more pronounced increase in PEP, than mildronate, respectively, on 23.7% and 18.9%. Losartan monotherapy results in a less pronounced decrease in the stiffness of the vessel wall.

Mesoporous organosilica nanotubes containing a chelating ligand in their walls

Energy Technology Data Exchange (ETDEWEB)

Liu, Xiao; Goto, Yasutomo; Maegawa, Yoshifumi; Inagaki, Shinji, E-mail: inagaki@mosk.tytlabs.co.jp [Toyota Central R and D Laboratories, Inc., Nagakute, Aichi 480-1192 (Japan); Japan Science and Technology Agency (JST)/ACT-C, Nagakute, Aichi, 480-1192 (Japan); Ohsuna, Tetsu [Toyota Central R and D Laboratories, Inc., Nagakute, Aichi 480-1192 (Japan)

2014-11-01

We report the synthesis of organosilica nanotubes containing 2,2′-bipyridine chelating ligands within their walls, employing a single-micelle-templating method. These nanotubes have an average pore diameter of 7.8 nm and lengths of several hundred nanometers. UV-vis absorption spectra and scanning transmission electron microscopy observations of immobilized nanotubes with an iridium complex on the bipyridine ligands showed that the 2,2′-bipyridine groups were homogeneously distributed in the benzene-silica walls. The iridium complex, thus, immobilized on the nanotubes exhibited efficient catalytic activity for water oxidation using Ce{sup 4+}, due to the ready access of reactants to the active sites in the nanotubes.

Synthetic Multiple-Imputation Procedure for Multistage Complex Samples

Directory of Open Access Journals (Sweden)

Zhou Hanzhi

2016-03-01

Full Text Available Multiple imputation (MI is commonly used when item-level missing data are present. However, MI requires that survey design information be built into the imputation models. For multistage stratified clustered designs, this requires dummy variables to represent strata as well as primary sampling units (PSUs nested within each stratum in the imputation model. Such a modeling strategy is not only operationally burdensome but also inferentially inefficient when there are many strata in the sample design. Complexity only increases when sampling weights need to be modeled. This article develops a generalpurpose analytic strategy for population inference from complex sample designs with item-level missingness. In a simulation study, the proposed procedures demonstrate efficient estimation and good coverage properties. We also consider an application to accommodate missing body mass index (BMI data in the analysis of BMI percentiles using National Health and Nutrition Examination Survey (NHANES III data. We argue that the proposed methods offer an easy-to-implement solution to problems that are not well-handled by current MI techniques. Note that, while the proposed method borrows from the MI framework to develop its inferential methods, it is not designed as an alternative strategy to release multiply imputed datasets for complex sample design data, but rather as an analytic strategy in and of itself.

Root Growth and Water distribution in living walls

DEFF Research Database (Denmark)

Jørgensen, Lars

of functional living walls and this thesis is a first step of understanding the essential but hidden part inside the growing medium, i.e. the roots. Ensuring successful performance of the plants in a living wall is complex and the choice of growing medium, plant species and planting position are important....... for root growth. This thesis investigates the correlations between the growing media and root and shoots growth, and studies root growth patterns of different plant species and effects of planting position and root interactions of plants growing in living walls. There are a number of challenges with living...... walls; the vertical orientation of the growing medium, plants are growing vertically above or below each other in a limited rooting volume; there is an increased exposure to weather and the plants can react differently to water conditions and competition from other plants. Plant growth is the core...

3d/4f Metal Complexes of Phenolic Oximes New Binding Sites on Anderson Polyoxometalates Metal Complexes of the New THAME Ligand

DEFF Research Database (Denmark)

Sethi, Waqas

to be coordinatedto SMMs as well as onto other transition metal complexes, via different synthetic strategies. These synthetic routes did not result in the crystallisation of any new compounds. A new hexadentate ligand tris(((2-hydroxyethyl)-amino)methyl)ethane (THAME) was synthesised and characterised. THAME...

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

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

Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project.

Science.gov (United States)

Sliva, Anna; Yang, Huanming; Boeke, Jef D; Mathews, Debra J H

2015-08-01

First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) PROJECT is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with this field of research and operate under a common set of principles. In this commentary, we survey the current ethics and regulatory landscape of synthetic biology and present the Sc2.0 Statement of Ethics and Governance to which all members of the project adhere. This statement focuses on four aspects of the Sc2.0 PROJECT: societal benefit, intellectual property, safety, and self-governance. We propose that such project-level agreements are an important, valuable, and flexible model of self-regulation for similar global, large-scale synthetic biology projects in order to maximize the benefits and minimize potential harms. Copyright © 2015 by the Genetics Society of America.

Connective tissue alteration in abdominal wall hernia

DEFF Research Database (Denmark)

Henriksen, N A; Yadete, D H; Sørensen, Lars Tue

2011-01-01

The aetiology and pathogenesis of abdominal wall hernia formation is complex. Optimal treatment of hernias depends on a full understanding of the pathophysiological mechanisms involved in their formation. The aim of this study was to review the literature on specific collagen alterations in abdom...

Synthetic Hydroxyapatite as a Biomimetic Oral Care Agent.

Science.gov (United States)

Enax, Joachim; Epple, Matthias

Human tooth enamel consists mostly of minerals, primarily hydroxyapatite, Ca10(PO4)6(OH)2, and thus synthetic hydroxyapatite can be used as a biomimetic oral care agent. This review describes the synthesis and characterization of hydroxyapatite from a chemist's perspective and provides an overview of its current use in oral care, with a focus on dentin hypersensitivity, caries, biofilm management, erosion, and enamel lesions. Reviews and original research papers published in English and German were included. The efficiency of synthetic hydroxyapatite in occluding open dentin tubules, resulting in a protection for sensitive teeth, has been well documented in a number of clinical studies. The first corresponding studies on caries, biofilm management and erosion have provided evidence for a positive effect of hydroxyapatite either as a main or synergistic agent in oral care products. However, more in situ and in vivo studies are needed due to the complexity of the oral milieu and to further clarify existing results. Due to its biocompatibility and similarity to biologically formed hydroxyapatite in natural tooth enamel, synthetic hydroxyapatite is a promising biomimetic oral care ingredient that may extend the scope of preventive dentistry.

Synthetic Botany.

Science.gov (United States)

Boehm, Christian R; Pollak, Bernardo; Purswani, Nuri; Patron, Nicola; Haseloff, Jim

2017-07-05

Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

Chest-wall reconstruction in case of infection of the operative site: is there any interest in titanium rib osteosynthesis?

Science.gov (United States)

Berthet, Jean-Philippe; Solovei, Laurence; Tiffet, Olivier; Gomez-Caro, Abel; Bommart, Sébastien; Canaud, Ludovic; Alric, Pierre; Marty-Ané, Charles-Henri

2013-11-01

To describe the management of thoracic reconstructions in the presence of primary chest-wall infection (PCWI) or secondary deep chest-wall infection (SCWI), focussing on local tolerance of a titanium rib osteosynthesis system. PCWI included infected chest wall tumours (CWT), infected T3 non-small-cell lung carcinoma (NSCLC) and open flail chest. SCWI was defined by deep infection of previous thoracic-wall reconstructions. Infection was identified by preoperative bacterial analysis of the tumour or surgical site. In PCWI, a one-step procedure combined extensive resection of infected tissues and rigid reconstruction of the defect; skeletal rigidity was achieved using titanium implants. In SCWI, we removed all synthetic material except titanium implants. In both groups, the surgical field was thoroughly cleaned and implants were wrapped or covered by flaps. From January 2005 to December 2011, 11 patients (54 ± 10.2 years) with either PCWI (3 CWT, 3 T3 NSCLC, 1 open flail chest) or SCWI (3 CWT, 1 funnel chest) were treated. Infection was polymicrobial in all but 1 case. Bacteria observed in PCWI patients were multidrug resistant. In PCWI, we resected 4.2 ± 0.6 ribs en bloc with the lung (n = 5), the skin and the pectoralis major and then used mesh and 2.1 ± 1.2 titanium implants for reconstruction (n = 6). The mean defect was 1154.4 ± 318 cm(3). Surgical SCWI management removed polytetrafluoroethylene-mesh and preserved the titanium implants. A Vicryl mesh (n = 3) and greater omentum flap (n = 3) were added. One of the 2 postoperative deaths in the PCWI group was related to infection recurrence. No other patient had infection at the 6-month follow-up with leucocyte-labelled scintigraphy. Titanium rib osteosynthesis is reliable in two complex and life-threatening situations: PCWIs and SCWIs. In combination with a flap, this allows rapid, reliable, rigid reconstruction of infected full-thickness chest-wall defects in a single-step procedure.

Beyond Cost-Benefit Analysis in the Governance of Synthetic Biology.

Science.gov (United States)

Wallach, Wendell; Saner, Marc; Marchant, Gary

2018-01-01

For many innovations, oversight fits nicely within existing governance mechanisms; nevertheless, others pose unique public health, environmental, and ethical challenges. Synthetic artemisinin, for example, has many precursors in laboratory-developed drugs that emulate natural forms of the same drug. The policy challenges posed by synthetic artemisinin do not differ significantly in kind from other laboratory-formulated drugs. Synthetic biofuels and gene drives, however, fit less clearly into existing governance structures. How many of the new categories of products require new forms of regulatory oversight, or at least extensive forms of testing, remains unclear. Any effort to improve the governance of synthetic biology should start with a rich understanding of the different possible science-policy interfaces that could help to inform governance. CBA falls into a subset of the overall range of possibilities, and which interface is appropriate may turn out to depend on context, on the demands of the decision at hand. In what follows, we lay out a typology of interfaces. After that, we turn to the question of how to draw upon the range of possible interfaces and effectively address the factual and moral complexities of emerging technologies. We propose a governance model built around structures that we call "governance coordinating committees." GCCs are intended to be mechanisms for accommodating the complexities of innovations that have far-ranging societal impacts. The production of biofuels, for example, could contaminate water supplies and have a destructive environmental impact if not managed correctly. The introduction of a gene drive could have economic and environmental impacts that are not restricted to one nation. Forging appropriate means for determining and evaluating those societal impacts, to the best of a corporation's, industry's, or government's ability, is central to responsible research and innovation. Public policy must be shaped in a manner that

Cell Wall Metabolism in Response to Abiotic Stress

Science.gov (United States)

Gall, Hyacinthe Le; Philippe, Florian; Domon, Jean-Marc; Gillet, Françoise; Pelloux, Jérôme; Rayon, Catherine

2015-01-01

This review focuses on the responses of the plant cell wall to several abiotic stresses including drought, flooding, heat, cold, salt, heavy metals, light, and air pollutants. The effects of stress on cell wall metabolism are discussed at the physiological (morphogenic), transcriptomic, proteomic and biochemical levels. The analysis of a large set of data shows that the plant response is highly complex. The overall effects of most abiotic stress are often dependent on the plant species, the genotype, the age of the plant, the timing of the stress application, and the intensity of this stress. This shows the difficulty of identifying a common pattern of stress response in cell wall architecture that could enable adaptation and/or resistance to abiotic stress. However, in most cases, two main mechanisms can be highlighted: (i) an increased level in xyloglucan endotransglucosylase/hydrolase (XTH) and expansin proteins, associated with an increase in the degree of rhamnogalacturonan I branching that maintains cell wall plasticity and (ii) an increased cell wall thickening by reinforcement of the secondary wall with hemicellulose and lignin deposition. Taken together, these results show the need to undertake large-scale analyses, using multidisciplinary approaches, to unravel the consequences of stress on the cell wall. This will help identify the key components that could be targeted to improve biomass production under stress conditions. PMID:27135320

Parameter Optimization of Multi-Element Synthetic Aperture Imaging Systems

Directory of Open Access Journals (Sweden)

Vera Behar

2007-03-01

Full Text Available In conventional ultrasound imaging systems with phased arrays, the further improvement of lateral resolution requires enlarging of the number of array elements that in turn increases both, the complexity and the cost, of imaging systems. Multi-element synthetic aperture focusing (MSAF systems are a very good alternative to conventional systems with phased arrays. The benefit of the synthetic aperture is in reduction of the system complexity, cost and acquisition time. In a MSAF system considered in the paper, a group of elements transmit and receive signals simultaneously, and the transmit beam is defocused to emulate a single element response. The echo received at each element of a receive sub-aperture is recorded in the computer memory. The process of transmission/reception is repeated for all positions of a transmit sub-aperture. All the data recordings associated with each corresponding pair "transmit-receive sub-aperture" are then focused synthetically producing a low-resolution image. The final high-resolution image is formed by summing of the all low-resolution images associated with transmit/receive sub-apertures. A problem of parameter optimization of a MSAF system is considered in this paper. The quality of imaging (lateral resolution and contrast is expressed in terms of the beam characteristics - beam width and side lobe level. The comparison between the MSAF system described in the paper and an equivalent conventional phased array system shows that the MSAF system acquires images of equivalent quality much faster using only a small part of the power per image.

Synthetic biology approaches to fluorinated polyketides.

Science.gov (United States)

Thuronyi, Benjamin W; Chang, Michelle C Y

2015-03-17

The catalytic diversity of living systems offers a broad range of opportunities for developing new methods to produce small molecule targets such as fuels, materials, and pharmaceuticals. In addition to providing cost-effective and renewable methods for large-scale commercial processes, the exploration of the unusual chemical phenotypes found in living organisms can also enable the expansion of chemical space for discovery of novel function by combining orthogonal attributes from both synthetic and biological chemistry. In this context, we have focused on the development of new fluorine chemistry using synthetic biology approaches. While fluorine has become an important feature in compounds of synthetic origin, the scope of biological fluorine chemistry in living systems is limited, with fewer than 20 organofluorine natural products identified to date. In order to expand the diversity of biosynthetically accessible organofluorines, we have begun to develop methods for the site-selective introduction of fluorine into complex natural products by engineering biosynthetic machinery to incorporate fluorinated building blocks. To gain insight into how both enzyme active sites and metabolic pathways can be evolved to manage and select for fluorinated compounds, we have studied one of the only characterized natural hosts for organofluorine biosynthesis, the soil microbe Streptomyces cattleya. This information provides a template for designing engineered organofluorine enzymes, pathways, and hosts and has allowed us to initiate construction of enzymatic and cellular pathways for the production of fluorinated polyketides.

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

Directory of Open Access Journals (Sweden)

Lihong Jiang

2018-06-01

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

A systematic design method for robust synthetic biology to satisfy design specifications.

Science.gov (United States)

Chen, Bor-Sen; Wu, Chih-Hung

2009-06-30

Synthetic biology is foreseen to have important applications in biotechnology and medicine, and is expected to contribute significantly to a better understanding of the functioning of complex biological systems. However, the development of synthetic gene networks is still difficult and most newly created gene networks are non-functioning due to intrinsic parameter uncertainties, external disturbances and functional variations of intra- and extra-cellular environments. The design method for a robust synthetic gene network that works properly in a host cell under these intrinsic parameter uncertainties and external disturbances is the most important topic in synthetic biology. In this study, we propose a stochastic model that includes parameter fluctuations and external disturbances to mimic the dynamic behaviors of a synthetic gene network in the host cell. Then, based on this stochastic model, four design specifications are introduced to guarantee that a synthetic gene network can achieve its desired steady state behavior in spite of parameter fluctuations, external disturbances and functional variations in the host cell. We propose a systematic method to select a set of appropriate design parameters for a synthetic gene network that will satisfy these design specifications so that the intrinsic parameter fluctuations can be tolerated, the external disturbances can be efficiently filtered, and most importantly, the desired steady states can be achieved. Thus the synthetic gene network can work properly in a host cell under intrinsic parameter uncertainties, external disturbances and functional variations. Finally, a design procedure for the robust synthetic gene network is developed and a design example is given in silico to confirm the performance of the proposed method. Based on four design specifications, a systematic design procedure is developed for designers to engineer a robust synthetic biology network that can achieve its desired steady state behavior

Ruthenium, osmium and rhodium complexes of polypyridyl ligands ...

Indian Academy of Sciences (India)

Unknown

Discipline of Silicates and Catalysis, Central Salt and Marine Chemicals ... However, synthetic methods have also been developed to prepare complexes with ... 3.2 Synthesis and characterisation of ruthenium(II) and osmium(II) complexes18, ...

Informing biological design by integration of systems and synthetic biology.

Science.gov (United States)

Smolke, Christina D; Silver, Pamela A

2011-03-18

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

Structural analysis of cell wall polysaccharides using PACE

Energy Technology Data Exchange (ETDEWEB)

Mortimer, Jennifer C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute

2017-01-01

The plant cell wall is composed of many complex polysaccharides. The composition and structure of the polysaccharides affect various cell properties including cell shape, cell function and cell adhesion. Many techniques to characterize polysaccharide structure are complicated, requiring expensive equipment and specialized operators e.g. NMR, MALDI-MS. PACE (Polysaccharide Analysis using Carbohydrate gel Electrophoresis) uses a simple, rapid technique to analyze polysaccharide quantity and structure (Goubet et al. 2002). Whilst the method here describes xylan analysis, it can be applied (by use of the appropriate glycosyl hydrolase) to any cell wall polysaccharide.

Mesoporous organosilica nanotubes containing a chelating ligand in their walls

Directory of Open Access Journals (Sweden)

Xiao Liu

2014-11-01

Full Text Available We report the synthesis of organosilica nanotubes containing 2,2′-bipyridine chelating ligands within their walls, employing a single-micelle-templating method. These nanotubes have an average pore diameter of 7.8 nm and lengths of several hundred nanometers. UV-vis absorption spectra and scanning transmission electron microscopy observations of immobilized nanotubes with an iridium complex on the bipyridine ligands showed that the 2,2′-bipyridine groups were homogeneously distributed in the benzene-silica walls. The iridium complex, thus, immobilized on the nanotubes exhibited efficient catalytic activity for water oxidation using Ce4+, due to the ready access of reactants to the active sites in the nanotubes.

Association Mapping of Cell Wall Synthesis Regulatory Genes and Cell Wall Quality in Switchgrass

Energy Technology Data Exchange (ETDEWEB)

Bartley, Laura [Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology; Wu, Y. [Oklahoma State Univ., Stillwater, OK (United States); Zhu, L. [Oklahoma State Univ., Stillwater, OK (United States); Brummer, E. C. [Noble Foundation, Ardmore, OK (United States); Saha, M. [Noble Foundation, Ardmore, OK (United States)

2016-05-31

transcription factors from the rice gene network. Eight of fifteen (53%) of these have not previously been examined for this function. Some of these may represent novel grass-diverged cell wall regulators, while others are likely to have this function across angiosperms. A parallel effort of this project to expand knowledge of enzymes that have evolved to function in grass cell wall synthesis, revealed that a grass-diverged enzyme in rice, OsAT₅, ferulates monolignols that are naturally incorporated into grass cell walls. This finding opens potential natural selection avenues for improving biomass composition for downstream processing by weak base pretreatment. Thus, this project has significantly expanded knowledge of cell wall synthesis and regulation in rice, information that can be used in reverse genetics and synthetic biology approaches to re-engineer cell walls for improved production of biofuel and high-value products. To lay the foundation for translating these results directly for switchgrass improvement, the project employed a comparative phylogenetic analysis of the major group of cell wall transcription factors that have been found to function in cell wall regulation, the R₂R₃ MYBs. This analysis concluded that known cell wall regulators are largely conserved across switchgrass, rice, maize, poplar, and Arabidopsis. This interpretation is also largely consistent with the gene network analysis described above, though both approaches provide evidence that some co-orthologs of Arabidopsis regulators have diminished or increased in importance based on gene expression patterns. Also, several clades containing dicot cell wall regulators have expanded, consistent with the evolution of new cell wall regulators. This latter result is supported by functional analysis of the R₂R₃ MYB protein SWAM₁ in a collaboration between this project and the DOE-funded group of Dr. S. Hazen at the University of

Synthetic environments

Science.gov (United States)

Lukes, George E.; Cain, Joel M.

1996-02-01

The Advanced Distributed Simulation (ADS) Synthetic Environments Program seeks to create robust virtual worlds from operational terrain and environmental data sources of sufficient fidelity and currency to interact with the real world. While some applications can be met by direct exploitation of standard digital terrain data, more demanding applications -- particularly those support operations 'close to the ground' -- are well-served by emerging capabilities for 'value-adding' by the user working with controlled imagery. For users to rigorously refine and exploit controlled imagery within functionally different workstations they must have a shared framework to allow interoperability within and between these environments in terms of passing image and object coordinates and other information using a variety of validated sensor models. The Synthetic Environments Program is now being expanded to address rapid construction of virtual worlds with research initiatives in digital mapping, softcopy workstations, and cartographic image understanding. The Synthetic Environments Program is also participating in a joint initiative for a sensor model applications programer's interface (API) to ensure that a common controlled imagery exploitation framework is available to all researchers, developers and users. This presentation provides an introduction to ADS and the associated requirements for synthetic environments to support synthetic theaters of war. It provides a technical rationale for exploring applications of image understanding technology to automated cartography in support of ADS and related programs benefitting from automated analysis of mapping, earth resources and reconnaissance imagery. And it provides an overview and status of the joint initiative for a sensor model API.

Synthetic biology devices and circuits for RNA-based 'smart vaccines': a propositional review.

Science.gov (United States)

Andries, Oliwia; Kitada, Tasuku; Bodner, Katie; Sanders, Niek N; Weiss, Ron

2015-02-01

Nucleic acid vaccines have been gaining attention as an alternative to the standard attenuated pathogen or protein based vaccine. However, an unrealized advantage of using such DNA or RNA based vaccination modalities is the ability to program within these nucleic acids regulatory devices that would provide an immunologist with the power to control the production of antigens and adjuvants in a desirable manner by administering small molecule drugs as chemical triggers. Advances in synthetic biology have resulted in the creation of highly predictable and modular genetic parts and devices that can be composed into synthetic gene circuits with complex behaviors. With the recent advent of modified RNA gene delivery methods and developments in the RNA replicon platform, we foresee a future in which mammalian synthetic biologists will create genetic circuits encoded exclusively on RNA. Here, we review the current repertoire of devices used in RNA synthetic biology and propose how programmable 'smart vaccines' will revolutionize the field of RNA vaccination.

Hybrid Synthetic Receptors on MOSFET Devices for Detection of Prostate Specific Antigen in Human Plasma.

Science.gov (United States)

Tamboli, Vibha K; Bhalla, Nikhil; Jolly, Pawan; Bowen, Chris R; Taylor, John T; Bowen, Jenna L; Allender, Chris J; Estrela, Pedro

2016-12-06

The study reports the use of extended gate field-effect transistors (FET) for the label-free and sensitive detection of prostate cancer (PCa) biomarkers in human plasma. The approach integrates for the first time hybrid synthetic receptors comprising of highly selective aptamer-lined pockets (apta-MIP) with FETs for sensitive detection of prostate specific antigen (PSA) at clinically relevant concentrations. The hybrid synthetic receptors were constructed by immobilizing an aptamer-PSA complex on gold and subjecting it to 13 cycles of dopamine electropolymerization. The polymerization resulted in the creation of highly selective polymeric cavities that retained the ability to recognize PSA post removal of the protein. The hybrid synthetic receptors were subsequently used in an extended gate FET setup for electrochemical detection of PSA. The sensor was reported to have a limit of detection of 0.1 pg/mL with a linear detection range from 0.1 pg/mL to 1 ng/mL PSA. Detection of 1-10 pg/mL PSA was also achieved in diluted human plasma. The present apta-MIP sensor developed in conjunction with FET devices demonstrates the potential for clinical application of synthetic hybrid receptors for the detection of clinically relevant biomarkers in complex samples.

Mechanochemical Polarization of Contiguous Cell Walls Shapes Plant Pavement Cells.

Science.gov (United States)

Majda, Mateusz; Grones, Peter; Sintorn, Ida-Maria; Vain, Thomas; Milani, Pascale; Krupinski, Pawel; Zagórska-Marek, Beata; Viotti, Corrado; Jönsson, Henrik; Mellerowicz, Ewa J; Hamant, Olivier; Robert, Stéphanie

2017-11-06

The epidermis of aerial plant organs is thought to be limiting for growth, because it acts as a continuous load-bearing layer, resisting tension. Leaf epidermis contains jigsaw puzzle piece-shaped pavement cells whose shape has been proposed to be a result of subcellular variations in expansion rate that induce local buckling events. Paradoxically, such local compressive buckling should not occur given the tensile stresses across the epidermis. Using computational modeling, we show that the simplest scenario to explain pavement cell shapes within an epidermis under tension must involve mechanical wall heterogeneities across and along the anticlinal pavement cell walls between adjacent cells. Combining genetics, atomic force microscopy, and immunolabeling, we demonstrate that contiguous cell walls indeed exhibit hybrid mechanochemical properties. Such biochemical wall heterogeneities precede wall bending. Altogether, this provides a possible mechanism for the generation of complex plant cell shapes. Copyright © 2017 Elsevier Inc. All rights reserved.

The adventitia: essential regulator of vascular wall structure and function.

Science.gov (United States)

Stenmark, Kurt R; Yeager, Michael E; El Kasmi, Karim C; Nozik-Grayck, Eva; Gerasimovskaya, Evgenia V; Li, Min; Riddle, Suzette R; Frid, Maria G

2013-01-01

The vascular adventitia acts as a biological processing center for the retrieval, integration, storage, and release of key regulators of vessel wall function. It is the most complex compartment of the vessel wall and is composed of a variety of cells, including fibroblasts, immunomodulatory cells (dendritic cells and macrophages), progenitor cells, vasa vasorum endothelial cells and pericytes, and adrenergic nerves. In response to vascular stress or injury, resident adventitial cells are often the first to be activated and reprogrammed to influence the tone and structure of the vessel wall; to initiate and perpetuate chronic vascular inflammation; and to stimulate expansion of the vasa vasorum, which can act as a conduit for continued inflammatory and progenitor cell delivery to the vessel wall. This review presents the current evidence demonstrating that the adventitia acts as a key regulator of vascular wall function and structure from the outside in.

The population genetics of X-autosome synthetic lethals and steriles.

Science.gov (United States)

Lachance, Joseph; Johnson, Norman A; True, John R

2011-11-01

Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.

YSAR: a compact low-cost synthetic aperture radar

Science.gov (United States)

Thompson, Douglas G.; Arnold, David V.; Long, David G.; Miner, Gayle F.; Karlinsey, Thomas W.; Robertson, Adam E.

1997-09-01

The Brigham Young University Synthetic Aperture Radar (YSAR) is a compact, inexpensive SAR system which can be flown on a small aircraft. The system has exhibited a resolution of approximately 0.8 m by 0.8 m in test flights in calm conditions. YSAR has been used to collect data over archeological sites in Israel. Using a relatively low frequency (2.1 GHz), we hope to be able to identify walls or other archeological features to assist in excavation. A large data set of radar and photographic data have been collected over sites at Tel Safi, Qumran, Tel Micnah, and the Zippori National Forest in Israel. We show sample images from the archeological data. We are currently working on improved autofocus algorithms for this data and are developing a small, low-cost interferometric SAR system (YINSAR) for operation from a small aircraft.

Post-synthetic modification of mesoporous zinc-adeninate framework with tris(2,2′-biprydine) ruthenium(II) complex and its electrochemiluminescence

Energy Technology Data Exchange (ETDEWEB)

Park, Ji Eun; Shin, Ik Soo [Dept. of Chemistry, Soongsil University, Seoul (Korea, Republic of); Oh, Hye Jae; An, Ji Hyun [Dept. of Chemistry Education, Seoul National University, Seoul (Korea, Republic of)

2017-04-15

Herein we report a redox-active metal-organic framework (MOF) via post-synthetic cation exchange with tris(2,2′-biprydine) ruthenium(II) complex (Ru(bpy){sub 3}{sup 2+}). A porous anionic zinc-adeninate framework (bMOF-100) is spacious enough to easily entrap 2.43 of Ru(bpy){sub 3}{sup 2+} cations within the mesopore. The encapsulation supported the framework structure preventing any distortion from a rapid solvent evaporation under SEM observation. Ru(bpy){sub 3}{sup 2+}@bMOF-100 was then immobilized on the surface of glassy carbon electrode, and its electrocatalytic and electrochemiluminescent (ECL) properties were investigated in aqueous and organic solution. Especially, Ru(bpy){sub 3}{sup 2+}@bMOF-100 showed the excellent electrochemical properties of Ru(bpy){sub 3}{sup 2+}, but gradual decomposition of the MOF structure was observed under electrochemical measurements because of the sluggish oxidation of adeninate ligand.

Synthetic biology in mammalian cells: Next generation research tools and therapeutics

Science.gov (United States)

Lienert, Florian; Lohmueller, Jason J; Garg, Abhishek; Silver, Pamela A

2014-01-01

Recent progress in DNA manipulation and gene circuit engineering has greatly improved our ability to programme and probe mammalian cell behaviour. These advances have led to a new generation of synthetic biology research tools and potential therapeutic applications. Programmable DNA-binding domains and RNA regulators are leading to unprecedented control of gene expression and elucidation of gene function. Rebuilding complex biological circuits such as T cell receptor signalling in isolation from their natural context has deepened our understanding of network motifs and signalling pathways. Synthetic biology is also leading to innovative therapeutic interventions based on cell-based therapies, protein drugs, vaccines and gene therapies. PMID:24434884

Controlling Ionic Transport for Device Design in Synthetic Nanopores

Science.gov (United States)

Kalman, Eric Boyd

Polymer nanopores present a number of behaviors not seen in microscale systems, such as ion current rectification, ionic selectivity, size exclusion and potential dependent ion concentrations in and near the pore. The existence of these effects stems from the small size of nanopores with respect to the characteristic length scales of surface interactions at the interface between the nanopore surface and the solution within it. The large surface-to-volume ratio due to the nanoscale geometry of a nanopore, as well as similarity in scale between geometry and interaction demands the solution interact with the nanopore walls. As surfaces in solution almost always carry residual charge, these surface forces are primarily the electrostatic interactions between the charge groups on the pore surface and the ions in solution. These interactions may be used by the experimentalist to control ionic transport through synthetic nanopores, and use them as a template for the construction of devices. In this research, we present our work on creating a number of ionic analogs to seminal electronic devices, specifically diodes, and transistors, by controlling ionic transport through the electrostatic interactions between a single synthetic nanopore and ions. Control is achieved by "doping" the effective charge carrier concentration in specific regions of the nanopore through manipulation of the pore's surface charge. This manipulation occurs through two mechanisms: chemical modification of the surface charge and electrostatic manipulation of the local internal nanopore potential using a gate electrode. Additionally, the innate selectivity of the charged nanopores walls allows for the separation of charges in solution. This well-known effect, which spawns measureable quantities, the streaming potential and current, has been used to create nanoscale water desalination membranes. We attempt to create a device using membranes with large nanopore densities for the desalination of water

Advancing the manufacture of complex geometry GFRC for today's building envelopes

Directory of Open Access Journals (Sweden)

Thomas Henriksen

2017-06-01

With this research the current architectural knowledge base has been advanced in terms of complex geometry thin-walled GFRC for building envelopes. The identified solutions should allow building with complex geometries to be realised using thin-walled GFRC as the envelope cladding.

Spatial Computing in Synthetic Bioware: Creating Bacterial Architectures

OpenAIRE

Pascalie , Jonathan; Potier , Martin; Kowaliw , Taras; Giavitto , Jean-Louis; Michel , Olivier; Spicher , Antoine; Doursat , René

2015-01-01

International audience; Synthetic biology is an emerging scientific field that promotes the standardized manufacturing of biological components without natural equivalents. Its goal is to create artificial living systems that can meet various needs in health care, nanotechnology and energy. Most works are currently focused on the individual bacterium as a chemical reactor. Our project, SynBioTIC, addresses a novel and more complex challenge: shape engineering, i.e. the redesign of natural mor...

Reprint of Design of synthetic microbial communities for biotechnological production processes.

Science.gov (United States)

Jagmann, Nina; Philipp, Bodo

2014-12-20

In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.

Hybrid RANS/LES applied to complex terrain

DEFF Research Database (Denmark)

Bechmann, Andreas; Sørensen, Niels N.

2011-01-01

Large Eddy Simulation (LES) of the wind in complex terrain is limited by computational cost. The number of computational grid points required to resolve the near-ground turbulent structures (eddies) are very high. The traditional solution to the problem has been to apply a wall function...... aspect ratio in the RANS layer and thereby resolve the mean near-wall velocity profile. The method is applicable to complex terrain and the benefits of traditional LES are kept intact. Using the hybrid method, simulations of the wind over a natural complex terrain near Wellington in New Zealand...... that accounts for the whole near-wall region. Recently, a hybrid method was proposed in which the eddies close to the ground were modelled in a Reynolds-averaged sense (RANS) and the eddies above this region were simulated using LES. The advantage of the approach is the ability to use shallow cells of high...

Opportunities in plant synthetic biology.

Science.gov (United States)

Cook, Charis; Martin, Lisa; Bastow, Ruth

2014-05-01

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

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

Science.gov (United States)

Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

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

Reconstrucción de defectos torácicos de espesor total: Presentación de 8 casos de especial complejidad Reconstruction of full thickness defects on the chest wall: Presentation of 8 complex cases

Directory of Open Access Journals (Sweden)

J.M. Lasso

2009-12-01

treatment require wide resection of the tumor or ischaemic or radiated tissue and control of the infection, but these principles could not be safely faced without the multiple reconstructive techniques that can afford the use of well vascularized, large or bulky tissues to reconstruct this anatomical area in combination with alloplastic materials, in order to give a solid stabilization. Thanks to these advances, we can actually perform our objectives in only one procedure. We present a selection of complex chest wall defects that have been operated in the last years by our surgical team. We will describe the solutions and the results obtained by means of a variety of possible flaps and synthetic materials.

Meeting the challenge of constructing a uniquely difficult barrier wall

International Nuclear Information System (INIS)

Stamnes, R.L.; Orlean, H.M.; Thompson, N.E.

1997-01-01

A soil-bentonite vertical barrier wall with intersecting and round corners was constructed in complex geology and steep terrain to enclose and dewater a 1.4 hectare (3.5 acre) area once used for hazardous waste lagoons and landfills at the Queen City Farms (QCF) Superfund site in Maple Valley, Washington. The barrier system, including cap and barrier wall, was designed to contain light non-aqueous phase liquid (LNAPL), in addition to subsurface soil and ground water contaminated with chromium, polychlorinated biphenyls, polyaromatic hydrocarbons, trichloroethylene, dichloroethylene and vinyl chloride in the dissolved-phase. These contaminants threaten a drinking water aquifer beneath the site. Constructing the vertical barrier was a challenge due to steep slopes of 20 percent along the alignment (19.2 meter elevation change in the top of the wall), a 22.5 meter (75 foot) design wall depth, heavily consolidated clays and silts, open works gravels (gravel without finer soils), and geologic discontinuity. The barrier wall is keyed into either a glacial till or thin clayey-silt aquitard. Extensive earth moving, stepped walls and many construction techniques were used to enable construction of this barrier wall. Commonly accepted constructability criteria would have discouraged the construction of this wall

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

Directory of Open Access Journals (Sweden)

Rosalind A. Le Feuvre

2018-06-01

Full Text Available Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal. Keywords: Synthetic biology, Materials, Biological materials, Biomaterials, Advanced materials

Synthetic biology and metabolic engineering.

Science.gov (United States)

Stephanopoulos, Gregory

2012-11-16

Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

Selection platforms for directed evolution in synthetic biology.

Science.gov (United States)

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

2016-08-15

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

Shell Scotsford's experience with a 100 per cent synthetic crude diet

International Nuclear Information System (INIS)

Margerum, M.

1997-01-01

A qualitative overview of Shell Canada's Scotford refinery was presented. The Scotford refinery is the only refinery in North America designed to run on 100 per cent synthetic crude. As a result, Scotford has a unique configuration and has faced some unique problems. Some of the challenges met in converting synthetic crude to today's products are described. The refinery's unique configuration is centered around a large hydrocracker and has high yield flexibility. The major units of the refinery are the crude unit, hydrocracker, naphtha hydrotreater and reformer, the aromatics complex, the distillate hydrogenator and the hydrogen plants. The refinery products include low sulphur gasoline, jet fuel and diesel fuel. Other products include LPG, FCC feed, benzene and solvents. Several process problems have been experienced at the Scotford refinery including hydrodenitrification of synthetic gasoline, PCA fouling, particulate fouling, crude unit fouling, and distillate lubricity. Solutions have been devised for most of these problems. 3 figs

The Complex Cell Wall Composition of Syncytia Induced by Plant Parasitic Cyst Nematodes Reflects Both Function and Host Plant

Directory of Open Access Journals (Sweden)

Li Zhang

2017-06-01

Full Text Available Plant–parasitic cyst nematodes induce the formation of specialized feeding structures, syncytia, within their host roots. These unique plant organs serve as the sole nutrient resource for development and reproduction throughout the biotrophic interaction. The multinucleate syncytium, which arises through local dissolution of cell walls and protoplast fusion of multiple adjacent cells, has dense cytoplasm containing numerous organelles, surrounded by thickened outer cell walls that must withstand high turgor pressure. However, little is known about how the constituents of the syncytial cell wall and their conformation support its role during nematode parasitism. We used a set of monoclonal antibodies, targeted to a range of plant cell wall components, to reveal the microstructures of syncytial cell walls induced by four of the most economically important cyst nematode species, Globodera pallida, Heterodera glycines, Heterodera avenae and Heterodera filipjevi, in their respective potato, soybean, and spring wheat host roots. In situ fluorescence analysis revealed highly similar cell wall composition of syncytia induced by G. pallida and H. glycines. Both consisted of abundant xyloglucan, methyl-esterified homogalacturonan and pectic arabinan. In contrast, the walls of syncytia induced in wheat roots by H. avenae and H. filipjevi contain little xyloglucan but are rich in feruloylated xylan and arabinan residues, with variable levels of mixed-linkage glucan. The overall chemical composition of syncytial cell walls reflected the general features of root cell walls of the different host plants. We relate specific components of syncytial cell walls, such as abundant arabinan, methyl-esterification status of pectic homogalacturonan and feruloylation of xylan, to their potential roles in forming a network to support both the strength and flexibility required for syncytium function.

The Complex Cell Wall Composition of Syncytia Induced by Plant Parasitic Cyst Nematodes Reflects Both Function and Host Plant.

Science.gov (United States)

Zhang, Li; Lilley, Catherine J; Imren, Mustafa; Knox, J Paul; Urwin, Peter E

2017-01-01

Plant-parasitic cyst nematodes induce the formation of specialized feeding structures, syncytia, within their host roots. These unique plant organs serve as the sole nutrient resource for development and reproduction throughout the biotrophic interaction. The multinucleate syncytium, which arises through local dissolution of cell walls and protoplast fusion of multiple adjacent cells, has dense cytoplasm containing numerous organelles, surrounded by thickened outer cell walls that must withstand high turgor pressure. However, little is known about how the constituents of the syncytial cell wall and their conformation support its role during nematode parasitism. We used a set of monoclonal antibodies, targeted to a range of plant cell wall components, to reveal the microstructures of syncytial cell walls induced by four of the most economically important cyst nematode species, Globodera pallida , Heterodera glycines , Heterodera avenae and Heterodera filipjevi , in their respective potato, soybean, and spring wheat host roots. In situ fluorescence analysis revealed highly similar cell wall composition of syncytia induced by G. pallida and H. glycines . Both consisted of abundant xyloglucan, methyl-esterified homogalacturonan and pectic arabinan. In contrast, the walls of syncytia induced in wheat roots by H. avenae and H. filipjevi contain little xyloglucan but are rich in feruloylated xylan and arabinan residues, with variable levels of mixed-linkage glucan. The overall chemical composition of syncytial cell walls reflected the general features of root cell walls of the different host plants. We relate specific components of syncytial cell walls, such as abundant arabinan, methyl-esterification status of pectic homogalacturonan and feruloylation of xylan, to their potential roles in forming a network to support both the strength and flexibility required for syncytium function.

Finite-size scaling functions for directed polymers confined between attracting walls

Energy Technology Data Exchange (ETDEWEB)

Owczarek, A L [Department of Mathematics and Statistics, University of Melbourne, Parkville, Victoria 3052 (Australia); Prellberg, T [School of Mathematical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS (United Kingdom); Rechnitzer, A [Department of Mathematics, University of British Columbia, Vancouver, BC V6T 1Z2 (Canada)

2008-01-25

The exact solution of directed self-avoiding walks confined to a slit of finite width and interacting with the walls of the slit via an attractive potential has been recently calculated. The walks can be considered to model the polymer-induced steric stabilization and sensitized flocculation of colloidal dispersions. The large-width asymptotics led to a phase diagram different to that of a polymer attached to, and attracted to, a single wall. The question that arises is: Can one interpolate between the single wall and two wall cases? In this paper, we calculate the exact scaling functions for the partition function by considering the two variable asymptotics of the partition function for simultaneous large length and large width. Consequently, we find the scaling functions for the force induced by the polymer on the walls. We find that these scaling functions are given by elliptic {theta} functions. In some parts of the phase diagram there is more a complex crossover between the single wall and two wall cases and we elucidate how this happens.

Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae.

Directory of Open Access Journals (Sweden)

Ido Yofe

2014-06-01

Full Text Available Introns are key regulators of eukaryotic gene expression and present a potentially powerful tool for the design of synthetic eukaryotic gene expression systems. However, intronic control over gene expression is governed by a multitude of complex, incompletely understood, regulatory mechanisms. Despite this lack of detailed mechanistic understanding, here we show how a relatively simple model enables accurate and predictable tuning of synthetic gene expression system in yeast using several predictive intron features such as transcript folding and sequence motifs. Using only natural Saccharomyces cerevisiae introns as regulators, we demonstrate fine and accurate control over gene expression spanning a 100 fold expression range. These results broaden the engineering toolbox of synthetic gene expression systems and provide a framework in which precise and robust tuning of gene expression is accomplished.

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

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

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems.

Science.gov (United States)

Bashor, Caleb J; Horwitz, Andrew A; Peisajovich, Sergio G; Lim, Wendell A

2010-01-01

The living cell is an incredibly complex entity, and the goal of predictively and quantitatively understanding its function is one of the next great challenges in biology. Much of what we know about the cell concerns its constituent parts, but to a great extent we have yet to decode how these parts are organized to yield complex physiological function. Classically, we have learned about the organization of cellular networks by disrupting them through genetic or chemical means. The emerging discipline of synthetic biology offers an additional, powerful approach to study systems. By rearranging the parts that comprise existing networks, we can gain valuable insight into the hierarchical logic of the networks and identify the modular building blocks that evolution uses to generate innovative function. In addition, by building minimal toy networks, one can systematically explore the relationship between network structure and function. Here, we outline recent work that uses synthetic biology approaches to investigate the organization and function of cellular networks, and describe a vision for a synthetic biology toolkit that could be used to interrogate the design principles of diverse systems.

Characteristics of wall pressure over wall with permeable coating

Energy Technology Data Exchange (ETDEWEB)

Song, Woo Seog; Shin, Seungyeol; Lee, Seungbae [Inha Univ., Incheon (Korea, Republic of)

2012-11-15

Fluctuating wall pressures were measured using an array of 16 piezoelectric transducers beneath a turbulent boundary layer. The coating used in this experiment was an open cell, urethane type foam with a porosity of approximately 50 ppi. The ultimate objective of the coating is to provide a mechanical filter to reduce the wall pressure fluctuations. The ultimate objective of the coating is to provide a mechanical filter to reduce the wall pressure fluctuations. The boundary layer on the flat plate was measured by using a hot wire probe, and the CPM method was used to determine the skin friction coefficient. The wall pressure autospectra and streamwise wavenumber frequency spectra were compared to assess the attenuation of the wall pressure field by the coating. The coating is shown to attenuate the convective wall pressure energy. However, the relatively rough surface of the coating in this investigation resulted in a higher mean wall shear stress, thicker boundary layer, and higher low frequency wall pressure spectral levels compared to a smooth wall.

Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

Science.gov (United States)

Kim, Juhyun; Salvador, Manuel; Saunders, Elizabeth; González, Jaime; Avignone-Rossa, Claudio

2016-01-01

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation. PMID:27903818

Enhanced fuel efficiency on tractor-trailers using synthetic jet-based active flow control

Science.gov (United States)

Amitay, Michael; Menicovich, David; Gallardo, Daniele

2016-04-01

The application of piezo-electrically-driven synthetic-jet-based active flow control to reduce drag on tractor-trailers was explored experimentally in wind tunnel testing as well as full-scale road tests. Aerodynamic drag accounts for more than 50% of the usable energy at highway speeds, a problem that applies primarily to trailer trucks. Therefore, a reduction in aerodynamic drag results in large saving of fuel and reduction in CO2 emissions. The active flow control technique that is being used relies on a modular system comprised of distributed, small, highly efficient actuators. These actuators, called synthetic jets, are jets that are synthesized at the edge of an orifice by a periodic motion of a piezoelectric diaphragm(s) mounted on one (or more) walls of a sealed cavity. The synthetic jet is zero net mass flux (ZNMF), but it allows momentum transfer to flow. It is typically driven near diaphragm and/or cavity resonance, and therefore, small electric input [O(10W)] is required. Another advantage of this actuator is that no plumbing is required. The system doesn't require changes to the body of the truck, can be easily reconfigured to various types of vehicles, and consumes small amounts of electrical power from the existing electrical system of the truck. Preliminary wind tunnel results showed up to 18% reduction in fuel consumption, whereas road tests also showed very promising results.

Antimicrobial Activity of Some Synthetic Compounds on Fungi Associated with Post Harvest Rot of Red Pepper (Capsicum annum

Directory of Open Access Journals (Sweden)

Matthew O. KOLAWOLE

2012-11-01

Full Text Available Rhizopus sp, Mucor sp, Collectotrichum capsici and Geotrichum candidum were isolated but pathogenic test revealed that Collectotrichum capsici and Geotrichum candidum were the most pathogenic of all the isolates. Ni2+ + Azo has the highest inhibitory effect, closely followed by Ni2+ + PAN while Copper (II complex of Thiourea has the lowest inhibitory effect. However, 10mg/ml concentration proved to be the most effective when radial mycelial growth of the test fungi was measured. The inhibitory effects of each complex on the isolates increases with increase in incubation period. There is the feasibility of using synthetic associated with the symptoms. The three synthetic compounds, Copper (II complex of Thiourea, Ni2+ + compounds as preservatives for harvested red pepper.

Bacterial glycobiology: rhamnose-containing cell wall polysaccharides in Gram-positive bacteria.

Science.gov (United States)

Mistou, Michel-Yves; Sutcliffe, Iain C; van Sorge, Nina M

2016-07-01

The composition of the Gram-positive cell wall is typically described as containing peptidoglycan, proteins and essential secondary cell wall structures called teichoic acids, which comprise approximately half of the cell wall mass. The cell walls of many species within the genera Streptococcus, Enterococcus and Lactococcus contain large amounts of the sugar rhamnose, which is incorporated in cell wall-anchored polysaccharides (CWP) that possibly function as homologues of well-studied wall teichoic acids (WTA). The presence and chemical structure of many rhamnose-containing cell wall polysaccharides (RhaCWP) has sometimes been known for decades. In contrast to WTA, insight into the biosynthesis and functional role of RhaCWP has been lacking. Recent studies in human streptococcal and enterococcal pathogens have highlighted critical roles for these complex polysaccharides in bacterial cell wall architecture and pathogenesis. In this review, we provide an overview of the RhaCWP with regards to their biosynthesis, genetics and biological function in species most relevant to human health. We also briefly discuss how increased knowledge in this field can provide interesting leads for new therapeutic compounds and improve biotechnological applications. © FEMS 2016.

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials.

Science.gov (United States)

Le Feuvre, Rosalind A; Scrutton, Nigel S

2018-06-01

Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials , where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

Fermion flavor in the soft-wall AdS model

International Nuclear Information System (INIS)

Gherghetta, Tony; Sword, Daniel

2009-01-01

The formalism for modeling multiple fermion generations in a warped extra dimension with a soft wall is presented. A bulk Higgs condensate is responsible for generating mass for the zero-mode fermions but leads to additional complexity from large mixing between different flavors. We extend existing single-generation analyses by considering new special cases in which analytical solutions can be derived. The general three-generation case is then treated using a simple numerical routine. Assuming anarchic 5D parameters, we find a fermion mass spectrum resembling the standard model quarks and leptons with highly degenerate couplings to Kaluza-Klein gauge bosons. This confirms that the soft-wall model has similar attractive features as that found in hard-wall models, providing a framework to generalize existing phenomenological analyses.

A laboratory investigation of the suspension, transport, and settling of silver carp eggs using synthetic surrogates

Science.gov (United States)

Garcia, Tatiana; Zuniga Zamalloa, Carlo; Jackson, P. Ryan; Murphy, Elizabeth A.; Garcia, Marcelo H.

2015-01-01

Asian carp eggs are semi-buoyant and must remain suspended in the water to survive, supported by the turbulence of the flow, until they hatch and develop the ability to swim. Analysis of the transport and dispersal patterns of Asian carp eggs will facilitate the development and implementation of control strategies to target the early life stages. Experimenting with Asian carp eggs is complicated due to practical issues of obtaining eggs in close proximity to experimental facilities and extensive handling of eggs tends to damage them. Herein, we describe laboratory experiments using styrene beads (4.85 mm diameter) as synthetic surrogate eggs to mimic the physical properties of water-hardened silver carp eggs. The first set of experiments was completed in a rectangular vertical column filled with salt water. The salinity of the water was adjusted in an iterative fashion to obtain a close approximation of the fall velocity of the styrene beads to the mean fall velocity of silver carp water-hardened eggs. The terminal fall velocity of synthetic eggs was measured using an image processing method. The second set of experiments was performed in a temperature-controlled recirculatory flume with a sediment bed. The flume was filled with salt water, and synthetic eggs were allowed to drift under different flow conditions. Drifting behavior, suspension conditions, and settling characteristics of synthetic eggs were observed. At high velocities, eggs were suspended and distributed through the water column. Eggs that touched the sediment bed were re-entrained by the flow. Eggs saltated when they touched the bed, especially at moderate velocities and with a relatively flat bed. At lower velocities, some settling of the eggs was observed. With lower velocities and a flat bed, eggs were trapped near the walls of the flume. When bedforms were present, eggs were trapped in the lee of the bedforms in addition to being trapped near the flume walls. Results of this research study

A Laboratory Investigation of the Suspension, Transport, and Settling of Silver Carp Eggs Using Synthetic Surrogates

Science.gov (United States)

Garcia, Tatiana; Zuniga Zamalloa, Carlo; Jackson, P. Ryan; Murphy, Elizabeth A.; Garcia, Marcelo H.

2015-01-01

Asian carp eggs are semi-buoyant and must remain suspended in the water to survive, supported by the turbulence of the flow, until they hatch and develop the ability to swim. Analysis of the transport and dispersal patterns of Asian carp eggs will facilitate the development and implementation of control strategies to target the early life stages. Experimenting with Asian carp eggs is complicated due to practical issues of obtaining eggs in close proximity to experimental facilities and extensive handling of eggs tends to damage them. Herein, we describe laboratory experiments using styrene beads (4.85 mm diameter) as synthetic surrogate eggs to mimic the physical properties of water-hardened silver carp eggs. The first set of experiments was completed in a rectangular vertical column filled with salt water. The salinity of the water was adjusted in an iterative fashion to obtain a close approximation of the fall velocity of the styrene beads to the mean fall velocity of silver carp water-hardened eggs. The terminal fall velocity of synthetic eggs was measured using an image processing method. The second set of experiments was performed in a temperature-controlled recirculatory flume with a sediment bed. The flume was filled with salt water, and synthetic eggs were allowed to drift under different flow conditions. Drifting behavior, suspension conditions, and settling characteristics of synthetic eggs were observed. At high velocities, eggs were suspended and distributed through the water column. Eggs that touched the sediment bed were re-entrained by the flow. Eggs saltated when they touched the bed, especially at moderate velocities and with a relatively flat bed. At lower velocities, some settling of the eggs was observed. With lower velocities and a flat bed, eggs were trapped near the walls of the flume. When bedforms were present, eggs were trapped in the lee of the bedforms in addition to being trapped near the flume walls. Results of this research study

A Laboratory Investigation of the Suspension, Transport, and Settling of Silver Carp Eggs Using Synthetic Surrogates.

Science.gov (United States)

Garcia, Tatiana; Zuniga Zamalloa, Carlo; Jackson, P Ryan; Murphy, Elizabeth A; Garcia, Marcelo H

2015-01-01

Asian carp eggs are semi-buoyant and must remain suspended in the water to survive, supported by the turbulence of the flow, until they hatch and develop the ability to swim. Analysis of the transport and dispersal patterns of Asian carp eggs will facilitate the development and implementation of control strategies to target the early life stages. Experimenting with Asian carp eggs is complicated due to practical issues of obtaining eggs in close proximity to experimental facilities and extensive handling of eggs tends to damage them. Herein, we describe laboratory experiments using styrene beads (4.85 mm diameter) as synthetic surrogate eggs to mimic the physical properties of water-hardened silver carp eggs. The first set of experiments was completed in a rectangular vertical column filled with salt water. The salinity of the water was adjusted in an iterative fashion to obtain a close approximation of the fall velocity of the styrene beads to the mean fall velocity of silver carp water-hardened eggs. The terminal fall velocity of synthetic eggs was measured using an image processing method. The second set of experiments was performed in a temperature-controlled recirculatory flume with a sediment bed. The flume was filled with salt water, and synthetic eggs were allowed to drift under different flow conditions. Drifting behavior, suspension conditions, and settling characteristics of synthetic eggs were observed. At high velocities, eggs were suspended and distributed through the water column. Eggs that touched the sediment bed were re-entrained by the flow. Eggs saltated when they touched the bed, especially at moderate velocities and with a relatively flat bed. At lower velocities, some settling of the eggs was observed. With lower velocities and a flat bed, eggs were trapped near the walls of the flume. When bedforms were present, eggs were trapped in the lee of the bedforms in addition to being trapped near the flume walls. Results of this research study

Synthetic biology and occupational risk.

Science.gov (United States)

Howard, John; Murashov, Vladimir; Schulte, Paul

2017-03-01

Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

Beta dosimetry in intraperitoneal administration of 166Ho-chitosan complex

International Nuclear Information System (INIS)

Kim, E. H.; Lim, S. M.; Park, K. B.

1998-01-01

Intraperitoneal administration of radioisotopes is suggested to treat the metastatic ovarian cancer in the peritoneal cavity. Administering beta-emitting radioisotopes into the peritoneal cavity allows the maximum energy delivery to the cancerous cells of the peritoneal wall surface while sparing the normal cells located in deep site of the peritoneal wall. In this study, dose estimates of the peritoneal wall are provided to be used for prescribing the amount of 166 Ho-chitosan complex administered. The 166 Ho-chitosan complex diffused in the peritoneal fluid may attach to the peritoneal wall surface. The attachment fraction of 166 Ho-chitosan complex to the peritoneal wall surface is obtained by simulating the ascites with Fischer rats. Both volume source in the peritoneal fluid and the surface source over the peritoneal wall surface are counted for the contribution to the peritoneal wall dose. The Monte Carlo code EGS4 is used to simulate the energy transfer of the beta particles emitted from 166 Ho. A plane geometrical model of semi-infinite volume describes the peritoneal cavity and the peritoneal wall. A semi-infinite plane of 10 μm in thickness at every 1 mm of depth in the peritoneal wall is taken as the target in dose estimation. Greater than 98 percents of attachment fraction has been observed from the experiments with Fischer rats. Given 1.3 μCi/cm 2 and 2.4 μCi/ml of uniform activity density, absorbed dose is 123 Gy, 8.59 Gy, 3.00 Gy, 1.03 Gy, and 327 Gy at 0 mm, 1 mm, 2 mm, 3 mm, and 4 mm in depth to the peritoneal wall, respectively

Synthetic Biology and Personalized Medicine

Science.gov (United States)

Jain, K.K.

2013-01-01

Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

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

Science.gov (United States)

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

2015-08-01

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

Plant synthetic biology: a new platform for industrial biotechnology.

Science.gov (United States)

Fesenko, Elena; Edwards, Robert

2014-05-01

Thirty years after the production of the first generation of genetically modified plants we are now set to move into a new era of recombinant crop technology through the application of synthetic biology to engineer new and complex input and output traits. The use of synthetic biology technologies will represent more than incremental additions of transgenes, but rather the directed design of completely new metabolic pathways, physiological traits, and developmental control strategies. The need to enhance our ability to improve crops through new engineering capability is now increasingly pressing as we turn to plants not just for food, but as a source of renewable feedstocks for industry. These accelerating and diversifying demands for new output traits coincide with a need to reduce inputs and improve agricultural sustainability. Faced with such challenges, existing technologies will need to be supplemented with new and far-more-directed approaches to turn valuable resources more efficiently into usable agricultural products. While these objectives are challenging enough, the use of synthetic biology in crop improvement will face public acceptance issues as a legacy of genetically modified technologies in many countries. Here we review some of the potential benefits of adopting synthetic biology approaches in improving plant input and output traits for their use as industrial chemical feedstocks, as linked to the rapidly developing biorefining industry. Several promising technologies and biotechnological targets are identified along with some of the key regulatory and societal challenges in the safe and acceptable introduction of such technology.

Tracking the emergence of synthetic biology.

Science.gov (United States)

Shapira, Philip; Kwon, Seokbeom; Youtie, Jan

2017-01-01

Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

International Nuclear Information System (INIS)

Lewis, Daniel D.; Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng

2014-01-01

As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

Energy Technology Data Exchange (ETDEWEB)

Lewis, Daniel D. [Integrative Genetics and Genomics, University of California Davis, Davis, CA (United States); Department of Biomedical Engineering, University of California Davis, Davis, CA (United States); Villarreal, Fernando D.; Wu, Fan; Tan, Cheemeng, E-mail: cmtan@ucdavis.edu [Department of Biomedical Engineering, University of California Davis, Davis, CA (United States)

2014-12-09

As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

[Use and versatility of titanium for the reconstruction of the thoracic wall].

Science.gov (United States)

Córcoles Padilla, Juan Manuel; Bolufer Nadal, Sergio; Kurowski, Krzysztof; Gálvez Muñoz, Carlos; Rodriguez Paniagua, José Manuel

2014-02-01

Chest wall deformities/defects and chest wall resections, as well as complex rib fractures require reconstruction with various prosthetic materials to ensure the basic functions of the chest wall. Titanium provides many features that make it an ideal material for this surgery. The aim is to present our initial results with this material in several diseases. From 2008 to 2012, 14 patients were operated on and titanium was used for reconstruction of the chest wall. A total of 7 patients had chest wall tumors, 2 with sternal resection, 4 patients with chest wall deformities/defects and 3 patients with severe rib injury due to traffic accident. The reconstruction was successful in all cases, with early extubation without detecting problems in the functionality of the chest wall at a respiratory level. Patients with chest wall tumors including sternal resections were extubated in the operating room as well as the chest wall deformities. Chest trauma cases were extubated within 24h from internal rib fixation. There were no complications related to the material used and the method of implementation. Titanium is an ideal material for reconstruction of the chest wall in several clinical situations allowing for great versatility and adaptability in different chest wall reconstructions. Copyright © 2013 AEC. Published by Elsevier Espana. All rights reserved.

Printability of Synthetic Papers by Electrophotography

Directory of Open Access Journals (Sweden)

Rozália Szentgyörgyvölgyi

2010-04-01

Full Text Available This paper deals with the printability of synthetic papers by the electrophotography technique. Prints of cmyk colour fields from 20% to 100% raster tone values were printed on three types of synthetic papers (one film synthetic paper and two fiber synthetic papers. The investigation of the appearance included densitometric measurement of the cmyk prints. The results have shown differences in the optical density and optical tone value between cmyk prints made on various synthetic papers. The highest optical density and the increase of the optical tone value were observed on the film synthetic paper, where cmyk prints were more saturated. The highest abrasion resistance of cmyk prints was obtained from the fibre synthetic paper.

Acute Intoxications Involving Synthetic Psychoactive Substances

Directory of Open Access Journals (Sweden)

Sergey A. Vasil'ev

2018-01-01

Full Text Available The purpose of this study was to evaluate the effectiveness of a succinic acid derivate, a substrate metabolic agent cytoflavin in patients with acute poisoning with synthetic psychoactive drugs.Materials and methods. A retrospective evaluation of effectiveness of a combined intensive care treatment protocol for 622 patients with acute narcotic poisoning (methadone and synthetic cannabinoids was carried out. All patients were divided into two groups. The main group (112 patients, median age 38.2±12.0 years included patients who, in addition to the basic treatment, received cytoflavin by intravenous drop infusion, 20–40 ml diluted in 400–500 ml of 10% glucose, for 5 days. Patients of the reference group (510 subjects, median age 37.6±14.1 years received treatment according to the «classical scheme». In addition to conventional examination, all patients underwent duplex scanning of cerebral vessels, examination of changes in the cerebral blood circulation and electroencephalogram findings. The severity of somatic disorders was assessed using criteria of the Glasgow coma scale. The severity of the asthenic syndrome was assessed according to the MFI-20 scale.Results. Compared to patients who received a standard therapy, patients of the main group had a significantly more rapid recovery from coma (by 1.5-fold: 23.5±3.1 days, versus 15.1±3.0 days, respectively, P0.05; the duration of psychotic disorders was shorter (by 1.8-fold: 15.5±4.2 hours vs 8.3±2.5 hours., respectively, P0.05, and the intensity of asthenic syndrome (by 2.8-fold: 64.1±3.3 rel. units vs 23.0±4,9 rel. units, respectively, P0.05 was also lower.Conclusion. Inclusion of cytoflavin in a protocol of a complex treatment of patients with synthetic drugs poisoning increased the effectiveness of the therapy. Data demonstrate that inclusion of the drug can be recommended for treatment of acute synthetic narcotic poisoning. 

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Programming Morphogenesis through Systems and Synthetic Biology.

Science.gov (United States)

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

2018-04-01

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

Contaminated glove remover for rubber or synthetic gloves

International Nuclear Information System (INIS)

Counit, G.; Charvolin, M.

1993-01-01

The glove remover, especially for protective rubber or synthetic gloves used to handle toxic materials in the nuclear, chemical and other industries, consist of a housing with a chamber into which the gloved hand is inserted, an outer depression chamber and a perforated wall between the two. A vacuum unit creates a low pressure inside the chamber enabling the hand to be withdrawn from the glove, which is then drawn through the pipe into a container for disposal. The open end of the chamber is covered by a diaphragm which surrounds and seals the arm which is inserted into it with the gloved hand. The diaphragm can occupy three positions: closed, where it surrounds and seals the arm; open, allowing the hand to be inserted or withdrawn, and intermediate, when air can pass from the outside between the hand and glove. A similar chamber is used for removing boots

Reinforcement mechanism of multi-anchor wall with double wall facing

Science.gov (United States)

Suzuki, Kouta; Kobayashi, Makoto; Miura, Kinya; Konami, Takeharu; Hayashi, Taketo

2017-10-01

The reinforced soil wall has high seismic performance as generally known. However, the seismic behavior has not been clarified accurately yet, especially on multi-anchor wall with double wall facing. Indefinite behavior of reinforced soil wall during earthquake make us complicated in case with adopting to the abutment, because of arrangement of anchor plate as reinforcement often different according to the width of roads. In this study, a series of centrifuge model tests were carried out to investigate the reinforcement mechanism of multi anchor wall with double wall facing from the perspective of the vertical earth pressure. Several types of reinforce arrangement and rigid wall were applied in order to verify the arch function in the reinforced regions. The test results show unique behavior of vertical earth pressure, which was affected by arch action. All the vertical earth pressure placed behind facing panel, are larger than that of middle part between facing panel despite of friction between backfill and facing panel. Similar results were obtained in case using rigid wall. On the other hands, the vertical earth pressure, which were measured at the 3cm high from bottom of model container, shows larger than that of bottom. This results show the existence of arch action between double walls. In addition, it implies that the wall facing of such soil structure confined the backfill as pseudo wall, which is very reason that the multi anchor wall with double wall facing has high seismic performance.

Assessment of Reynolds stresses tensor reconstruction methods for synthetic turbulent inflow conditions. Application to hybrid RANS/LES methods

International Nuclear Information System (INIS)

Laraufie, Romain; Deck, Sébastien

2013-01-01

Highlights: • Present various Reynolds stresses reconstruction methods from a RANS-SA flow field. • Quantify the accuracy of the reconstruction methods for a wide range of Reynolds. • Evaluate the capabilities of the overall process (Reconstruction + SEM). • Provide practical guidelines to realize a streamwise RANS/LES (or WMLES) transition. -- Abstract: Hybrid or zonal RANS/LES approaches are recognized as the most promising way to accurately simulate complex unsteady flows under current computational limitations. One still open issue concerns the transition from a RANS to a LES or WMLES resolution in the stream-wise direction, when near wall turbulence is involved. Turbulence content has then to be prescribed at the transition to prevent from turbulence decay leading to possible flow relaminarization. The present paper aims to propose an efficient way to generate this switch, within the flow, based on a synthetic turbulence inflow condition, named Synthetic Eddy Method (SEM). As the knowledge of the whole Reynolds stresses is often missing, the scope of this paper is focused on generating the quantities required at the SEM inlet from a RANS calculation, namely the first and second order statistics of the aerodynamic field. Three different methods based on two different approaches are presented and their capability to accurately generate the needed aerodynamic values is investigated. Then, the ability of the combination SEM + Reconstruction method to manufacture well-behaved turbulence is demonstrated through spatially developing flat plate turbulent boundary layers. In the mean time, important intrinsic features of the Synthetic Eddy method are pointed out. The necessity of introducing, within the SEM, accurate data, with regards to the outer part of the boundary layer, is illustrated. Finally, user’s guidelines are given depending on the Reynolds number based on the momentum thickness, since one method is suitable for low Reynolds number while the

Reward-based hypertension control by a synthetic brain-dopamine interface.

Science.gov (United States)

Rössger, Katrin; Charpin-El Hamri, Ghislaine; Fussenegger, Martin

2013-11-05

Synthetic biology has significantly advanced the design of synthetic trigger-controlled devices that can reprogram mammalian cells to interface with complex metabolic activities. In the brain, the neurotransmitter dopamine coordinates communication with target neurons via a set of dopamine receptors that control behavior associated with reward-driven learning. This dopamine transmission has recently been suggested to increase central sympathetic outflow, resulting in plasma dopamine levels that correlate with corresponding brain activities. By functionally rewiring the human dopamine receptor D1 (DRD1) via the second messenger cyclic adenosine monophosphate (cAMP) to synthetic promoters containing cAMP response element-binding protein 1(CREB1)-specific cAMP-responsive operator modules, we have designed a synthetic dopamine-sensitive transcription controller that reversibly fine-tunes specific target gene expression at physiologically relevant brain-derived plasma dopamine levels. Following implantation of circuit-transgenic human cell lines insulated by semipermeable immunoprotective microcontainers into mice, the designer device interfaced with dopamine-specific brain activities and produced a systemic expression response when the animal's reward system was stimulated by food, sexual arousal, or addictive drugs. Reward-triggered brain activities were able to remotely program peripheral therapeutic implants to produce sufficient amounts of the atrial natriuretic peptide, which reduced the blood pressure of hypertensive mice to the normal physiologic range. Seamless control of therapeutic transgenes by subconscious behavior may provide opportunities for treatment strategies of the future.

Evolvable synthetic neural system

Science.gov (United States)

Curtis, Steven A. (Inventor)

2009-01-01

An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

Seismic capacities of masonry walls at the big rock point nuclear generating plant

International Nuclear Information System (INIS)

Wesley, D.A.; Bunon, H.; Jenkins, R.B.

1984-01-01

An evaluation to determine the ability of selected concrete block walls in the vicinity of essential equipment to withstand seismic excitation was conducted. The seismic input to the walls was developed in accordance with the Systematic Evaluation Program (SEP) site-specific response spectra for the site. Time-history inputs to the walls were determined from the response of the turbine building complex. Analyses were performed to determine the capacities of the walls to withstand both in-plane and transverse seismic loads. Transverse load capacities were determined from time-history analyses of nonlinear two-dimensional analytical models of the walls. Separate inputs were used at the tops and bottoms of the walls to reflect the amplification through the building. The walls were unreinforced vertically with one exception, and have unsupported heights as high as 20'-8''. Also, cantilever walls as high as 11'-2'' were included in the evaluation. Factors of safety based on stability of the walls were determined for the transverse response, and on code allowable stresses (Reference 1) for the in-plane response

Adaptive wall treatment for a second moment closure in the industrial context

International Nuclear Information System (INIS)

Wald, Jean-Francois

2016-01-01

CFD computations of turbulent flows always begin with a complex meshing process (upper plenum, fuel assembly in the nuclear industry for example). Geometrical constraints are the first ones to be satisfied (level of details, important zones to refine regarding 'user experiences'). One has however to satisfy constraints that are inherent to the RANS model (Reynolds Averaged Navier Stokes) used for the computation. For example, if a 'High-Reynolds' (κ-ε standard, SSG,...) model is used one should only have wall cells with a dimensionless distance to the wall greater or equal to 20 to justify the use of the universal 'law of the wall'. On the other hand, if a 'Low-Reynolds' (BL-v"2/k, EB-RSM,...) model is used, one should only find wall cells with a dimensionless distance to the wall below 1. If those models are used in an inappropriate way the results could be dramatic (computations can either diverge or give unphysical results). This thesis proposes the development of a new turbulence model with adaptive wall treatments that gives satisfactory results on all types of meshes. In particular, the model will be able to cope with meshes containing both 'High-Reynolds' and 'Low-Reynolds' wall cells. Given the complex flows encountered in the nuclear industry this thesis will use a model known for its good behavior: the EB-RSM model. This model is able to reproduce the anisotropy of the turbulence and give more satisfactory results than eddy viscosity models in different configurations. This model is available in Code Saturne, an open source code developed at EDF. All the developments are made in this code. (author)

IL-6/IL-12 Cytokine Receptor Shuffling of Extra- and Intracellular Domains Reveals Canonical STAT Activation via Synthetic IL-35 and IL-39 Signaling.

Science.gov (United States)

Floss, D M; Schönberg, M; Franke, M; Horstmeier, F C; Engelowski, E; Schneider, A; Rosenfeldt, E M; Scheller, J

2017-11-09

IL-35 and IL-39 are recently discovered shared members of the IL-6- and IL-12-type cytokine family with immune-suppressive capacity. IL-35 has been reported to induce the formation of four different receptor complexes: gp130:IL-12β2, gp130:gp130, IL-12β2:IL-12β2, and IL-12β2:WSX-1. IL-39 was proposed to form a gp130:IL-23R receptor complex. IL-35, but not IL-39, has been reported to activate non-conventional STAT signaling, depending on the receptor complex and target cell. Analyses of IL-35 and IL-39 are, however, hampered by the lack of biologically active recombinant IL-35 and IL-39 proteins. Therefore, we engineered chimeric cytokine receptors to accomplish synthetic IL-35 and IL- 39 signaling by shuffling the extra- and intracellular domains of IL-6/IL-12-type cytokine receptors, resulting in biological activity for all previously described IL-35 receptor complexes. Moreover, we found that the proposed IL-39 receptor complex is biologically active and discovered two additional biologically active synthetic receptor combinations, gp130/IL-12Rβ1 and IL-23R/IL-12Rβ2. Surprisingly, synthetic IL-35 activation led to more canonical STAT signaling of all receptor complexes. In summary, our receptor shuffling approach highlights an interchangeable, modular domain structure among IL-6- and IL-12-type cytokine receptors and enabled synthetic IL-35 and IL-39 signaling.

Integrative systems and synthetic biology of cell-matrix adhesion sites.

Science.gov (United States)

Zamir, Eli

2016-09-02

The complexity of cell-matrix adhesion convolves its roles in the development and functioning of multicellular organisms and their evolutionary tinkering. Cell-matrix adhesion is mediated by sites along the plasma membrane that anchor the actin cytoskeleton to the matrix via a large number of proteins, collectively called the integrin adhesome. Fundamental challenges for understanding how cell-matrix adhesion sites assemble and function arise from their multi-functionality, rapid dynamics, large number of components and molecular diversity. Systems biology faces these challenges in its strive to understand how the integrin adhesome gives rise to functional adhesion sites. Synthetic biology enables engineering intracellular modules and circuits with properties of interest. In this review I discuss some of the fundamental questions in systems biology of cell-matrix adhesion and how synthetic biology can help addressing them.

Evaluation of a Porcine Dermal Collagen (Permacol Implant for Abdominal Wall Reconstruction in a Pediatric Multitrauma Patient

Directory of Open Access Journals (Sweden)

Idit Melnik

2014-01-01

Full Text Available The presence of a contaminated surgical field in abdominal wall defects caused by trauma presents a challenge for surgeons. Both primary suture and synthetic meshes are strongly discouraged as surgical treatments in such cases. We describe the use of a porcine dermal collagen (Permacol implant in an eight-year-old patient with multiple injuries. Three months after discharge, the child remains well with good cosmetic results. He is free of pain and has returned to full activity levels with complete wound closure and without any evidence of residual hernia. In conclusion, our experience indicates that the use of Permacol can be considered an efficient technique for reconstructing an infected abdominal wall defect of a pediatric multitrauma patient.

Synthetic Cathinones ("Bath Salts")

Science.gov (United States)

... Alcohol Club Drugs Cocaine Fentanyl Hallucinogens Inhalants Heroin Marijuana MDMA (Ecstasy/Molly) Methamphetamine Opioids Over-the-Counter Medicines Prescription Medicines Steroids (Anabolic) Synthetic Cannabinoids (K2/Spice) Synthetic Cathinones (Bath Salts) Tobacco/ ...

Cell-wall recovery after irreversible deformation of wood

Science.gov (United States)

Keckes, Jozef; Burgert, Ingo; Frühmann, Klaus; Müller, Martin; Kölln, Klaas; Hamilton, Myles; Burghammer, Manfred; Roth, Stephan V.; Stanzl-Tschegg, Stefanie; Fratzl, Peter

2003-12-01

The remarkable mechanical properties of biological materials reside in their complex hierarchical architecture and in specific molecular mechanistic phenomena. The fundamental importance of molecular interactions and bond recovery has been suggested by studies on deformation and fracture of bone and nacre. Like these mineral-based materials, wood also represents a complex nanocomposite with excellent mechanical performance, despite the fact that it is mainly based on polymers. In wood, however, the mechanistic contribution of processes in the cell wall is not fully understood. Here we have combined tensile tests on individual wood cells and on wood foils with simultaneous synchrotron X-ray diffraction analysis in order to separate deformation mechanisms inside the cell wall from those mediated by cell-cell interactions. We show that tensile deformation beyond the yield point does not deteriorate the stiffness of either individual cells or foils. This indicates that there is a dominant recovery mechanism that re-forms the amorphous matrix between the cellulose microfibrils within the cell wall, maintaining its mechanical properties. This stick-slip mechanism, rather like Velcro operating at the nanometre level, provides a 'plastic response' similar to that effected by moving dislocations in metals. We suggest that the molecular recovery mechanism in the cell matrix is a universal phenomenon dominating the tensile deformation of different wood tissue types.

Wall adjustment strategy software for use with the NASA Langley 0.3-meter transonic cryogenic tunnel adaptive wall test section

Science.gov (United States)

Wolf, Stephen W. D.

1988-01-01

The Wall Adjustment Strategy (WAS) software provides successful on-line control of the 2-D flexible walled test section of the Langley 0.3-m Transonic Cryogenic Tunnel. This software package allows the level of operator intervention to be regulated as necessary for research and production type 2-D testing using and Adaptive Wall Test Section (AWTS). The software is designed to accept modification for future requirements, such as 3-D testing, with a minimum of complexity. The WAS software described is an attempt to provide a user friendly package which could be used to control any flexible walled AWTS. Control system constraints influence the details of data transfer, not the data type. Then this entire software package could be used in different control systems, if suitable interface software is available. A complete overview of the software highlights the data flow paths, the modular architecture of the software and the various operating and analysis modes available. A detailed description of the software modules includes listings of the code. A user's manual is provided to explain task generation, operating environment, user options and what to expect at execution.

Complex and unexpected dynamics in simple genetic regulatory networks

Science.gov (United States)

Borg, Yanika; Ullner, Ekkehard; Alagha, Afnan; Alsaedi, Ahmed; Nesbeth, Darren; Zaikin, Alexey

2014-03-01

One aim of synthetic biology is to construct increasingly complex genetic networks from interconnected simpler ones to address challenges in medicine and biotechnology. However, as systems increase in size and complexity, emergent properties lead to unexpected and complex dynamics due to nonlinear and nonequilibrium properties from component interactions. We focus on four different studies of biological systems which exhibit complex and unexpected dynamics. Using simple synthetic genetic networks, small and large populations of phase-coupled quorum sensing repressilators, Goodwin oscillators, and bistable switches, we review how coupled and stochastic components can result in clustering, chaos, noise-induced coherence and speed-dependent decision making. A system of repressilators exhibits oscillations, limit cycles, steady states or chaos depending on the nature and strength of the coupling mechanism. In large repressilator networks, rich dynamics can also be exhibited, such as clustering and chaos. In populations of Goodwin oscillators, noise can induce coherent oscillations. In bistable systems, the speed with which incoming external signals reach steady state can bias the network towards particular attractors. These studies showcase the range of dynamical behavior that simple synthetic genetic networks can exhibit. In addition, they demonstrate the ability of mathematical modeling to analyze nonlinearity and inhomogeneity within these systems.

Wind tunnels with adapted walls for reducing wall interference

Science.gov (United States)

Ganzer, U.

1979-01-01

The basic principle of adaptable wind tunnel walls is explained. First results of an investigation carried out at the Aero-Space Institute of Berlin Technical University are presented for two dimensional flexible walls and a NACA 0012 airfoil. With five examples exhibiting very different flow conditions it is demonstrated that it is possible to reduce wall interference and to avoid blockage at transonic speeds by wall adaptation.

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

New designer drugs (synthetic cannabinoids and synthetic cathinones): review of literature.

Science.gov (United States)

Cottencin, Olivier; Rolland, Benjamin; Karila, Laurent

2014-01-01

New designer drugs (synthetic cannabinoids and synthetic cathinones) are new "legal highs" that are sold online for recreational public or private use. Synthetic cannabinoids are psychoactive herbal and chemical products that mimic the effects of cannabis when used. These drugs are available on the Internet or in head shops as incense or air fresheners to circumvent the law. Cathinone is a naturally occurring beta-ketone amphetamine analog found in the leaves of the Catha edulis plant. Synthetic cathinones are phenylalkylamine derivatives that may possess amphetamine-like properties. These drugs are sold online as bath salts. Designer drugs are often labeled as "not for human consumption" to circumvent drug abuse legislation. The absence of legal risks, the ease of obtaining these drugs, the moderate cost, and the availability via the Internet are the main features that attract users, but the number of intoxicated people presenting with emergencies is increasing. There is evidence that negative health and social consequences may affect recreational and chronic users. The addictive potential of designer drugs is not negligible.

Inverse measurement of wall pressure field in flexible-wall wind tunnels using global wall deformation data

Science.gov (United States)

Brown, Kenneth; Brown, Julian; Patil, Mayuresh; Devenport, William

2018-02-01

The Kevlar-wall anechoic wind tunnel offers great value to the aeroacoustics research community, affording the capability to make simultaneous aeroacoustic and aerodynamic measurements. While the aeroacoustic potential of the Kevlar-wall test section is already being leveraged, the aerodynamic capability of these test sections is still to be fully realized. The flexibility of the Kevlar walls suggests the possibility that the internal test section flow may be characterized by precisely measuring small deflections of the flexible walls. Treating the Kevlar fabric walls as tensioned membranes with known pre-tension and material properties, an inverse stress problem arises where the pressure distribution over the wall is sought as a function of the measured wall deflection. Experimental wall deformations produced by the wind loading of an airfoil model are measured using digital image correlation and subsequently projected onto polynomial basis functions which have been formulated to mitigate the impact of measurement noise based on a finite-element study. Inserting analytic derivatives of the basis functions into the equilibrium relations for a membrane, full-field pressure distributions across the Kevlar walls are computed. These inversely calculated pressures, after being validated against an independent measurement technique, can then be integrated along the length of the test section to give the sectional lift of the airfoil. Notably, these first-time results are achieved with a non-contact technique and in an anechoic environment.

Current status of synthetic epikeratoplasty.

Science.gov (United States)

Thompson, K P; Hanna, K; Waring, G O; Gipson, I; Liu, Y; Gailitis, R P; Johnson-Wint, B; Green, K

1991-01-01

Many of the deficiencies with human tissue epikeratoplasty might be improved by the use of a suitable synthetic lenticule. Potential biomaterials for epikeratoplasty include collagen (types I, III, or IV), collagen-hydrogel copolymers, bioactive synthetics, and coated hydrogels. The biomaterial must be engineered to achieve strict specifications of optical clarity, support of epithelial migration and adhesion, permeability to solutes, and stability to corneal proteases. Attaching synthetic lenticules to the cornea without cutting Bowman's layer by adhesives, laser welding, or direct adhesion may also improve the efficacy of synthetic epikeratoplasty.

Life after the synthetic cell

DEFF Research Database (Denmark)

Rasmussen, Steen

2010-01-01

Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self-replicating ......Nature asked eight synthetic-biology experts about the implications for science and society of the “synthetic cell” made by the J. Craig Venter Institute (JCVI). The institute's team assembled, modified and implanted a synthesized genome into a DNA-free bacterial shell to make a self...

Designing synthetic networks in silico: a generalised evolutionary algorithm approach.

Science.gov (United States)

Smith, Robert W; van Sluijs, Bob; Fleck, Christian

2017-12-02

Evolution has led to the development of biological networks that are shaped by environmental signals. Elucidating, understanding and then reconstructing important network motifs is one of the principal aims of Systems & Synthetic Biology. Consequently, previous research has focused on finding optimal network structures and reaction rates that respond to pulses or produce stable oscillations. In this work we present a generalised in silico evolutionary algorithm that simultaneously finds network structures and reaction rates (genotypes) that can satisfy multiple defined objectives (phenotypes). The key step to our approach is to translate a schema/binary-based description of biological networks into systems of ordinary differential equations (ODEs). The ODEs can then be solved numerically to provide dynamic information about an evolved networks functionality. Initially we benchmark algorithm performance by finding optimal networks that can recapitulate concentration time-series data and perform parameter optimisation on oscillatory dynamics of the Repressilator. We go on to show the utility of our algorithm by finding new designs for robust synthetic oscillators, and by performing multi-objective optimisation to find a set of oscillators and feed-forward loops that are optimal at balancing different system properties. In sum, our results not only confirm and build on previous observations but we also provide new designs of synthetic oscillators for experimental construction. In this work we have presented and tested an evolutionary algorithm that can design a biological network to produce desired output. Given that previous designs of synthetic networks have been limited to subregions of network- and parameter-space, the use of our evolutionary optimisation algorithm will enable Synthetic Biologists to construct new systems with the potential to display a wider range of complex responses.

A Statistical Approach For Modeling Tropical Cyclones. Synthetic Hurricanes Generator Model

Energy Technology Data Exchange (ETDEWEB)

Pasqualini, Donatella [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2016-05-11

This manuscript brie y describes a statistical ap- proach to generate synthetic tropical cyclone tracks to be used in risk evaluations. The Synthetic Hur- ricane Generator (SynHurG) model allows model- ing hurricane risk in the United States supporting decision makers and implementations of adaptation strategies to extreme weather. In the literature there are mainly two approaches to model hurricane hazard for risk prediction: deterministic-statistical approaches, where the storm key physical parameters are calculated using physi- cal complex climate models and the tracks are usually determined statistically from historical data; and sta- tistical approaches, where both variables and tracks are estimated stochastically using historical records. SynHurG falls in the second category adopting a pure stochastic approach.

Genetic complexity of miscanthus cell wall composition and biomass quality for biofuels.

Science.gov (United States)

van der Weijde, Tim; Kamei, Claire L Alvim; Severing, Edouard I; Torres, Andres F; Gomez, Leonardo D; Dolstra, Oene; Maliepaard, Chris A; McQueen-Mason, Simon J; Visser, Richard G F; Trindade, Luisa M

2017-05-25

Miscanthus sinensis is a high yielding perennial grass species with great potential as a bioenergy feedstock. One of the challenges that currently impedes commercial cellulosic biofuel production is the technical difficulty to efficiently convert lignocellulosic biomass into biofuel. The development of feedstocks with better biomass quality will improve conversion efficiency and the sustainability of the value-chain. Progress in the genetic improvement of biomass quality may be substantially expedited by the development of genetic markers associated to quality traits, which can be used in a marker-assisted selection program. To this end, a mapping population was developed by crossing two parents of contrasting cell wall composition. The performance of 182 F1 offspring individuals along with the parents was evaluated in a field trial with a randomized block design with three replicates. Plants were phenotyped for cell wall composition and conversion efficiency characters in the second and third growth season after establishment. A new SNP-based genetic map for M. sinensis was built using a genotyping-by-sequencing (GBS) approach, which resulted in 464 short-sequence uniparental markers that formed 16 linkage groups in the male map and 17 linkage groups in the female map. A total of 86 QTLs for a variety of biomass quality characteristics were identified, 20 of which were detected in both growth seasons. Twenty QTLs were directly associated to different conversion efficiency characters. Marker sequences were aligned to the sorghum reference genome to facilitate cross-species comparisons. Analyses revealed that for some traits previously identified QTLs in sorghum occurred in homologous regions on the same chromosome. In this work we report for the first time the genetic mapping of cell wall composition and bioconversion traits in the bioenergy crop miscanthus. These results are a first step towards the development of marker-assisted selection programs in miscanthus

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

Science.gov (United States)

Shi, Zhenyu; Vickers, Claudia E

2016-12-01

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

Protein scaffolds and higher-order complexes in synthetic biology

NARCIS (Netherlands)

den Hamer, A.; Rosier, B.J.H.M.; Brunsveld, L.; de Greef, T.F.A.; Ryadnov, M.; Brunsveld, L.; Suga, H.

2017-01-01

Interactions between proteins control molecular functions such as signalling or metabolic activity. Assembly of proteins via scaffold proteins or in higher-order complexes is a key regulatory mechanism. Understanding and functionally applying this concept requires the construction, study, and

Non-electrostatic complexes with DNA: towards novel synthetic gene delivery systems.

Science.gov (United States)

Soto, J; Bessodes, M; Pitard, B; Mailhe, P; Scherman, D; Byk, G

2000-05-01

We have developed new DNA complexing amphiphile based on Hoechst 33258 interaction with DNA grooves. The synthesis and physicochemical characterisation of lipid/DNA complexes, as compared to that of classical lipopolyamine for gene delivery, are described and discussed.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

Science.gov (United States)

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

WD40-repeat proteins in plant cell wall formation: current evidence and research prospects

Directory of Open Access Journals (Sweden)

Gea eGuerriero

2015-12-01

Full Text Available The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR proteins often function as molecular hubs mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico aproaches, such as analyses of co-expression, interactome and conserved gene neighbourhood. Notably, some WDR genes are frequently genomic neighbours of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CESAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.

Plant cell wall glycosyltransferases: High-throughput recombinant expression screening and general requirements for these challenging enzymes

DEFF Research Database (Denmark)

Welner, Ditte Hededam; Shin, David; Tomaleri, Giovani P.

2017-01-01

Molecular characterization of plant cell wall glycosyltransferases is a critical step towards understanding the biosynthesis of the complex plant cell wall, and ultimately for efficient engineering of biofuel and agricultural crops. The majority of these enzymes have proven very difficult to obta...

Beam, vacuum and walls, a 3-body interaction

International Nuclear Information System (INIS)

Arianer, J.

2002-11-01

The interactions between beams of accelerated particles, residual gas and walls involve complex physical processes. In most cases these interactions affect the quality of the vacuum and the value of the pressure. This course reviews all these interactions in a pedagogical and practical way that may be useful for any user of devices involving beams of particles. This document is made up of 6 chapters: 1) basic notions (Maxwell-Boltzmann distribution, kinematics of charged particles, collisions, excitation and ionization), 2) properties of beams (emittance, local effects, and synchrotron radiation), 3) interactions between residual gas and particle beams (Bremsstrahlung radiation, energy loss due to ionization, charge shift of ion beams, photo-absorption and photo-ionization, and slowing-down in a plasma), 4) surface properties (crystal structure, and interaction between surface and the residual gas), 5) interaction between the beam and walls (reflection and diffraction of electrons, secondary emission of electrons, desorption induced by electron and ion impacts, photon production, ion-wall interaction, sputtering, ion penetration, surface ionization and thermal-ionization), and 6) radiation-wall interaction (diffusion, damping, photo-electric effect, desorption induced by photons, pair production and laser-surface interaction). (A.C.)

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

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

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

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

Explicitly represented polygon wall boundary model for the explicit MPS method

Science.gov (United States)

Mitsume, Naoto; Yoshimura, Shinobu; Murotani, Kohei; Yamada, Tomonori

2015-05-01

This study presents an accurate and robust boundary model, the explicitly represented polygon (ERP) wall boundary model, to treat arbitrarily shaped wall boundaries in the explicit moving particle simulation (E-MPS) method, which is a mesh-free particle method for strong form partial differential equations. The ERP model expresses wall boundaries as polygons, which are explicitly represented without using the distance function. These are derived so that for viscous fluids, and with less computational cost, they satisfy the Neumann boundary condition for the pressure and the slip/no-slip condition on the wall surface. The proposed model is verified and validated by comparing computed results with the theoretical solution, results obtained by other models, and experimental results. Two simulations with complex boundary movements are conducted to demonstrate the applicability of the E-MPS method to the ERP model.

Synthetic genome engineering forging new frontiers for wine yeast.

Science.gov (United States)

Pretorius, Isak S

2017-02-01

Over the past 15 years, the seismic shifts caused by the convergence of biomolecular, chemical, physical, mathematical, and computational sciences alongside cutting-edge developments in information technology and engineering have erupted into a new field of scientific endeavor dubbed Synthetic Biology. Recent rapid advances in high-throughput DNA sequencing and DNA synthesis techniques are enabling the design and construction of new biological parts (genes), devices (gene networks) and modules (biosynthetic pathways), and the redesign of biological systems (cells and organisms) for useful purposes. In 2014, the budding yeast Saccharomyces cerevisiae became the first eukaryotic cell to be equipped with a fully functional synthetic chromosome. This was achieved following the synthesis of the first viral (poliovirus in 2002 and bacteriophage Phi-X174 in 2003) and bacterial (Mycoplasma genitalium in 2008 and Mycoplasma mycoides in 2010) genomes, and less than two decades after revealing the full genome sequence of a laboratory (S288c in 1996) and wine (AWRI1631 in 2008) yeast strain. A large international project - the Synthetic Yeast Genome (Sc2.0) Project - is now underway to synthesize all 16 chromosomes (∼12 Mb carrying ∼6000 genes) of the sequenced S288c laboratory strain by 2018. If successful, S. cerevisiae will become the first eukaryote to cross the horizon of in silico design of complex cells through de novo synthesis, reshuffling, and editing of genomes. In the meantime, yeasts are being used as cell factories for the semi-synthetic production of high-value compounds, such as the potent antimalarial artemisinin, and food ingredients, such as resveratrol, vanillin, stevia, nootkatone, and saffron. As a continuum of previously genetically engineered industrially important yeast strains, precision genome engineering is bound to also impact the study and development of wine yeast strains supercharged with synthetic DNA. The first taste of what the future

Synthetic biology: Emerging bioengineering in Indonesia

Science.gov (United States)

Suhandono, Sony

2017-05-01

The development of synthetic biology will shape the new era of science and technology. It is an emerging bioengineering technique involving genetic engineering which can alter the phenotype and behavior of the cell or the new product. Synthetic biology may produce biomaterials, drugs, vaccines, biosensors, and even a recombinant secondary metabolite used in herbal and complementary medicine, such as artemisinin, a malaria drug which is usually extracted from the plant Artemisia annua. The power of synthetic biology has encouraged scientists in Indonesia, and is still in early development. This paper also covers some research from an Indonesian research institute in synthetic biology such as observing the production of bio surfactants and the enhanced production of artemisinin using a transient expression system. Synthetic biology development in Indonesia may also be related to the iGEM competition, a large synthetic biology research competition which was attended by several universities in Indonesia. The application of synthetic biology for drug discovery will be discussed.

Slurry walls and slurry trenches - construction quality control

International Nuclear Information System (INIS)

Poletto, R.J.; Good, D.R.

1997-01-01

Slurry (panel) walls and slurry trenches have become conventional methods for construction of deep underground structures, interceptor trenches and hydraulic (cutoff) barriers. More recently polymers mixed with water are used to stabilize the excavation instead of bentonite slurry. Slurry walls are typically excavated in short panel segments, 2 to 7 m (7 to 23 ft) long, and backfilled with structural materials; whereas slurry trenches are fairly continuous excavations with concurrent backfilling of blended soils, or cement-bentonite mixtures. Slurry trench techniques have also been used to construct interceptor trenches. Currently no national standards exist for the design and/or construction of slurry walls/trenches. Government agencies, private consultants, contractors and trade groups have published specifications for construction of slurry walls/trenches. These specifications vary in complexity and quality of standards. Some place excessive emphasis on the preparation and control of bentonite or polymer slurry used for excavation, with insufficient emphasis placed on quality control of bottom cleaning, tremie concrete, backfill placement or requirements for the finished product. This has led to numerous quality problems, particularly with regard to identification of key depths, bottom sediments and proper backfill placement. This paper will discuss the inspection of slurry wall/trench construction process, identifying those areas which require special scrutiny. New approaches to inspection of slurry stabilized excavations are discussed

Proteomic analysis of cell walls of two developmental stages of alfalfa stems

Directory of Open Access Journals (Sweden)

Julian C Verdonk

2012-12-01

Full Text Available Cell walls are important for the growth and development of all plants. They are also valuable resources for feed and fiber, and more recently as a potential feedstock for bioenergy production. Cell wall proteins comprise only a fraction of the cell wall, but play important roles in establishing the walls and in the chemical interactions (e.g. crosslinking of cell wall components. This crosslinking provides structure, but restricts digestibility of cell wall complex carbohydrates, limiting available energy in animal and bioenergy production systems. Manipulation of cell wall proteins could be a strategy to improve digestibility. An analysis of the cell wall proteome of apical alfalfa stems (less mature, more digestible and basal alfalfa stems (more mature, less digestible was conducted using a recently developed low-salt/density gradient method for the isolation of cell walls. Walls were subsequently subjected to a modified extraction utilizing EGTA to remove pectins, followed by a LiCl extraction to isolate more tightly bound proteins. Recovered proteins were identified using shotgun proteomics. We identified 272 proteins in the alfalfa stem cell wall proteome, 153 of which had not previously been identified in cell wall proteomic analyses. Nearly 70% percent of the identified proteins were predicted to be secreted, as would be expected for most cell wall proteins, an improvement over previously published studies using traditional cell wall isolation methods. A comparison of our and several other cell wall proteomic studies indicates little overlap in identified proteins among them, which may be largely due to differences in the tissues used as well as differences in experimental approach.

Repair of large abdominal wall defects with expanded polytetrafluoroethylene (PTFE).

Science.gov (United States)

Bauer, J J; Salky, B A; Gelernt, I M; Kreel, I

1987-01-01

Most abdominal wall incisional hernias can be repaired by primary closure. However, where the defect is large or there is tension on the closure, the use of a prosthetic material is indicated. Expanded polytetrafluoroethylene (PTFE) patches were used to repair incisional hernias in 28 patients between November 1983 and December 1986. Twelve of these patients (43%) had a prior failure of a primary repair. Reherniation occurred in three patients (10.7%). Wound infections developed in two patients (7.1%), both of whom had existing intestinal stomas, one with an intercurrent pelvic abscess. The prosthetic patch was removed in the patient with the abscess, but the infection was resolved in the other without sequelae. Septic complications did not occur after any operations performed in uncontaminated fields. None of the patients exhibited any undue discomfort, wound pain, erythema, or induration. Complications related to adhesions, erosion of the patch material into the viscera, bowel obstruction, or fistula formation did not occur. Based on this clinical experience, the authors believe that the PTFE patch appears to represent an advance in synthetic abdominal wall substitutes. Images Fig. 1. Fig. 2(left)., Fig. 3(right). PMID:3689012

Data Assimilation of AirSWOT and Synthetically Derived SWOT Observations of Water Surface Elevation in a Multichannel River

Science.gov (United States)

Altenau, E. H.; Pavelsky, T.; Andreadis, K.; Bates, P. D.; Neal, J. C.

2017-12-01

Multichannel rivers continue to be challenging features to quantify, especially at regional and global scales, which is problematic because accurate representations of such environments are needed to properly monitor the earth's water cycle as it adjusts to climate change. It has been demonstrated that higher-complexity, 2D models outperform lower-complexity, 1D models in simulating multichannel river hydraulics at regional scales due to the inclusion of the channel network's connectivity. However, new remote sensing measurements from the future Surface Water and Ocean Topography (SWOT) mission and it's airborne analog AirSWOT offer new observations that can be used to try and improve the lower-complexity, 1D models to achieve accuracies closer to the higher-complexity, 2D codes. Here, we use an Ensemble Kalman Filter (EnKF) to assimilate AirSWOT water surface elevation (WSE) measurements from a 2015 field campaign into a 1D hydrodynamic model along a 90 km reach of Tanana River, AK. This work is the first to test data assimilation methods using real SWOT-like data from AirSWOT. Additionally, synthetic SWOT observations of WSE are generated across the same study site using a fine-resolution 2D model and assimilated into the coarser-resolution 1D model. Lastly, we compare the abilities of AirSWOT and the synthetic-SWOT observations to improve spatial and temporal model outputs in WSEs. Results indicate 1D model outputs of spatially distributed WSEs improve as observational coverage increases, and improvements in temporal fluctuations in WSEs depend on the number of observations. Furthermore, results reveal that assimilation of AirSWOT observations produce greater error reductions in 1D model outputs compared to synthetic SWOT observations due to lower measurement errors. Both AirSWOT and the synthetic SWOT observations significantly lower spatial and temporal errors in 1D model outputs of WSEs.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Science.gov (United States)

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

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

Science.gov (United States)

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

2014-03-27

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

Generation and analyses of human synthetic antibody libraries and their application for protein microarrays

DEFF Research Database (Denmark)

Säll, Anna; Walle, Maria; Wingren, Christer

2016-01-01

in a high-throughput manner. To address this we designed and constructed two human synthetic antibody fragment (scFv) libraries denoted HelL-11 and HelL-13. By the use of phage display technology, in total 466 unique scFv antibodies specific for 114 different antigens were generated. The specificities......Antibody-based proteomics offers distinct advantages in the analysis of complex samples for discovery and validation of biomarkers associated with disease. However, its large-scale implementation requires tools and technologies that allow development of suitable antibody or antibody fragments...... for diagnostics and therapeutics. In addition, this work provides a great example on how a synthetic approach can be used to optimize library designs. By having precise control of the diversity introduced into the antigen-binding sites, synthetic libraries offer increased understanding of how different diversity...

Interaction between plasma synthetic jet and subsonic turbulent boundary layer

Science.gov (United States)

Zong, Haohua; Kotsonis, Marios

2017-04-01

This paper experimentally investigates the interaction between a plasma synthetic jet (PSJ) and a subsonic turbulent boundary layer (TBL) using a hotwire anemometer and phase-locked particle imaging velocimetry. The PSJ is interacting with a fully developed turbulent boundary layer developing on the flat wall of a square wind tunnel section of 1.7 m length. The Reynolds number based on the freestream velocity (U∞ = 20 m/s) and the boundary layer thickness (δ99 = 34.5 mm) at the location of interaction is 44 400. A large-volume (1696 mm3) three-electrode plasma synthetic jet actuator (PSJA) with a round exit orifice (D = 2 mm) is adopted to produce high-speed (92 m/s) and short-duration (Tjet = 1 ms) pulsed jets. The exit velocity variation of the adopted PSJA in a crossflow is shown to remain almost identical to that in quiescent conditions. However, the flow structures emanating from the interaction between the PSJ and the TBL are significantly different from what were observed in quiescent conditions. In the midspan xy plane (z = 0 mm), the erupted jet body initially follows a wall-normal trajectory accompanied by the formation of a distinctive front vortex ring. After three convective time scales the jet bends to the crossflow, thus limiting the peak penetration depth to approximately 0.58δ99. Comparison of the normalized jet trajectories indicates that the penetration ability of the PSJ is less than steady jets with the same momentum flow velocity. Prior to the jet diminishing, a recirculation region is observed in the leeward side of the jet body, experiencing first an expansion and then a contraction in the area. In the cross-stream yz plane, the signature structure of jets in a crossflow, the counter-rotating vortex pair (CVP), transports high-momentum flow from the outer layer to the near-wall region, leading to a fuller velocity profile and a drop in the boundary layer shape factor (1.3 to 1.2). In contrast to steady jets, the CVP produced by the PSJ

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Science.gov (United States)

Brown, Bonnie L; Watson, Mick; Minot, Samuel S; Rivera, Maria C; Franklin, Rima B

2017-03-01

Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up

A Canadian refiner's perspective of synthetic crudes

International Nuclear Information System (INIS)

Halford, T.L.; McIntosh, A.P.; Rasmussen

1997-01-01

Some of the factors affecting a refiner's choice of crude oil include refinery hardware, particularly gas oil crackers, products slate and product specifications, crude availability, relative crude price and crude quality. An overview of synthetic crude, the use of synthetic crude combined with other crudes and a comparison of synthetic crude with conventional crude oil was given. The two main users of synthetic crude are basically two groups of refiners, those large groups who use synthetic crude combined with other crudes, and a smaller group who run synthetic crude on specially designed units as a sole feed. The effects of changes in fuel legislation were reviewed. It was predicted that the changes will have a mixed impact on the value of synthetic crude, but low sulphur diesel regulations and gasoline sulphur regulations will make current synthetic crudes attractive. The big future change with a negative impact will be diesel cetane increases to reduce engine emissions. This will reduce synthetic crude attractiveness due to distillate yields and quality and high gas oil yields. Similarly, any legislation limiting aromatics in diesel fuel will also make synthetic crudes less attractive. Problems experienced by refiners with hardware dedicated to synthetic crude (salt, naphthenic acid, fouling, quality variations) were also reviewed. 3 tabs

Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms

KAUST Repository

Braguy, Justine

2016-05-26

Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of inter-connectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks. This article is protected by copyright. All rights reserved.

Branched pectic galactan in phloem-sieve-element cell walls: implications for cell mechanics

DEFF Research Database (Denmark)

Torode, Thomas A.; O'Neill, Rachel E.; Marcus, Susan E.

2018-01-01

A major question in plant biology concerns the specification and functional differentiation of cell types. This is in the context of constraints imposed by networks of cell walls that both adhere cells and contribute to the form and function of developing organs. Here, we report the identification...... is an important factor for the study of phloem unloading of sucrose. Using microarrays of synthetic oligosaccharides, the LM26 epitope has been identified as a β-1,6-galactosyl substitution of β-1,4-galactan requiring more than three backbone residues for optimized recognition. This branched galactan structure...

Wall-based identification of coherent structures in wall-bounded turbulence

Science.gov (United States)

Sanmiguel Vila, C.; Flores, O.

2018-04-01

During the last decades, a number of reduced order models based on coherent structures have been proposed to describe wall-bounded turbulence. Many of these models emphasize the importance of coherent wall-normal velocity eddies (ν-eddies), which drive the generation of the very long streamwise velocity structures observed in the logarithmic and outer region. In order to use these models to improve our ability to control wall-bounded turbulence in realistic applications, these ν-eddies need to be identified from the wall in a non-intrusive way. In this paper, the possibility of using the pressure signal at the wall to identify these ν-eddies is explored, analyzing the cross-correlation between the wall-normal velocity component and the pressure fluctuations at the wall in a DNS of a turbulent channel flow at Reτ = 939. The results show that the cross-correlation has a region of negative correlation upstream, and a region of positive correlation backwards. In the spanwise direction the correlation decays monotonously, except very close to the wall where a change of sign of the correlation coefficient is observed. Moreover, filtering the pressure fluctuations at the wall in space results in an increase of the region where the cross-correlation is strong, both for the positively and the negatively correlated regions. The use of a time filter for the pressure fluctuations at the wall yields different results, displacing the regions of strong correlation without changing much their sizes. The results suggest that space-filtering the pressure at the wall is a feasible way to identify ν-eddies of different sizes, which could be used to trigger turbulent control strategies.

Effect of chemical composition on the flocculation dynamics of latex-based synthetic activated sludge

International Nuclear Information System (INIS)

Tan Phong Nguyen; Hankins, Nicholas P.; Hilal, Nidal

2007-01-01

This study investigates the effect of calcium, alginate, fibrous cellulose, and pH on the flocculation dynamics and final properties of synthetic activated sludges. A laboratory-scale batch reactor, fed with standard synthetic sludges was used. The effects of varying calcium concentration (5-25 mM), alginate concentration (25-125 mg/L), fibrous cellulose concentration (0.2-0.8 g/L) and pH (3-9) on the sludge characteristics were studied by varying one parameter whilst keeping the others constant. The results from experiments indicated that the calcium, alginate, fibrous cellulose, and pH had the critical effect on the aggregation rate, flocs size, and made the improvement of the final properties of sludge. Dynamic measurements have established the optimum conditions for floc formation and can accurately reflect the state of formation of the synthetic activated sludge flocs. These correlate well with measurements of settleability and turbidity of the synthetic activated sludge. The results of this study support the bonding theory and indicate that formation of cations-polymer complexes and polymer gelation are important means of flocculation. The development of synthetic activated sludges is suggested also to be a possible surrogate for studying the final properties of activated sludge

Finding Hope in Synthetic Biology.

Science.gov (United States)

Takala, Tuija

2017-04-01

For some, synthetic biology represents great hope in offering possible solutions to many of the world's biggest problems, from hunger to sustainable development. Others remain fearful of the harmful uses, such as bioweapons, that synthetic biology can lend itself to, and most hold that issues of biosafety are of utmost importance. In this article, I will evaluate these points of view and conclude that although the biggest promises of synthetic biology are unlikely to become reality, and the probability of accidents is fairly substantial, synthetic biology could still be seen to benefit humanity by enhancing our ethical understanding and by offering a boost to world economy.

Geo synthetic-reinforced Pavement systems

International Nuclear Information System (INIS)

Zornberg, J. G.

2014-01-01

Geo synthetics have been used as reinforcement inclusions to improve pavement performance. while there are clear field evidence of the benefit of using geo synthetic reinforcements, the specific conditions or mechanisms that govern the reinforcement of pavements are, at best, unclear and have remained largely unmeasured. Significant research has been recently conducted with the objectives of: (i) determining the relevant properties of geo synthetics that contribute to the enhanced performance of pavement systems, (ii) developing appropriate analytical, laboratory and field methods capable of quantifying the pavement performance, and (iii) enabling the prediction of pavement performance as a function of the properties of the various types of geo synthetics. (Author)

Characterisation of a complex thin walled structure fabricated by selective laser melting using a ferritic oxide dispersion strengthened steel

Energy Technology Data Exchange (ETDEWEB)

Boegelein, Thomas, E-mail: t.boegelein@liv.ac.uk; Louvis, Eleftherios; Dawson, Karl; Tatlock, Gordon J.; Jones, Andy R.

2016-02-15

Oxide dispersion strengthened (ODS) alloys exhibit superior mechanical and physical properties due to the presence of nanoscopic Y(Al, Ti) oxide precipitates, but their manufacturing process is complex. The present study is aimed at further investigation of the application of an alternative, Additive Manufacturing (AM) technique, Selective Laser Melting (SLM), to the production of consolidated ODS alloy components. Mechanically alloyed PM2000 (ODS-FeCrAl) powders have been consolidated and a fine dispersion of Y-containing precipitates were observed in an as built thin-walled component, but these particles were typically poly-crystalline and contained a variety of elements including O, Al, Ti, Cr and Fe. Application of post-build heat treatments resulted in the modification of particle structures and compositions; in the annealed condition most precipitates were transformed to single crystal yttrium aluminium oxides. During the annealing treatment, precipitate distributions homogenised and localised variations in number density were diminished. The resulting volume fractions of those precipitates were 25–40% lower than have been reported in conventionally processed PM2000, which was attributed to Y-rich slag-like surface features and inclusions formed during SLM. - Highlights: • A wall structure was grown from ODS steel powder using selective laser melting. • A fine dispersion of nano-precipitates was apparent in as-build material. • Precipitates were multi-phased containing several elements, e.g. O, Ti, Al, Fe, Cr, Y. • Post-build annealing changed those into typically single-crystalline Y–Al–O. • The anneal also reduced and stabilised the volume fraction of precipitates to ~ 0.006.

Examining an underappreciated control on lignin decomposition in soils? Effects of reactive manganese species on intact plant cell walls

Science.gov (United States)

Keiluweit, M.; Bougoure, J.; Pett-Ridge, J.; Kleber, M.; Nico, P. S.

2011-12-01

Lignin comprises a dominant proportion of carbon fluxes into the soil (representing up to 50% of plant litter and roots). Two lines of evidence suggest that manganese (Mn) acts as a strong controlling factor on the residence time of lignin in soil ecosystems. First, Mn content is highly correlated with litter decomposition in temperate and boreal forest soil ecosystems and, second, microbial agents of lignin degradation have been reported to rely on reactive Mn(III)-complexes to specifically oxidize lignin. However, few attempts have been made to isolate the mechanisms responsible for the apparent Mn-dependence of lignin decomposition in soils. Here we tested the hypothesis that Mn(III)-oxalate complexes may act as a perforating 'pretreatment' for structurally intact plant cell walls. We propose that these diffusible oxidizers are small enough to penetrate and react with non-porous ligno-cellulose in cell walls. This process was investigated by reacting single Zinnia elegans tracheary elements with Mn(III)-oxalate complexes in a continuous flow-through microreactor. The uniformity of cultured tracheary elements allowed us to examine Mn(III)-induced changes in cell wall chemistry and ultrastructure on the micro-scale using fluorescence and electron microscopy as well as synchrotron-based infrared and X-ray spectromicroscopy. Our results show that Mn(III)-complexes substantially oxidize specific lignin components of the cell wall, solubilize decomposition products, severely undermine the cell wall integrity, and cause cell lysis. We conclude that Mn(III)-complexes induce oxidative damage in plant cell walls that renders ligno-cellulose substrates more accessible for microbial lignin- and cellulose-decomposing enzymes. Implications of our results for the rate limiting impact of soil Mn speciation and availability on litter decomposition in forest soils will be discussed.

Oxide nanomaterials: synthetic developments, mechanistic studies, and technological innovations.

Science.gov (United States)

Patzke, Greta R; Zhou, Ying; Kontic, Roman; Conrad, Franziska

2011-01-24

Oxide nanomaterials are indispensable for nanotechnological innovations, because they combine an infinite variety of structural motifs and properties with manifold morphological features. Given that new oxide materials are almost reported on a daily basis, considerable synthetic and technological work remains to be done to fully exploit this ever increasing family of compounds for innovative nano-applications. This calls for reliable and scalable preparative approaches to oxide nanomaterials and their development remains a challenge for many complex nanostructured oxides. Oxide nanomaterials with special physicochemical features and unusual morphologies are still difficult to access by classic synthetic pathways. The limitless options for creating nano-oxide building blocks open up new technological perspectives with the potential to revolutionize areas ranging from data processing to biocatalysis. Oxide nanotechnology of the 21st century thus needs a strong interplay of preparative creativity, analytical skills, and new ideas for synergistic implementations. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Micro/nanofabricated environments for synthetic biology.

Science.gov (United States)

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Ferroelectricity and piezoelectricity in soft biological tissue: Porcine aortic walls revisited

NARCIS (Netherlands)

Lenz, T.; Hummel,R.; Katsouras,I.; Groen, W.A.; Nijemeisland, M.; Ruemmler,R.; Schäfer, M.K.E.; Leeuw, D.M. de

2017-01-01

Recently reported piezoresponse force microscopy (PFM) measurements have proposed that porcine aortic walls are ferroelectric. This finding may have great implications for understanding biophysical properties of cardiovascular diseases such as arteriosclerosis. However, the complex anatomical

I. Redox chemistry of bimetallic fulvalene complexes II. Oligocyclopentadienyl complexes

Energy Technology Data Exchange (ETDEWEB)

Brown, David Stephen [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley Lab., CA (United States). Chemical Sciences Div.

1993-11-01

The electrochemistry of the heterobimetallic complexes (fulvalene)WFe(CO)₅ (30) and (fulvalene)WRu(CO)₅ (31) has been investigated. Compound 30 is reduced in two one-electron processes, and this behavior was exploited synthetically to prepare a tetranuclear dimer by selective metal reduction. Complex 31 displayed a distinction between the metals upon reoxidation of the dianion, allowing the formation of a dimer by selective metal anion oxidation. The redox behavior of 30 led to an investigation of the use of electrocatalysis to effect metal-specific ligand substitution. It was found that reduction of 30 with a catalytic amount of CpFe(C₆Me₆) (97) in the presence of excess P(OMe)₃ or PMe₅ led to the formation of the zwitterions (fulvalene)[W(CO)₃^-][Fe(CO)PR₃⁺] (107, R = P(OMe)₃; 108, R = PMe₃). Compound 31 also displayed unique behavior with different reducing agents, as the monosubstituted zwitterion (fulvalene)[W(CO)₃^-][Ru(CO)₂(PMe₃⁺] was obtained when 97 was used while the disubstituted complex (fulvalene) [W(CO)₃^-] [Ru(CO)(PMe₃)₂⁺] was produced when Cp*Fe(C₆Me₆) was the catalyst. Potential synthetic routes to quatercyclopentadienyl complexes were also explored. Various attempts to couple heterobimetallic fulvalene compounds proved to be unsuccessful. 138 refs.

A Laboratory Investigation of the Suspension, Transport, and Settling of Silver Carp Eggs Using Synthetic Surrogates.

Directory of Open Access Journals (Sweden)

Tatiana Garcia

Full Text Available Asian carp eggs are semi-buoyant and must remain suspended in the water to survive, supported by the turbulence of the flow, until they hatch and develop the ability to swim. Analysis of the transport and dispersal patterns of Asian carp eggs will facilitate the development and implementation of control strategies to target the early life stages. Experimenting with Asian carp eggs is complicated due to practical issues of obtaining eggs in close proximity to experimental facilities and extensive handling of eggs tends to damage them. Herein, we describe laboratory experiments using styrene beads (4.85 mm diameter as synthetic surrogate eggs to mimic the physical properties of water-hardened silver carp eggs. The first set of experiments was completed in a rectangular vertical column filled with salt water. The salinity of the water was adjusted in an iterative fashion to obtain a close approximation of the fall velocity of the styrene beads to the mean fall velocity of silver carp water-hardened eggs. The terminal fall velocity of synthetic eggs was measured using an image processing method. The second set of experiments was performed in a temperature-controlled recirculatory flume with a sediment bed. The flume was filled with salt water, and synthetic eggs were allowed to drift under different flow conditions. Drifting behavior, suspension conditions, and settling characteristics of synthetic eggs were observed. At high velocities, eggs were suspended and distributed through the water column. Eggs that touched the sediment bed were re-entrained by the flow. Eggs saltated when they touched the bed, especially at moderate velocities and with a relatively flat bed. At lower velocities, some settling of the eggs was observed. With lower velocities and a flat bed, eggs were trapped near the walls of the flume. When bedforms were present, eggs were trapped in the lee of the bedforms in addition to being trapped near the flume walls. Results of this

COMPARATIVE EFFICACY OF SYNTHETIC AND BOTANICAL INSECTICIDES AGAINST SUCKING INSECT PEST AND THEIR NATURAL ENEMIES ON COTTON CROP

OpenAIRE

M. A. Baker; A. H. Makhdum; M. Nasir; A. Imran; A. Ahmad; F. Tufail

2016-01-01

The Synthetic and botanical insecticides are relatively safer for environment and beneficial insects. The study was conducted in Rahim Yar Khan during the cotton cropping season 2014 to evaluate the comparative efficacy of two Synthetic insecticides i.e. Nitenpyram (Jasper 10% SL) and Pyriproxyfen (Bruce 10.8% EC) and two botanical extracts of Calotropic procera and Azadirachta indica, against sucking insect pest complex of cotton and their natural enemies. Upon reaching economic thresholds, ...

Isolation of a novel cell wall architecture mutant of rice with defective Arabidopsis COBL4 ortholog BC1 required for regulated deposition of secondary cell wall components.

Science.gov (United States)

Sato, Kanna; Suzuki, Ryu; Nishikubo, Nobuyuki; Takenouchi, Sachi; Ito, Sachiko; Nakano, Yoshimi; Nakaba, Satoshi; Sano, Yuzou; Funada, Ryo; Kajita, Shinya; Kitano, Hidemi; Katayama, Yoshihiro

2010-06-01

The plant secondary cell wall is a highly ordered structure composed of various polysaccharides, phenolic components and proteins. Its coordinated regulation of a number of complex metabolic pathways and assembly has not been resolved. To understand the molecular mechanisms that regulate secondary cell wall synthesis, we isolated a novel rice mutant, cell wall architecture1 (cwa1), that exhibits an irregular thickening pattern in the secondary cell wall of sclerenchyma, as well as culm brittleness and reduced cellulose content in mature internodes. Light and transmission electron microscopy revealed that the cwa1 mutant plant has regions of local aggregation in the secondary cell walls of the cortical fibers in its internodes, showing uneven thickness. Ultraviolet microscopic observation indicated that localization of cell wall phenolic components was perturbed and that these components abundantly deposited at the aggregated cell wall regions in sclerenchyma. Therefore, regulation of deposition and assembly of secondary cell wall materials, i.e. phenolic components, appear to be disturbed by mutation of the cwa1 gene. Genetic analysis showed that cwa1 is allelic to brittle culm1 (bc1), which encodes the glycosylphosphatidylinositol-anchored COBRA-like protein specifically in plants. BC1 is known as a regulator that controls the culm mechanical strength and cellulose content in the secondary cell walls of sclerenchyma, but the precise function of BC1 has not been resolved. Our results suggest that CWA1/BC1 has an essential role in assembling cell wall constituents at their appropriate sites, thereby enabling synthesis of solid and flexible internodes in rice.

Nitric oxide reduction over a synthetic coal char

Energy Technology Data Exchange (ETDEWEB)

C. Pevida; A. Arenillas; F. Rubiera; J.J. Pis [Instituto Nacional del Carbon, CSIC, Oviedo (Spain)

2003-07-01

In the present work, the mechanisms involved in the NO heterogeneous reduction have been investigated. A synthetic coal char was used as the carbon source. This synthetic coal was made from a mixture of model compounds and provides well-known functionalities, including nitrogenated ones, similar to those found in a high volatile bituminous coal. The char was obtained by pyrolysis of the synthetic coal, up to 1123 K, under helium atmosphere in a fixed bed reactor. Char texture and structure were characterised by N{sub 2} and CO{sub 2} adsorption isotherms at 77 and 273 K, respectively, X-ray diffraction, immersion calorimetry in C{sub 6}H{sub 6} and scanning electron microscopy (SEM). Temperature programmed reactions (TPR) were carried out in a thermogravimetric analyser using 400 ppm NO diluted in Ar as the reactant gas. The char was heated at 15 K min{sup -1} from room temperature to 1273 K. Gaseous products were simultaneously analysed by mass spectrometry (MS) and Fourier transform infrared spectroscopy (FTIR). The influence of nitrogen in the solid phase on the reduction mechanism was evaluated by comparing the results for chars with and without nitrogen in their composition. The results of this preliminary study showed that the presence of nitrogen in the chars composition did not favour the heterogeneous NO reduction. In addition, low temperature NO chemisorption on the carbon surface creates complexes that take an active part in the subsequent reactions with NO. 5 refs., 4 figs., 3 tabs.

Customizable Generation of Synthetically Accessible, Local Chemical Subspaces.

Science.gov (United States)

Pottel, Joshua; Moitessier, Nicolas

2017-03-27

Screening large libraries of chemicals has been an efficient strategy to discover bioactive compounds; however a portion of the potential for success is limited to the available libraries. Synergizing combinatorial and computational chemistries has emerged as a time-efficient strategy to explore the chemical space more widely. Ideally, streamlining the evaluation process for larger, feasible chemical libraries would become commonplace. Thus, combinatorial tools and, for example, docking methods would be integrated to identify novel bioactive entities. The idea is simple in nature, but much more complex in practice; combinatorial chemistry is more than the coupling of chemicals into products: synthetic feasibility includes chemoselectivity, stereoselectivity, protecting group chemistry, and chemical availability which must all be considered for combinatorial library design. In addition, intuitive interfaces and simple user manipulation is key for optimal use of such tools by organic chemists-crucial for the integration of such software in medicinal chemistry laboratories. We present herein Finders and React2D-integrated into the Virtual Chemist platform, a modular software suite. This approach enhances virtual combinatorial chemistry by identifying available chemicals compatible with a user-defined chemical transformation and by carrying out the reaction leading to libraries of realistic, synthetically accessible chemicals-all with a completely automated, black-box, and efficient design. We demonstrate its utility by generating ∼40 million synthetically accessible, stereochemically accurate compounds from a single library of 100 000 purchasable molecules and 56 well-characterized chemical reactions.

Synthetic approaches to uniform polymers.

Science.gov (United States)

Ali, Monzur; Brocchini, Steve

2006-12-30

Uniform polymers are characterised by a narrow molecular weight distribution (MWD). Uniformity is also defined by chemical structure in respect of (1) monomer orientation, sequence and stereo-regularity, (2) polymer shape and morphology and (3) chemical functionality. The function of natural polymers such as polypeptides and polynucleotides is related to their conformational structure (e.g. folded tertiary structure). This is only possible because of their high degree of uniformity. While completely uniform synthetic polymers are rare, polymers with broad structure and MWD are widely used in medicine and the biomedical sciences. They are integral components in final dosage forms, drug delivery systems (DDS) and in implantable devices. Increasingly uniform polymers are being used to develop more complex medicines (e.g. delivery of biopharmaceuticals, enhanced formulations or DDS's for existing actives). In addition to the function imparted by any new polymer it will be required to meet stringent specifications in terms of cost containment, scalability, biocompatibility and performance. Synthetic polymers with therapeutic activity are also being developed to exploit their polyvalent properties, which is not possible with low molecular weight molecules. There is need to utilise uniform polymers for applications where the polymer may interact with the systemic circulation, tissues or cellular environment. There are also potential applications (e.g. stimuli responsive coatings) where uniform polymers may be used for their more defined property profile. While it is not yet practical to prepare synthetic polymers to the same high degree of uniformity as proteins, nature also effectively utilises many polymers with lower degrees of uniformity (e.g. polysaccharides, poly(amino acids), polyhydroxyalkanoates). In recent years it has become possible to prepare with practical experimental protocols sufficient quantities of polymers that display many aspects of uniformity. This

Models for synthetic biology.

Science.gov (United States)

Kaznessis, Yiannis N

2007-11-06

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

Ultimate shearing strength of aseismatic walls with many small holes for reactor buildings

International Nuclear Information System (INIS)

Yoshizaki, Seiji; Ezaki, Tetsuro; Korenaga, Takeyoshi; Sotomura, Kentaro.

1984-01-01

The aseismatic walls for reactor buildings have complicated forms, and are characterized by large wall thickness and high reinforcement ratio as compared with ordinary aseismatic walls. The forms are mainly box, cylinder or irregular polygonal prism and their combination. The design of the walls with many small holes has been performed on the basis of the reinforced concrete structure calculation standard of the Architectural Institute of Japan, following the case with large opening. When there are many small holes, the arrangement of reinforcement for the openings becomes complex, and the construction is difficult. It is necessary to rationalize the design and to simplify the reinforcement work. Under the background like this, the experiment to examine the shearing property in bending of the aseismatic walls with many small holes for reactor buildings was carried out, and horizontal loading test was performed on 43 specimens. The method of calculating the ultimate shearing strength of a wall without opening was proposed, and the method of applying it to a wall with many small holes is shown. The experimental method and the results, the examination of the experimental results, and the ultimate shearing strength of the aseismatic walls are reported. (Kako, I.)

Investigation of Plant Cell Wall Properties: A Study of Contributions from the Nanoscale to the Macroscale Impacting Cell Wall Recalcitrance

Science.gov (United States)

Crowe, Jacob Dillon

Biochemical conversion of lignocellulosic biomass to fuel ethanol is one of a few challenging, yet opportune technologies that can reduce the consumption of petroleum-derived transportation fuels, while providing parallel reductions in greenhouse gas emissions. Biomass recalcitrance, or resistance to deconstruction, is a major technical challenge that limits effective conversion of biomass to fermentable sugars, often requiring a costly thermochemical pretreatment step to improve biomass deconstruction. Biomass recalcitrance is imparted largely by the secondary cell wall, a complex polymeric matrix of cell wall polysaccharides and aromatic heteropolymers, that provides structural stability to cells and enables plant upright growth. Polymers within the cell wall can vary both compositionally and structurally depending upon plant species and anatomical fraction, and have varied responses to thermochemical pretreatments. Cell wall properties impacting recalcitrance are still not well understood, and as a result, the goal of this dissertation is to investigate structural features of the cell wall contributing to recalcitrance (1) in diverse anatomical fractions of a single species, (2) in response to diverse pretreatments, and (3) resulting from genetic modification. In the first study, feedstock cell wall heterogeneity was investigated in anatomical (stem, leaf sheaths, and leaf blades) and internode fractions of switchgrass at varying tissue maturities. Lignin content was observed as the key contributor to recalcitrance in maturing stem tissues only, with non-cellulosic substituted glucuronoarabinoxylans and pectic polysaccharides contributing to cell wall recalcitrance in leaf sheath and leaf blades. Hydroxycinnamate (i.e., saponifiable p-coumarate and ferulate) content along with xylan and pectin extractability decreased with tissue maturity, suggesting lignification is only one component imparting maturity specific cell wall recalcitrance. In the second study

Ferroelectricity and piezoelectricity in soft biological tissue : Porcine aortic walls revisited

NARCIS (Netherlands)

Lenz, Thomas; Hummel, Regina; Katsouras, Ilias; Groen, W.A.; Nijemeisland, M.; Ruemmler, Robert; Schäfer, Michael K.E.; de Leeuw, D.M.

2017-01-01

Recently reported piezoresponse force microscopy (PFM) measurements have proposed that porcine aortic walls are ferroelectric. This finding may have great implications for understanding biophysical properties of cardiovascular diseases such as arteriosclerosis. However, the complex anatomical

Ambiguous walls

DEFF Research Database (Denmark)

Mody, Astrid

2012-01-01

The introduction of Light Emitting Diodes (LEDs) in the built environment has encouraged myriad applications, often embedded in surfaces as an integrated part of the architecture. Thus the wall as responsive luminous skin is becoming, if not common, at least familiar. Taking into account how walls...... have encouraged architectural thinking of enclosure, materiality, construction and inhabitation in architectural history, the paper’s aim is to define new directions for the integration of LEDs in walls, challenging the thinking of inhabitation and program. This paper introduces the notion...... of “ambiguous walls” as a more “critical” approach to design [1]. The concept of ambiguous walls refers to the diffuse status a lumious and possibly responsive wall will have. Instead of confining it can open up. Instead of having a static appearance, it becomes a context over time. Instead of being hard...

Subclavian vein aneurysm secondary to a benign vessel wall hamartoma

Energy Technology Data Exchange (ETDEWEB)

Warren, Patrick [Nationwide Children' s Hospital, Section of Pediatric Interventional Radiology, Columbus, OH (United States); Spaeth, Maya [Nationwide Children' s Hospital, Section of Plastic and Reconstructive Surgery, Columbus, OH (United States); Prasad, Vinay [Nationwide Children' s Hospital, Section of Pediatric Pathology, Columbus, OH (United States); McConnell, Patrick [Nationwide Children' s Hospital, Section of Cardiothoracic Surgery, Columbus, OH (United States)

2013-11-15

Venous aneurysms are rare clinical entities, particularly in children, and their presentation and natural history often depend on the anatomical location and underlying etiology. We present a single case of a 12-year-old girl who presented with a palpable right supraclavicular mass. Imaging evaluation with CT, conventional venography, MRI and sonography revealed a large fusiform subclavian vein aneurysm with an unusual, mass-like fibrofatty component incorporated into the vessel wall. The girl ultimately required complete resection of the right subclavian vein with placement of a synthetic interposition graft. This case provides a radiology/pathology correlation of an entity that has not previously been described as well as an example of the utility of multiple imaging modalities to aid diagnosis and preoperative planning. (orig.)

Heterologous Expression of Plant Cell Wall Degrading Enzymes for Effective Production of Cellulosic Biofuels

Science.gov (United States)

Jung, Sang-Kyu; Parisutham, Vinuselvi; Jeong, Seong Hun; Lee, Sung Kuk

2012-01-01

A major technical challenge in the cost-effective production of cellulosic biofuel is the need to lower the cost of plant cell wall degrading enzymes (PCDE), which is required for the production of sugars from biomass. Several competitive, low-cost technologies have been developed to produce PCDE in different host organisms such as Escherichia coli, Zymomonas mobilis, and plant. Selection of an ideal host organism is very important, because each host organism has its own unique features. Synthetic biology-aided tools enable heterologous expression of PCDE in recombinant E. coli or Z. mobilis and allow successful consolidated bioprocessing (CBP) in these microorganisms. In-planta expression provides an opportunity to simplify the process of enzyme production and plant biomass processing and leads to self-deconstruction of plant cell walls. Although the future of currently available technologies is difficult to predict, a complete and viable platform will most likely be available through the integration of the existing approaches with the development of breakthrough technologies. PMID:22911272

Full-thickness skin graft vs. synthetic mesh in the repair of giant incisional hernia: a randomized controlled multicenter study.

Science.gov (United States)

Clay, L; Stark, B; Gunnarsson, U; Strigård, K

2018-04-01

Repair of large incisional hernias includes the implantation of a synthetic mesh, but this may lead to pain, stiffness, infection and enterocutaneous fistulae. Autologous full-thickness skin graft as on-lay reinforcement has been tested in eight high-risk patients in a proof-of-concept study, with satisfactory results. In this multicenter randomized study, the use of skin graft was compared to synthetic mesh in giant ventral hernia repair. Non-smoking patients with a ventral hernia > 10 cm wide were randomized to repair using an on-lay autologous full-thickness skin graft or a synthetic mesh. The primary endpoint was surgical site complications during the first 3 months. A secondary endpoint was patient comfort. Fifty-three patients were included. Clinical evaluation was performed at a 3-month follow-up appointment. There were fewer patients in the skin graft group reporting discomfort: 3 (13%) vs. 12 (43%) (p = 0.016). Skin graft patients had less pain and a better general improvement. No difference was seen regarding seroma; 13 (54%) vs. 13 (46%), or subcutaneous wound infection; 5 (20%) vs. 7 (25%). One recurrence appeared in each group. Three patients in the skin graft group and two in the synthetic mesh group were admitted to the intensive care unit. No difference was seen for the primary endpoint short-term surgical complication. Full-thickness skin graft appears to be a reliable material for ventral hernia repair producing no more complications than when using synthetic mesh. Patients repaired with a skin graft have less subjective abdominal wall symptoms.

High-R Walls for Remodeling: Wall Cavity Moisture Monitoring

Energy Technology Data Exchange (ETDEWEB)

Wiehagen, J.; Kochkin, V.

2012-12-01

The focus of the study is on the performance of wall systems, and in particular, the moisture characteristics inside the wall cavity and in the wood sheathing. Furthermore, while this research will initially address new home construction, the goal is to address potential moisture issues in wall cavities of existing homes when insulation and air sealing improvements are made.

High-R Walls for Remodeling. Wall Cavity Moisture Monitoring

Energy Technology Data Exchange (ETDEWEB)

Wiehagen, J. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States); Kochkin, V. [NAHB Research Center Industry Partnership, Upper Marlboro, MD (United States)

2012-12-01

The focus of the study is on the performance of wall systems, and in particular, the moisture characteristics inside the wall cavity and in the wood sheathing. Furthermore, while this research will initially address new home construction, the goal is to address potential moisture issues in wall cavities of existing homes when insulation and air sealing improvements are made.

Chemical and Physical Analysis Methods for Characterizing Tire Crumb Rubber Used in Synthetic Turf Fields

Science.gov (United States)

Tire crumb rubber from recycled tires is widely used as infill material in synthetic turf fields in the United States. Recycled crumb rubber is a complex and potentially variable matrix with many metal, VOC, and SVOC constituents, presenting challenges for characterization and ex...

The interaction of synthetic jets with turbulent boundary layers

Science.gov (United States)

Cui, Jing

In recent years, a promising approach to the control of wall bounded as well as free shear flows, using synthetic jet (oscillatory jet with zero-net-mass-flux) actuators, has received a great deal of attention. A variety of impressive flow control results have been achieved experimentally by many researchers including the vectoring of conventional propulsive jets, modification of aerodynamic characteristics of bluff bodies, control of lift and drag of airfoils, reduction of skin-friction of a flat plate boundary layer, enhanced mixing in circular jets, and control of external as well as internal flow separation and of cavity oscillations. More recently, attempts have been made to numerically simulate some of these flowfields. Numerically several of the above mentioned flow fields have been simulated primarily by employing the Unsteady Reynolds-Averaged Navier Stokes (URANS) equations with a turbulence model and a limited few by Direct Numerical Simulation (DNS). In simulations, both the simplified boundary conditions at the exit of the jet as well as the details of the cavity and lip have been included. In this dissertation, I describe the results of simulations for several two- and three-dimensional flowfields dealing with the interaction of a synthetic jet with a turbulent boundary layer and control of separation. These simulations have been performed using the URANS equations in conjunction with either one- or a two-equation turbulence model. 2D simulations correspond to the experiments performed by Honohan at Georgia Tech. and 3D simulations correspond to the CFD validation test cases proposed in the NASA Langley Research Center Workshop---"CFD Validation of Synthetic Jets and Turbulent Separation Control" held at Williamsburg VA in March 2004. The sources of uncertainty due to grid resolution, time step, boundary conditions, turbulence modeling etc. have been examined during the computations. Extensive comparisons for various flow variables are made with the

Predicting Complex Organic Molecule Emission from TW Hya

Science.gov (United States)

Vissapragada, Shreyas; Walsh, Catherine

2017-01-01

The Atacama Large Millimeter/submillimeter Array (ALMA) has significantly increased our ability to observe the rich chemical inventory of star and planet formation. ALMA has recently been used to detect CH3OH (methanol) and CH3CN (methyl cyanide) in protoplanetary disks; these molecules may be vital indicators of the complex organic ice reservoir in the comet-forming zone. We have constructed a physiochemical model of TW Hya, a well-studied protoplanetary disk, to explore the different formation mechanisms of complex ices. By running our model through a radiative transfer code and convolving with beam sizes appropriate for ALMA, we have obtained synthetic observations of methanol and methyl cyanide. Here, we compare and comment on these synthetic observations, and provide astrochemical justification for their spatial distributions.

Biological interaction of living cells with COSAN-based synthetic vesicles.

Science.gov (United States)

Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J

2015-01-15

Cobaltabisdicarbollide (COSAN) [3,3'-Co(1,2-C2B9H11)2](-), is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes.

Liquid Wall Chambers

Energy Technology Data Exchange (ETDEWEB)

Meier, W R

2011-02-24

The key feature of liquid wall chambers is the use of a renewable liquid layer to protect chamber structures from target emissions. Two primary options have been proposed and studied: wetted wall chambers and thick liquid wall (TLW) chambers. With wetted wall designs, a thin layer of liquid shields the structural first wall from short ranged target emissions (x-rays, ions and debris) but not neutrons. Various schemes have been proposed to establish and renew the liquid layer between shots including flow-guiding porous fabrics (e.g., Osiris, HIBALL), porous rigid structures (Prometheus) and thin film flows (KOYO). The thin liquid layer can be the tritium breeding material (e.g., flibe, PbLi, or Li) or another liquid metal such as Pb. TLWs use liquid jets injected by stationary or oscillating nozzles to form a neutronically thick layer (typically with an effective thickness of {approx}50 cm) of liquid between the target and first structural wall. In addition to absorbing short ranged emissions, the thick liquid layer degrades the neutron flux and energy reaching the first wall, typically by {approx}10 x x, so that steel walls can survive for the life of the plant ({approx}30-60 yrs). The thick liquid serves as the primary coolant and tritium breeding material (most recent designs use flibe, but the earliest concepts used Li). In essence, the TLW places the fusion blanket inside the first wall instead of behind the first wall.

The method to design the length of thin-wall flexible rotor

International Nuclear Information System (INIS)

Zhang Yue; Yao Zengzhong; Baigu Lafu

2014-01-01

Thin-wall flexible rotor is frequently used in rotating machinery. For this rotor the vibration is very complex under the working speed. So the composition design is very difficult. In this paper, for a thin-wall flexible rotor, the material and rotor diameter are determined from spatial structure, the working speed is determined from strength of the material, the first bending critical speed is determined from working speed, then the influence of length on the critical speed is researched. According to the influence of critical speed on the vibration, the length design method is researched, the design steps and methods are given, the safety margin of vibration is analysed. Design validity is established by test. The method is generally suitable for thin-wall flexible rotor. (authors)

Geometric Relations for CYLEX Test Tube-Wall Motion

Science.gov (United States)

Hill, Larry

2015-06-01

The CYLinder EXpansion (CYLEX) test is a (precision, instrumented, high-purity annealed copper) pipe bomb. Its essential measured quantities are detonation speed and tube-wall motion. Its main purpose is to calibrate detonation product equations of state (EOS) by measuring how product fluid pushes metal. In its full complexity, CYLEX is an integral test, for which EOS calibration requires the entire system to be computationally modeled and compared to salient data. Stripped to its essence, CYLEX is a non-integral test for which one may perform the inverse problem, to infer the EOS directly from data. CYLEX analysis can be simplified by the fact that the test constituents achieve a steady traveling wave structure; this allows derivation of several useful geometric relationships regarding tube wall motion. The first such treatment was by G.I. Taylor. Although his analysis was limited to small wall deflection angles, he asserted that the results remain valid for arbitrary ones. I confirm this attribute and present additional useful relationships. In the past decade, CYLEX wall-motion instrumentation has migrated almost entirely from streak camera to PDV, yet discrepancies remain between the two methods. I further present geometric relationships that shed light on this issue. Work supported by the U.S. DOE.

Evidence for land plant cell wall biosynthetic mechanisms in charophyte green algae

DEFF Research Database (Denmark)

Mikkelsen, Maria Dalgaard; Harholt, Jesper; Ulvskov, Peter

2014-01-01

in CGA is currently unknown, as no genomes are available, so this study sought to give insight into the evolution of the biosynthetic machinery of CGA through an analysis of available transcriptomes. METHODS: Available CGA transcriptomes were mined for cell wall biosynthesis GTs and compared with GTs...... to colonize land. These cell walls provide support and protection, are a source of signalling molecules, and provide developmental cues for cell differentiation and elongation. The cell wall of land plants is a highly complex fibre composite, characterized by cellulose cross-linked by non......-cellulosic polysaccharides, such as xyloglucan, embedded in a matrix of pectic polysaccharides. How the land plant cell wall evolved is currently unknown: early-divergent chlorophyte and prasinophyte algae genomes contain a low number of glycosyl transferases (GTs), while land plants contain hundreds. The number of GTs...

Rising damp in building walls: the wall base ventilation system

Energy Technology Data Exchange (ETDEWEB)

Guimaraes, A.S.; Delgado, J.M.P.Q.; Freitas, V.P. de [Faculdade de Engenharia da Universidade do Porto, Laboratorio de Fisica das Construcoes (LFC), Departamento de Engenharia Civil, Porto (Portugal)

2012-12-15

This work intends to validate a new system for treating rising damp in historic buildings walls. The results of laboratory experiments show that an efficient way of treating rising damp is by ventilating the wall base, using the HUMIVENT technique. The analytical model presented describes very well the observed features of rising damp in walls, verified by laboratory tests, who contributed for a simple sizing of the wall base ventilation system that will be implemented in historic buildings. (orig.)

Derivation and application of an analytical rock displacement solution on rectangular cavern wall using the inverse mapping method.

Directory of Open Access Journals (Sweden)

Mingzhong Gao

Full Text Available Rectangular caverns are increasingly used in underground engineering projects, the failure mechanism of rectangular cavern wall rock is significantly different as a result of the cross-sectional shape and variations in wall stress distributions. However, the conventional computational method always results in a long-winded computational process and multiple displacement solutions of internal rectangular wall rock. This paper uses a Laurent series complex method to obtain a mapping function expression based on complex variable function theory and conformal transformation. This method is combined with the Schwarz-Christoffel method to calculate the mapping function coefficient and to determine the rectangular cavern wall rock deformation. With regard to the inverse mapping concept, the mapping relation between the polar coordinate system within plane ς and a corresponding unique plane coordinate point inside the cavern wall rock is discussed. The disadvantage of multiple solutions when mapping from the plane to the polar coordinate system is addressed. This theoretical formula is used to calculate wall rock boundary deformation and displacement field nephograms inside the wall rock for a given cavern height and width. A comparison with ANSYS numerical software results suggests that the theoretical solution and numerical solution exhibit identical trends, thereby demonstrating the method's validity. This method greatly improves the computing accuracy and reduces the difficulty in solving for cavern boundary and internal wall rock displacements. The proposed method provides a theoretical guide for controlling cavern wall rock deformation failure.

Meeting Report: Synthetic Biology Jamboree for Undergraduates

Science.gov (United States)

Campbell, A. Malcolm

2005-01-01

The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

21 CFR 73.1200 - Synthetic iron oxide.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Synthetic iron oxide. 73.1200 Section 73.1200 Food... COLOR ADDITIVES EXEMPT FROM CERTIFICATION Drugs § 73.1200 Synthetic iron oxide. (a) Identity. (1) The color additive synthetic iron oxide consists of any one or any combination of synthetically prepared...

21 CFR 73.200 - Synthetic iron oxide.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Synthetic iron oxide. 73.200 Section 73.200 Food... COLOR ADDITIVES EXEMPT FROM CERTIFICATION Foods § 73.200 Synthetic iron oxide. (a) Identity. (1) The color additive synthetic iron oxide consists of any one or any combination of synthetically prepared...

21 CFR 172.888 - Synthetic petroleum wax.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Synthetic petroleum wax. 172.888 Section 172.888... CONSUMPTION Multipurpose Additives § 172.888 Synthetic petroleum wax. Synthetic petroleum wax may be safely used in or on foods in accordance with the following conditions: (a) Synthetic petroleum wax is a...

A mobility based vibroacoustic energy transmission simulation into an enclosure through a double-wall panel.

Science.gov (United States)

Sahu, Atanu; Bhattacharya, Partha; Niyogi, Arup Guha; Rose, Michael

2017-06-01

Double-wall panels are known for their superior sound insulation properties over single wall panels as a sound barrier. The sound transmission phenomenon through a double-wall structure is a complex process involving vibroacoustic interaction between structural panels, the air-cushion in between, and the secondary acoustic domain. It is in this context a versatile and a fully coupled technique based on the finite-element-boundary element model is developed that enables estimation of sound transfer through a double-wall panel into an adjacent enclosure while satisfying the displacement compatibility across the interface. The contribution of individual components in the transmitted energy is identified through numerical simulations.

Longevity in vivo of primary cell wall cellulose synthases.

Science.gov (United States)

Hill, Joseph Lee; Josephs, Cooper; Barnes, William J; Anderson, Charles T; Tien, Ming

2018-02-01

Our work focuses on understanding the lifetime and thus stability of the three main cellulose synthase (CESA) proteins involved in primary cell wall synthesis of Arabidopsis. It had long been thought that a major means of CESA regulation was via their rapid degradation. However, our studies here have uncovered that AtCESA proteins are not rapidly degraded. Rather, they persist for an extended time in the plant cell. Plant cellulose is synthesized by membrane-embedded cellulose synthase complexes (CSCs). The CSC is composed of cellulose synthases (CESAs), of which three distinct isozymes form the primary cell wall CSC and another set of three isozymes form the secondary cell wall CSC. We determined the stability over time of primary cell wall (PCW) CESAs in Arabidopsis thaliana seedlings, using immunoblotting after inhibiting protein synthesis with cycloheximide treatment. Our work reveals very slow turnover for the Arabidopsis PCW CESAs in vivo. Additionally, we show that the stability of all three CESAs within the PCW CSC is altered by mutations in individual CESAs, elevated temperature, and light conditions. Together, these results suggest that CESA proteins are very stable in vivo, but that their lifetimes can be modulated by intrinsic and environmental cues.

Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology

Science.gov (United States)

Blount, Benjamin A.; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

2012-01-01

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex “multi-wire” logic functions. PMID:22442681

Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology.

Science.gov (United States)

Blount, Benjamin A; Weenink, Tim; Vasylechko, Serge; Ellis, Tom

2012-01-01

Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis. In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library. TetR regulation was introduced into PFY1p to create a synthetic inducible promoter (iPFY1p) that functions in an inverter device. Orthogonal and scalable regulation of synthetic promoters was then demonstrated for the first time using customisable Transcription Activator-Like Effectors (TALEs) modified and designed to act as orthogonal repressors for specific PFY1-based promoters. The ability to diversify a promoter at its core sequences and then independently target Transcription Activator-Like Orthogonal Repressors (TALORs) to virtually any of these sequences shows great promise toward the design and construction of future synthetic gene networks that encode complex "multi-wire" logic functions.

Role of Synthetic and Dimensional Synthetic Organic Chemistry in Block Copolymer Micelle Nanosensor Engineering

DEFF Research Database (Denmark)

Ek, Pramod Kumar

This thesis investigated the role of amphiphilic triblock copolymer micelle nanomaterials in nanosensors, with emphasis on the synthesis of micelle particle sensors. The thesis is focused on the role of synthetic and dimensional synthetic organic chemistry in amphiphilic triblock core-shellcorona...

Word selection affects perceptions of synthetic biology

Directory of Open Access Journals (Sweden)

Tonidandel Scott

2011-07-01

Full Text Available Abstract Members of the synthetic biology community have discussed the significance of word selection when describing synthetic biology to the general public. In particular, many leaders proposed the word "create" was laden with negative connotations. We found that word choice and framing does affect public perception of synthetic biology. In a controlled experiment, participants perceived synthetic biology more negatively when "create" was used to describe the field compared to "construct" (p = 0.008. Contrary to popular opinion among synthetic biologists, however, low religiosity individuals were more influenced negatively by the framing manipulation than high religiosity people. Our results suggest that synthetic biologists directly influence public perception of their field through avoidance of the word "create".

Bifurcating Particle Swarms in Smooth-Walled Fractures

Science.gov (United States)

Pyrak-Nolte, L. J.; Sun, H.

2010-12-01

Particle swarms can occur naturally or from industrial processes where small liquid drops containing thousands to millions of micron-size to colloidal-size particles are released over time from seepage or leaks into fractured rock. The behavior of these particle swarms as they fall under gravity are affected by particle interactions as well as interactions with the walls of the fractures. In this paper, we present experimental results on the effect of fractures on the cohesiveness of the swarm and the formation of bifurcation structures as they fall under gravity and interact with the fracture walls. A transparent cubic sample (100 mm x 100 mm x 100 mm) containing a synthetic fracture with uniform aperture distributions was optically imaged to quantify the effect of confinement within fractures on particle swarm formation, swarm velocity, and swarm geometry. A fracture with a uniform aperture distribution was fabricated from two polished rectangular prisms of acrylic. A series of experiments were performed to determine how swarm movement and geometry are affected as the walls of the fracture are brought closer together from 50 mm to 1 mm. During the experiments, the fracture was fully saturated with water. We created the swarms using two different particle sizes in dilute suspension (~ 1.0% by mass). The particles were 3 micron diameter fluorescent polymer beads and 25 micron diameter soda-lime glass beads. Experiments were performed using swarms that ranged in size from 5 µl to 60 µl. The swarm behavior was imaged using an optical fluorescent imaging system composed of a CCD camera illuminated by a 100 mW diode-pumped doubled YAG laser. As a swarm falls in an open-tank of water, it forms a torroidal shape that is stable as long as no ambient or background currents exist in the water tank. When a swarm is released into a fracture with an aperture less than 5 mm, the swarm forms the torroidal shape but it is distorted because of the presence of the walls. The

The Craterostigma plantagineum glycine-rich protein CpGRP1 interacts with a cell wall-associated protein kinase 1 (CpWAK1) and accumulates in leaf cell walls during dehydration.

Science.gov (United States)

Giarola, Valentino; Krey, Stephanie; von den Driesch, Barbara; Bartels, Dorothea

2016-04-01

Craterostigma plantagineum tolerates extreme desiccation. Leaves of this plant shrink and extensively fold during dehydration and expand again during rehydration, preserving their structural integrity. Genes were analysed that may participate in the reversible folding mechanism. Analysis of transcripts abundantly expressed in desiccated leaves identified a gene putatively coding for an apoplastic glycine-rich protein (CpGRP1). We studied the expression, regulation and subcellular localization of CpGRP1 and its ability to interact with a cell wall-associated protein kinase (CpWAK1) to understand the role of CpGRP1 in the cell wall during dehydration. The CpGRP1 protein accumulates in the apoplast of desiccated leaves. Analysis of the promoter revealed that the gene expression is mainly regulated at the transcriptional level, is independent of abscisic acid (ABA) and involves a drought-responsive cis-element (DRE). CpGRP1 interacts with CpWAK1 which is down-regulated in response to dehydration. Our data suggest a role of the CpGRP1-CpWAK1 complex in dehydration-induced morphological changes in the cell wall during dehydration in C. plantagineum. Cell wall pectins and dehydration-induced pectin modifications are predicted to be involved in the activity of the CpGRP1-CpWAK1 complex. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Velocity distribution in a turbulent flow near a rough wall

Science.gov (United States)

Korsun, A. S.; Pisarevsky, M. I.; Fedoseev, V. N.; Kreps, M. V.

2017-11-01

Velocity distribution in the zone of developed wall turbulence, regardless of the conditions on the wall, is described by the well-known Prandtl logarithmic profile. In this distribution, the constant, that determines the value of the velocity, is determined by the nature of the interaction of the flow with the wall and depends on the viscosity of the fluid, the dynamic velocity, and the parameters of the wall roughness.In extreme cases depending on the ratio between the thickness of the viscous sublayer and the size of the roughness the constant takes on a value that does not depend on viscosity, or leads to a ratio for a smooth wall.It is essential that this logarithmic profile is the result not only of the Prandtl theory, but can be derived from general considerations of the theory of dimensions, and also follows from the condition of local equilibrium of generation and dissipation of turbulent energy in the wall area. This allows us to consider the profile as a universal law of velocity distribution in the wall area of a turbulent flow.The profile approximation up to the maximum speed line with subsequent integration makes possible to obtain the resistance law for channels of simple shape. For channels of complex shape with rough walls, the universal profile can be used to formulate the boundary condition when applied to the calculation of turbulence models.This paper presents an empirical model for determining the constant of the universal logarithmic profile. The zone of roughness is described by a set of parameters and is considered as a porous structure with variable porosity.

Attenuation in Rectangular Waveguides with Finite Conductivity Walls

Directory of Open Access Journals (Sweden)

K. C. Yeong

2011-06-01

Full Text Available We present a fundamental and accurate approach to compute the attenuation of electromagnetic waves propagating in rectangular waveguides with finite conductivity walls. The wavenumbers kx and ky in the x and y directions respectively, are obtained as roots of a set of transcendental equations derived by matching the tangential component of the electric field (E and the magnetic field (H at the surface of the waveguide walls. The electrical properties of the wall material are determined by the complex permittivity ε, permeability μ, and conductivity σ. We have examined the validity of our model by carrying out measurements on the loss arising from the fundamental TE10 mode near the cutoff frequency. We also found good agreement between our results and those obtained by others including Papadopoulos’ perturbation method across a wide range of frequencies, in particular in the vicinity of cutoff. In the presence of degenerate modes however, our method gives higher losses, which we attribute to the coupling between modes as a result of dispersion.

Ion-surface interaction: simulation of plasma-wall interaction (ITER)

International Nuclear Information System (INIS)

Salou, Pierre

2013-01-01

The wall materials of magnetic confinement in fusion machines are exposed to an aggressive environment; the reactor blanket is bombarded with a high flux of particles extracted from the plasma, leading to the sputtering of surface material. This sputtering causes wall erosion as well as plasma contamination problems. In order to control fusion reactions in complex reactors, it is thus imperative to well understand the plasma-wall interactions. This work proposes the study of the sputtering of fusion relevant materials. We propose to simulate the charged particles influx by few keV single-charged ion beams. This study is based on the catcher method; to avoid any problem of pollution (especially in the case of carbon) we designed a new setup allowing an in situ Auger electron spectroscopy analysis. The results provide the evolution of the angular distribution of the sputtering yield as a function of the ion mass (from helium to xenon) and its energy (from 3 keV to 9 keV). (author) [fr

Synthetic Biology for Specialty Chemicals.

Science.gov (United States)

Markham, Kelly A; Alper, Hal S

2015-01-01

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

Protease-sensitive synthetic prions.

Directory of Open Access Journals (Sweden)

David W Colby

2010-01-01

Full Text Available Prions arise when the cellular prion protein (PrP(C undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrP(Sc. Frequently, PrP(Sc is protease-resistant but protease-sensitive (s prions have been isolated in humans and other animals. We report here that protease-sensitive, synthetic prions were generated in vitro during polymerization of recombinant (rec PrP into amyloid fibers. In 22 independent experiments, recPrP amyloid preparations, but not recPrP monomers or oligomers, transmitted disease to transgenic mice (n = 164, denoted Tg9949 mice, that overexpress N-terminally truncated PrP. Tg9949 control mice (n = 174 did not spontaneously generate prions although they were prone to late-onset spontaneous neurological dysfunction. When synthetic prion isolates from infected Tg9949 mice were serially transmitted in the same line of mice, they exhibited sPrP(Sc and caused neurodegeneration. Interestingly, these protease-sensitive prions did not shorten the life span of Tg9949 mice despite causing extensive neurodegeneration. We inoculated three synthetic prion isolates into Tg4053 mice that overexpress full-length PrP; Tg4053 mice are not prone to developing spontaneous neurological dysfunction. The synthetic prion isolates caused disease in 600-750 days in Tg4053 mice, which exhibited sPrP(Sc. These novel synthetic prions demonstrate that conformational changes in wild-type PrP can produce mouse prions composed exclusively of sPrP(Sc.

Materials Manufactured from 3D Printed Synthetic Biology Arrays

Science.gov (United States)

Gentry, Diana; Micks, Ashley

2013-01-01

Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but are unsuitable for space-related applications due to production, manufacturing, or processing limitations. Large-scale ecosystem-based production, such as raising and harvesting trees for wood, is impractical in a self-contained habitat such as a space station or potential Mars colony. Manufacturing requirements, such as the specialized equipment needed to harvest and process cotton, add too much upmass for current launch technology. Cells in nature are already highly specialized for making complex biological materials on a micro scale. We envision combining these strengths with the recently emergent technologies of synthetic biology and 3D printing to create 3D-structured arrays of cells that are bioengineered to secrete different materials in a specified three-dimensional pattern.

Complex Dynamic Development of Poliovirus Membranous Replication Complexes

Science.gov (United States)

Nair, Vinod; Hansen, Bryan T.; Hoyt, Forrest H.; Fischer, Elizabeth R.; Ehrenfeld, Ellie

2012-01-01

Replication of all positive-strand RNA viruses is intimately associated with membranes. Here we utilize electron tomography and other methods to investigate the remodeling of membranes in poliovirus-infected cells. We found that the viral replication structures previously described as “vesicles” are in fact convoluted, branching chambers with complex and dynamic morphology. They are likely to originate from cis-Golgi membranes and are represented during the early stages of infection by single-walled connecting and branching tubular compartments. These early viral organelles gradually transform into double-membrane structures by extension of membranous walls and/or collapsing of the luminal cavity of the single-membrane structures. As the double-membrane regions develop, they enclose cytoplasmic material. At this stage, a continuous membranous structure may have double- and single-walled membrane morphology at adjacent cross-sections. In the late stages of the replication cycle, the structures are represented mostly by double-membrane vesicles. Viral replication proteins, double-stranded RNA species, and actively replicating RNA are associated with both double- and single-membrane structures. However, the exponential phase of viral RNA synthesis occurs when single-membrane formations are predominant in the cell. It has been shown previously that replication complexes of some other positive-strand RNA viruses form on membrane invaginations, which result from negative membrane curvature. Our data show that the remodeling of cellular membranes in poliovirus-infected cells produces structures with positive curvature of membranes. Thus, it is likely that there is a fundamental divergence in the requirements for the supporting cellular membrane-shaping machinery among different groups of positive-strand RNA viruses. PMID:22072780

Single-walled carbon nanotubes as near-infrared optical biosensors for life sciences and biomedicine.

Science.gov (United States)

Jain, Astha; Homayoun, Aida; Bannister, Christopher W; Yum, Kyungsuk

2015-03-01

Single-walled carbon nanotubes that emit photostable near-infrared fluorescence have emerged as near-infrared optical biosensors for life sciences and biomedicine. Since the discovery of their near-infrared fluorescence, researchers have engineered single-walled carbon nanotubes to function as an optical biosensor that selectively modulates its fluorescence upon binding of target molecules. Here we review the recent advances in the single-walled carbon nanotube-based optical sensing technology for life sciences and biomedicine. We discuss the structure and optical properties of single-walled carbon nanotubes, the mechanisms for molecular recognition and signal transduction in single-walled carbon nanotube complexes, and the recent development of various single-walled carbon nanotube-based optical biosensors. We also discuss the opportunities and challenges to translate this emerging technology into biomedical research and clinical use, including the biological safety of single-walled carbon nanotubes. The advances in single-walled carbon nanotube-based near-infrared optical sensing technology open up a new avenue for in vitro and in vivo biosensing with high sensitivity and high spatial resolution, beneficial for many areas of life sciences and biomedicine. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synergistic Synthetic Biology: Units in Concert

Science.gov (United States)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

Synergistic Synthetic Biology: Units in Concert

International Nuclear Information System (INIS)

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

Simulating wall and corner fire tests on wood products with the OSU room fire model

Science.gov (United States)

H. C. Tran

1994-01-01

This work demonstrates the complexity of modeling wall and corner fires in a compartment. The model chosen for this purpose is the Ohio State University (OSU) room fire model. This model was designed to simulate fire growth on walls in a compartment and therefore lends itself to direct comparison with standard room test results. The model input were bench-scale data...

Synthetic real estate: bringing corporate finance to health care.

Science.gov (United States)

Varwig, D; Smith, J

1998-01-01

The changing landscape of health care has caused hospitals, health care systems, and other health care organizations to look for ways to finance expansions and acquisitions without "tainting" their balance sheets. This search has led health care executives to a financing technique that has been already embraced by Fortune 500 companies for most of this decade and more recently adopted by high-tech companies: synthetic real estate. Select case studies provide examples of the more creative financial structures currently being employed to meet rapidly growing and increasingly complex funding needs.

Purity and Defect Characterization of Single-Wall Carbon Nanotubes Using Raman Spectroscopy

Directory of Open Access Journals (Sweden)

Yasumitsu Miyata

2011-01-01

Full Text Available We investigated the purity and defects of single-wall carbon nanotubes (SWCNTs produced by various synthetic methods including chemical vapor deposition, arc discharge, and laser ablation. The SWCNT samples were characterized using scanning electron microscopy (SEM, thermogravimetric analysis (TGA, and Raman spectroscopy. Quantitative analysis of SEM images suggested that the G-band Raman intensity serves as an index for the purity. By contrast, the intensity ratio of G-band to D-band (G/D ratio reflects both the purity and the defect density of SWCNTs. The combination of G-band intensity and G/D ratio is useful for a quick, nondestructive evaluation of the purity and defect density of a SWCNT sample.

Design of magnetic coordination complexes for quantum computing.

Science.gov (United States)

Aromí, Guillem; Aguilà, David; Gamez, Patrick; Luis, Fernando; Roubeau, Olivier

2012-01-21

A very exciting prospect in coordination chemistry is to manipulate spins within magnetic complexes for the realization of quantum logic operations. An introduction to the requirements for a paramagnetic molecule to act as a 2-qubit quantum gate is provided in this tutorial review. We propose synthetic methods aimed at accessing such type of functional molecules, based on ligand design and inorganic synthesis. Two strategies are presented: (i) the first consists in targeting molecules containing a pair of well-defined and weakly coupled paramagnetic metal aggregates, each acting as a carrier of one potential qubit, (ii) the second is the design of dinuclear complexes of anisotropic metal ions, exhibiting dissimilar environments and feeble magnetic coupling. The first systems obtained from this synthetic program are presented here and their properties are discussed.

Synthetic biology, metaphors and responsibility.

Science.gov (United States)

McLeod, Carmen; Nerlich, Brigitte

2017-08-29

Metaphors are not just decorative rhetorical devices that make speech pretty. They are fundamental tools for thinking about the world and acting on the world. The language we use to make a better world matters; words matter; metaphors matter. Words have consequences - ethical, social and legal ones, as well as political and economic ones. They need to be used 'responsibly'. They also need to be studied carefully - this is what we want to do through this editorial and the related thematic collection. In the context of synthetic biology, natural and social scientists have become increasingly interested in metaphors, a wave of interest that we want to exploit and amplify. We want to build on emerging articles and books on synthetic biology, metaphors of life and the ethical and moral implications of such metaphors. This editorial provides a brief introduction to synthetic biology and responsible innovation, as well as a comprehensive review of literature on the social, cultural and ethical impacts of metaphor use in genomics and synthetic biology. Our aim is to stimulate an interdisciplinary and international discussion on the impact that metaphors can have on science, policy and publics in the context of synthetic biology.

Approaches to chemical synthetic biology.

Science.gov (United States)

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

2012-07-16

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

Synthetic Aperture Sequential Beamforming

DEFF Research Database (Denmark)

Kortbek, Jacob; Jensen, Jørgen Arendt; Gammelmark, Kim Løkke

2008-01-01

A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective is to im......A synthetic aperture focusing (SAF) technique denoted Synthetic Aperture Sequential Beamforming (SASB) suitable for 2D and 3D imaging is presented. The technique differ from prior art of SAF in the sense that SAF is performed on pre-beamformed data contrary to channel data. The objective...... is to improve and obtain a more range independent lateral resolution compared to conventional dynamic receive focusing (DRF) without compromising frame rate. SASB is a two-stage procedure using two separate beamformers. First a set of Bmode image lines using a single focal point in both transmit and receive...... is stored. The second stage applies the focused image lines from the first stage as input data. The SASB method has been investigated using simulations in Field II and by off-line processing of data acquired with a commercial scanner. The performance of SASB with a static image object is compared with DRF...

Towards a synthetic chloroplast.

Directory of Open Access Journals (Sweden)

Christina M Agapakis

2011-04-01

Full Text Available The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner.We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages.Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

Dependence of the Casimir-Polder interaction between an atom and a cavity wall on atomic and material properties

International Nuclear Information System (INIS)

Mostepanenko, V M; Babb, J F; Caride, A O; Klimchitskaya, G L; Zanette, S I

2006-01-01

The Casimir-Polder and van der Waals interactions between an atom and a flat cavity wall are investigated under the influence of real conditions including the dynamic polarizability of the atom, actual conductivity of the wall material and nonzero temperature of the wall. The cases of different atoms near metal and dielectric walls are considered. It is shown that to obtain accurate results for the atom-wall interaction at short separations, one should use the complete tabulated optical data for the complex refractive index of the wall material and the accurate dynamic polarizability of an atom. At relatively large separations in the case of a metal wall, one may use the plasma model dielectric function to describe the dielectric properties of the wall material. The obtained results are important for the theoretical interpretation of experiments on quantum reflection and Bose-Einstein condensation

Dependences of the van der Waals atom-wall interaction on atomic and material properties

International Nuclear Information System (INIS)

Caride, A.O.; Klimchitskaya, G.L.; Mostepanenko, V.M.; Zanette, S.I.

2005-01-01

The 1%-accurate calculations of the van der Waals interaction between an atom and a cavity wall are performed in the separation region from 3 nm to 150 nm. The cases of metastable He * and Na atoms near metal, semiconductor, and dielectric walls are considered. Different approximations to the description of wall material and atomic dynamic polarizability are carefully compared. The smooth transition to the Casimir-Polder interaction is verified. It is shown that to obtain accurate results for the atom-wall van der Waals interaction at short separations with an error less than 1% one should use the complete optical-tabulated data for the complex refractive index of the wall material and the accurate dynamic polarizability of an atom. The obtained results may be useful for the theoretical interpretation of recent experiments on quantum reflection and Bose-Einstein condensation of ultracold atoms on or near surfaces of different kinds

Prenatal sonographic diagnosis of limb-body wall complex: case series of a rare congenital anomaly

Directory of Open Access Journals (Sweden)

Arshad Bhat, MBBS, DMRD

2016-06-01

Full Text Available Three case reports of a rare congenital anomaly “limb-body wall complex” also known as “body stalk syndrome” are presented with prenatal ultrasonographic diagnostic features, immediate after delivery evaluation, and histopathologic analysis.

Centralized coordinated control to protect the JET ITER-like wall

International Nuclear Information System (INIS)

Stephen, A.V.; Arnoux, G.; Budd, T.; Card, P.; Felton, R.; Goodyear, A.; Harling, J.; Kinna, D.; Lomas, P.; McCullen, P.; Thomas, P.; Young, I.; Zastrow, K.D.; Neto, A.; Alves, D.; Valcarcel, D.F.; Jachmich, S.; Devaux, S.

2012-01-01

The JET ITER-like wall project (ILW) replaces the first wall carbon fibre composite tiles with beryllium and tungsten tiles which should have improved fuel retention characteristics but are less thermally robust. An enhanced protection system using new control and diagnostic systems has been designed which can modify the pre-planned experimental control to protect the new wall. Key design challenges were to extend the Level-1 supervisory control system to allow configurable responses to thermal problems to be defined without introducing excessive complexity, and to integrate the new functionality with existing control and protection systems efficiently and reliably. Alarms are generated by the vessel thermal map (VTM) system if infra-red camera measurements of tile temperatures are too high and by the plasma wall load system (WALLS) if component power limits are exceeded. The design introduces two new concepts: local protection, which inhibits individual heating components but allows the discharge to proceed, and stop responses, which allow highly configurable early termination of the pulse in the safest way for the plasma conditions and type of alarm. These are implemented via the new real-time protection system (RTPS), a centralized controller which responds to the VTM and WALLS alarms by providing override commands to the plasma shape, current, density and heating controllers. This paper describes the design and implementation of the RTPS system which is built with the Multi-threaded Application Real-Time executor (MARTe) and will present results from initial operations. (authors)

Plant cell wall sugars: sweeteners for a bio-based economy.

Science.gov (United States)

Van de Wouwer, Dorien; Boerjan, Wout; Vanholme, Bartel

2018-02-12

Global warming and the consequent climate change is one of the major environmental challenges we are facing today. The driving force behind the rise in temperature is our fossil-based economy, which releases massive amounts of the greenhouse gas carbon dioxide into the atmosphere. In order to reduce greenhouse gas emission, we need to scale down our dependency on fossil resources, implying that we need other sources for energy and chemicals to feed our economy. Here, plants have an important role to play; by means of photosynthesis, plants capture solar energy to split water and fix carbon derived from atmospheric carbon dioxide. A significant fraction of the fixed carbon ends up as polysaccharides in the plant cell wall. Fermentable sugars derived from cell wall polysaccharides form an ideal carbon source for the production of bio-platform molecules. However, a major limiting factor in the use of plant biomass as feedstock for the bio-based economy is the complexity of the plant cell wall and its recalcitrance towards deconstruction. To facilitate the release of fermentable sugars during downstream biomass processing, the composition and structure of the cell wall can be engineered. Different strategies to reduce cell wall recalcitrance will be described in this review. The ultimate goal is to obtain a tailor-made biomass, derived from plants with a cell wall optimized for particular industrial or agricultural applications, without affecting plant growth and development. This article is protected by copyright. All rights reserved.

Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity.

Directory of Open Access Journals (Sweden)

Miles Miller

Full Text Available Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeneity' that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism, demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a 'phenotypic sensitivity analysis' method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in

Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity.

Science.gov (United States)

Miller, Miles; Hafner, Marc; Sontag, Eduardo; Davidsohn, Noah; Subramanian, Sairam; Purnick, Priscilla E M; Lauffenburger, Douglas; Weiss, Ron

2012-01-01

Synthetic biology efforts have largely focused on small engineered gene networks, yet understanding how to integrate multiple synthetic modules and interface them with endogenous pathways remains a challenge. Here we present the design, system integration, and analysis of several large scale synthetic gene circuits for artificial tissue homeostasis. Diabetes therapy represents a possible application for engineered homeostasis, where genetically programmed stem cells maintain a steady population of β-cells despite continuous turnover. We develop a new iterative process that incorporates modular design principles with hierarchical performance optimization targeted for environments with uncertainty and incomplete information. We employ theoretical analysis and computational simulations of multicellular reaction/diffusion models to design and understand system behavior, and find that certain features often associated with robustness (e.g., multicellular synchronization and noise attenuation) are actually detrimental for tissue homeostasis. We overcome these problems by engineering a new class of genetic modules for 'synthetic cellular heterogeneity' that function to generate beneficial population diversity. We design two such modules (an asynchronous genetic oscillator and a signaling throttle mechanism), demonstrate their capacity for enhancing robust control, and provide guidance for experimental implementation with various computational techniques. We found that designing modules for synthetic heterogeneity can be complex, and in general requires a framework for non-linear and multifactorial analysis. Consequently, we adapt a 'phenotypic sensitivity analysis' method to determine how functional module behaviors combine to achieve optimal system performance. We ultimately combine this analysis with Bayesian network inference to extract critical, causal relationships between a module's biochemical rate-constants, its high level functional behavior in isolation, and

Evidence for a structural role for acid-fast lipids in oocyst walls of Cryptosporidium, Toxoplasma, and Eimeria.

Science.gov (United States)

Bushkin, G Guy; Motari, Edwin; Carpentieri, Andrea; Dubey, Jitender P; Costello, Catherine E; Robbins, Phillips W; Samuelson, John

2013-09-03

Coccidia are protozoan parasites that cause significant human disease and are of major agricultural importance. Cryptosporidium spp. cause diarrhea in humans and animals, while Toxoplasma causes disseminated infections in fetuses and untreated AIDS patients. Eimeria is a major pathogen of commercial chickens. Oocysts, which are the infectious form of Cryptosporidium and Eimeria and one of two infectious forms of Toxoplasma (the other is tissue cysts in undercooked meat), have a multilayered wall. Recently we showed that the inner layer of the oocyst walls of Toxoplasma and Eimeria is a porous scaffold of fibers of β-1,3-glucan, which are also present in fungal walls but are absent from Cryptosporidium oocyst walls. Here we present evidence for a structural role for lipids in the oocyst walls of Cryptosporidium, Toxoplasma, and Eimeria. Briefly, oocyst walls of each organism label with acid-fast stains that bind to lipids in the walls of mycobacteria. Polyketide synthases similar to those that make mycobacterial wall lipids are abundant in oocysts of Toxoplasma and Eimeria and are predicted in Cryptosporidium. The outer layer of oocyst wall of Eimeria and the entire oocyst wall of Cryptosporidium are dissolved by organic solvents. Oocyst wall lipids are complex mixtures of triglycerides, some of which contain polyhydroxy fatty acyl chains like those present in plant cutin or elongated fatty acyl chains like mycolic acids. We propose a two-layered model of the oocyst wall (glucan and acid-fast lipids) that resembles the two-layered walls of mycobacteria (peptidoglycan and acid-fast lipids) and plants (cellulose and cutin). Oocysts, which are essential for the fecal-oral spread of coccidia, have a wall that is thought responsible for their survival in the environment and for their transit through the stomach and small intestine. While oocyst walls of Toxoplasma and Eimeria are strengthened by a porous scaffold of fibrils of β-1,3-glucan and by proteins cross

Solution-phase synthesis of chromium-functionalized single-walled carbon nanotubes

KAUST Repository

Kalinina, Irina V.; Al-Hadeethi, Yas Fadel; Bekyarova, Elena; Zhao, Chao; Wang, Qingxiao; Zhang, Xixiang; Al-Zahrani, Ali; Al-Agel, Faisal Abdulaziz M; Al-Marzouki, Fahad M.; Haddon, Robert C.

2015-01-01

The solution phase reactions of single-walled carbon nanotubes (SWNTs) with Cr(CO)6 and benzene-Cr(CO)3 can lead to the formation of small chromium clusters. The cluster size can be varied from less than 1 nm to about 4 nm by increasing the reaction time. TEM images suggest that the clusters are deposited predominantly on the exterior walls of the nanotubes. TGA analysis was used to obtain the Cr content and carbon to chromium ratio in the Cr-complexed SWNTs. It is suggested that the carbon nanotube benzenoid structure templates the condensation of chromium atoms and facilitates the loss of carbon monoxide leading to well defined metal clusters.

Solution-phase synthesis of chromium-functionalized single-walled carbon nanotubes

KAUST Repository

Kalinina, Irina V.

2015-03-01

The solution phase reactions of single-walled carbon nanotubes (SWNTs) with Cr(CO)6 and benzene-Cr(CO)3 can lead to the formation of small chromium clusters. The cluster size can be varied from less than 1 nm to about 4 nm by increasing the reaction time. TEM images suggest that the clusters are deposited predominantly on the exterior walls of the nanotubes. TGA analysis was used to obtain the Cr content and carbon to chromium ratio in the Cr-complexed SWNTs. It is suggested that the carbon nanotube benzenoid structure templates the condensation of chromium atoms and facilitates the loss of carbon monoxide leading to well defined metal clusters.

Synthesis and self-assembly of complex hollow materials

KAUST Repository

Zeng, Hua Chun

2011-01-01

Hollow materials with interiors or voids and pores are a class of lightweight nanostructured matters that promise many future technological applications, and they have received significant research attention in recent years. On the basis of well-known physicochemical phenomena and principles, for example, several solution-based protocols have been developed for the general preparation of these complex materials under mild reaction conditions. This article is thus a short introductory review on the synthetic aspects of this field of development. The synthetic methodologies can be broadly divided into three major categories: (i) template-assisted synthesis, (ii) self-assembly with primary building blocks, and (iii) induced matter relocations. In most cases, both synthesis and self-assembly are involved in the above processes. Further combinations of these methodologies appear to be very important, as they will allow one to prepare functional materials at a higher level of complexity and precision. The synthetic strategies are introduced through some simple case studies with schematic illustrations. Salient features of the methods developed have been summarized, and some urgent issues of this field have also been indicated. © 2011 The Royal Society of Chemistry.

Synthetic Biology: Advancing Biological Frontiers by Building Synthetic Systems

OpenAIRE

Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D

2012-01-01

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

Magnetic forces on a ferromagnetic HT-9 first wall/blanket and coolant pipe

International Nuclear Information System (INIS)

Lechtenberg, T.A.; Dahms, C.; Attaya, H.; Univ. of Wisconsin, Madison)

1984-01-01

The GFUN 3D code was used to model the toroidal fields and determine the magnetic body forces on the STARFIRE design for coolant pipes exiting the first wall sector and first wall/blanket modules. The HT-9 coolant pipes were modeled on the basis of a square bar having the same length and material volume as the coolant pipes. The stress analysis was performed using these magnetic forces applied to a pipe of 4 meters length, 8.25 cm O.D., and 0.75 cm thickness by the MODSAP stress analysis code. For the first wall/blanket module, GFUN 3D does not allow full modeling of the complex thin-walled structure or numerous small tubes because of the element aspect ratio limitations. Therefore, to obtain three dimensional loads, a solid homogeneous equivalent structure was used

Synthetic biology: an emerging engineering discipline.

Science.gov (United States)

Cheng, Allen A; Lu, Timothy K

2012-01-01

Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

Synthetic peptides for antibody production

NARCIS (Netherlands)

N.D. Zegers (Netty)

1995-01-01

textabstractSynthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps

Synthetic LDL as targeted drug delivery vehicle

Science.gov (United States)

Forte, Trudy M [Berkeley, CA; Nikanjam, Mina [Richmond, CA

2012-08-28

The present invention provides a synthetic LDL nanoparticle comprising a lipid moiety and a synthetic chimeric peptide so as to be capable of binding the LDL receptor. The synthetic LDL nanoparticle of the present invention is capable of incorporating and targeting therapeutics to cells expressing the LDL receptor for diseases associated with the expression of the LDL receptor such as central nervous system diseases. The invention further provides methods of using such synthetic LDL nanoparticles.

Programming languages for synthetic biology.

Science.gov (United States)

Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

2010-12-01

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

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

Science.gov (United States)

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.

To retouch or not to retouch – reflections on the aesthetic completion of wall paintings

DEFF Research Database (Denmark)

Brajer, Isabelle Eve

2015-01-01

Decision-making regarding the aesthetic treatment of wall paintings can be a difficult and complex process due to the multifaceted issues that influence the choices. In addition, local views and national value assignations make it difficult to apply general guidelines for retouching. This paper...... describes general theoretical concerns presented on the backdrop of specific examples, illustrating a wide range of aesthetic solutions for wall paintings....

High frame rate synthetic aperture vector flow imaging for transthoracic echocardiography

Science.gov (United States)

Villagómez-Hoyos, Carlos A.; Stuart, Matthias B.; Bechsgaard, Thor; Nielsen, Michael Bachmann; Jensen, Jørgen Arendt

2016-04-01

This work presents the first in vivo results of 2-D high frame rate vector velocity imaging for transthoracic cardiac imaging. Measurements are made on a healthy volunteer using the SARUS experimental ultrasound scanner connected to an intercostal phased-array probe. Two parasternal long-axis view (PLAX) are obtained, one centred at the aortic valve and another centred at the left ventricle. The acquisition sequence was composed of 3 diverging waves for high frame rate synthetic aperture flow imaging. For verification a phantom measurement is performed on a transverse straight 5 mm diameter vessel at a depth of 100 mm in a tissue-mimicking phantom. A flow pump produced a 2 ml/s constant flow with a peak velocity of 0.2 m/s. The average estimated flow angle in the ROI was 86.22° +/- 6.66° with a true flow angle of 90°. A relative velocity bias of -39% with a standard deviation of 13% was found. In-vivo acquisitions show complex flow patterns in the heart. In the aortic valve view, blood is seen exiting the left ventricle cavity through the aortic valve into the aorta during the systolic phase of the cardiac cycle. In the left ventricle view, blood flow is seen entering the left ventricle cavity through the mitral valve and splitting in two ways when approximating the left ventricle wall. The work presents 2-D velocity estimates on the heart from a non-invasive transthoracic scan. The ability of the method detecting flow regardless of the beam angle could potentially reveal a more complete view of the flow patterns presented on the heart.

Synthetic biology as red herring.

Science.gov (United States)

Preston, Beth

2013-12-01

It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy. Copyright © 2013 Elsevier Ltd. All rights reserved.

US Competitiveness in Synthetic Biology.

Science.gov (United States)

Gronvall, Gigi Kwik

2015-01-01

Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

Cell Wall Remodeling Enzymes Modulate Fungal Cell Wall Elasticity and Osmotic Stress Resistance.

Science.gov (United States)

Ene, Iuliana V; Walker, Louise A; Schiavone, Marion; Lee, Keunsook K; Martin-Yken, Hélène; Dague, Etienne; Gow, Neil A R; Munro, Carol A; Brown, Alistair J P

2015-07-28

The fungal cell wall confers cell morphology and protection against environmental insults. For fungal pathogens, the cell wall is a key immunological modulator and an ideal therapeutic target. Yeast cell walls possess an inner matrix of interlinked β-glucan and chitin that is thought to provide tensile strength and rigidity. Yeast cells remodel their walls over time in response to environmental change, a process controlled by evolutionarily conserved stress (Hog1) and cell integrity (Mkc1, Cek1) signaling pathways. These mitogen-activated protein kinase (MAPK) pathways modulate cell wall gene expression, leading to the construction of a new, modified cell wall. We show that the cell wall is not rigid but elastic, displaying rapid structural realignments that impact survival following osmotic shock. Lactate-grown Candida albicans cells are more resistant to hyperosmotic shock than glucose-grown cells. We show that this elevated resistance is not dependent on Hog1 or Mkc1 signaling and that most cell death occurs within 10 min of osmotic shock. Sudden decreases in cell volume drive rapid increases in cell wall thickness. The elevated stress resistance of lactate-grown cells correlates with reduced cell wall elasticity, reflected in slower changes in cell volume following hyperosmotic shock. The cell wall elasticity of lactate-grown cells is increased by a triple mutation that inactivates the Crh family of cell wall cross-linking enzymes, leading to increased sensitivity to hyperosmotic shock. Overexpressing Crh family members in glucose-grown cells reduces cell wall elasticity, providing partial protection against hyperosmotic shock. These changes correlate with structural realignment of the cell wall and with the ability of cells to withstand osmotic shock. The C. albicans cell wall is the first line of defense against external insults, the site of immune recognition by the host, and an attractive target for antifungal therapy. Its tensile strength is conferred by

Synthetic Biology: Mapping the Scientific Landscape

Science.gov (United States)

Oldham, Paul; Hall, Stephen; Burton, Geoff

2012-01-01

This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves. PMID:22539946

Mass spectrometry for characterizing plant cell wall polysaccharides

Directory of Open Access Journals (Sweden)

Stefan eBauer

2012-03-01

Full Text Available Mass spectrometry is a selective and powerful technique to obtain identification and structural information on compounds present in complex mixtures. Since it requires only small sample amount it is an excellent tool for researchers interested in detecting changes in composition of complex carbohydrates of plants. This mini-review gives an overview of common mass spectrometry techniques applied to the analysis of plant cell wall carbohydrates. It presents examples in which mass spectrometry has been used to elucidate the structure of oligosaccharides derived from hemicelluloses and pectins and illustrates how information on sequence, linkages, branching and modifications are obtained from characteristic fragmentation patterns.

Solar Walls in tsbi3

DEFF Research Database (Denmark)

Wittchen, Kim Bjarne

tsbi3 is a user-friendly and flexible computer program, which provides support to the design team in the analysis of the indoor climate and the energy performance of buildings. The solar wall module gives tsbi3 the capability of simulating solar walls and their interaction with the building....... This version, C, of tsbi3 is capable of simulating five types of solar walls say: mass-walls, Trombe-walls, double Trombe-walls, internally ventilated walls and solar walls for preheating ventilation air. The user's guide gives a description of the capabilities and how to simulate solar walls in tsbi3....

Lipoproteins/peptides are sepsis-inducing toxins from bacteria that can be neutralized by synthetic anti-endotoxin peptides.

Science.gov (United States)

Martinez de Tejada, Guillermo; Heinbockel, Lena; Ferrer-Espada, Raquel; Heine, Holger; Alexander, Christian; Bárcena-Varela, Sergio; Goldmann, Torsten; Correa, Wilmar; Wiesmüller, Karl-Heinz; Gisch, Nicolas; Sánchez-Gómez, Susana; Fukuoka, Satoshi; Schürholz, Tobias; Gutsmann, Thomas; Brandenburg, Klaus

2015-09-22

Sepsis, a life-threatening syndrome with increasing incidence worldwide, is triggered by an overwhelming inflammation induced by microbial toxins released into the bloodstream during infection. A well-known sepsis-inducing factor is the membrane constituent of Gram-negative bacteria, lipopolysaccharide (LPS), signalling via Toll-like receptor-4. Although sepsis is caused in more than 50% cases by Gram-positive and mycoplasma cells, the causative compounds are still poorly described. In contradicting investigations lipoproteins/-peptides (LP), lipoteichoic acids (LTA), and peptidoglycans (PGN), were made responsible for eliciting this pathology. Here, we used human mononuclear cells from healthy donors to determine the cytokine-inducing activity of various LPs from different bacterial origin, synthetic and natural, and compared their activity with that of natural LTA and PGN. We demonstrate that LP are the most potent non-LPS pro-inflammatory toxins of the bacterial cell walls, signalling via Toll-like receptor-2, not only in vitro, but also when inoculated into mice: A synthetic LP caused sepsis-related pathological symptoms in a dose-response manner. Additionally, these mice produced pro-inflammatory cytokines characteristic of a septic reaction. Importantly, the recently designed polypeptide Aspidasept(®) which has been proven to efficiently neutralize LPS in vivo, inhibited cytokines induced by the various non-LPS compounds protecting animals from the pro-inflammatory activity of synthetic LP.

Synthetic peptides for antibody production

NARCIS (Netherlands)

Zegers, N.D.

1995-01-01

Synthetic peptides are useful tools for the generation of antibodies. The use of antibodies as specific reagents in inununochemical assays is widely applied. In this chapter, the application of synthetic peptides for the generation of antibodies is described. The different steps that lead to the

The Ethics of Synthetic Biology

DEFF Research Database (Denmark)

Christiansen, Andreas

The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

Content metamorphosis in synthetic holography

International Nuclear Information System (INIS)

Desbiens, Jacques

2013-01-01

A synthetic hologram is an optical system made of hundreds of images amalgamated in a structure of holographic cells. Each of these images represents a point of view on a three-dimensional space which makes us consider synthetic holography as a multiple points of view perspective system. In the composition of a computer graphics scene for a synthetic hologram, the field of view of the holographic image can be divided into several viewing zones. We can attribute these divisions to any object or image feature independently and operate different transformations on image content. In computer generated holography, we tend to consider content variations as a continuous animation much like a short movie. However, by composing sequential variations of image features in relation with spatial divisions, we can build new narrative forms distinct from linear cinematographic narration. When observers move freely and change their viewing positions, they travel from one field of view division to another. In synthetic holography, metamorphoses of image content are within the observer's path. In all imaging Medias, the transformation of image features in synchronisation with the observer's position is a rare occurrence. However, this is a predominant characteristic of synthetic holography. This paper describes some of my experimental works in the development of metamorphic holographic images.

Plant cell walls throughout evolution: towards a molecular understanding of their design principles.

Science.gov (United States)

Sarkar, Purbasha; Bosneaga, Elena; Auer, Manfred

2009-01-01

Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche, which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are constantly remodelled and reconstructed during the development of an individual plant, and in response to environmental stress or pathogen attacks. Carbohydrate-rich cell walls display complex designs, which together with the presence of phenolic polymers constitutes a barrier for microbes, fungi, and animals. Throughout evolution microbes have co-evolved strategies for efficient breakdown of cell walls. Our current understanding of cell walls and their evolutionary changes are limited as our knowledge is mainly derived from biochemical and genetic studies, complemented by a few targeted yet very informative imaging studies. Comprehensive plant cell wall models will aid in the re-design of plant cell walls for the purpose of commercially viable lignocellulosic biofuel production as well as for the timber, textile, and paper industries. Such knowledge will also be of great interest in the context of agriculture and to plant biologists in general. It is expected that detailed plant cell wall models will require integrated correlative multimodal, multiscale imaging and modelling approaches, which are currently underway.

Plant cell walls throughout evolution: towards a molecular understanding of their design principles

Energy Technology Data Exchange (ETDEWEB)

Sarkar, Purbasha; Bosneaga, Elena; Auer, Manfred

2009-02-16

Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche,which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are constantly remodelled and reconstructed during the development of an individual plant, and in response to environmental stress or pathogen attacks. Carbohydrate-rich cell walls display complex designs, which together with the presence of phenolic polymers constitutes a barrier for microbes, fungi, and animals. Throughout evolution microbes have co-evolved strategies for efficient breakdown of cell walls. Our current understanding of cell walls and their evolutionary changes are limited as our knowledge is mainly derived from biochemical and genetic studies, complemented by a few targeted yet very informative imaging studies. Comprehensive plant cell wall models will aid in the re-design of plant cell walls for the purpose of commercially viable lignocellulosic biofuel production as well as for the timber, textile, and paper industries. Such knowledge will also be of great interest in the context of agriculture and to plant biologists in general. It is expected that detailed plant cell wall models will require integrated correlative multimodal, multiscale imaging and modelling approaches, which are currently underway.

Multiply-Imputed Synthetic Data: Advice to the Imputer

Directory of Open Access Journals (Sweden)

Loong Bronwyn

2017-12-01

Full Text Available Several statistical agencies have started to use multiply-imputed synthetic microdata to create public-use data in major surveys. The purpose of doing this is to protect the confidentiality of respondents’ identities and sensitive attributes, while allowing standard complete-data analyses of microdata. A key challenge, faced by advocates of synthetic data, is demonstrating that valid statistical inferences can be obtained from such synthetic data for non-confidential questions. Large discrepancies between observed-data and synthetic-data analytic results for such questions may arise because of uncongeniality; that is, differences in the types of inputs available to the imputer, who has access to the actual data, and to the analyst, who has access only to the synthetic data. Here, we discuss a simple, but possibly canonical, example of uncongeniality when using multiple imputation to create synthetic data, which specifically addresses the choices made by the imputer. An initial, unanticipated but not surprising, conclusion is that non-confidential design information used to impute synthetic data should be released with the confidential synthetic data to allow users of synthetic data to avoid possible grossly conservative inferences.

Detection of extracellular neutrophil elastase in hamster lungs after intratracheal instillation of E. coli lipopolysaccharide using a fluorogenic, elastase-specific, synthetic substrate.

Science.gov (United States)

Rudolphus, A.; Stolk, J.; van Twisk, C.; van Noorden, C. J.; Dijkman, J. H.; Kramps, J. A.

1992-01-01

Repeated intratracheal instillations of E. coli lipopolysaccharide (LPS) in hamster lungs cause an influx of polymorphonuclear leukocytes (PMNs) into the alveolar walls, with concomitant development of severe emphysema. It has been suggested that elastase, released by these PMNs, is involved in the development of emphysema. This study demonstrates the release of elastase from recruited PMNs in cryostat sections of hamster lungs, after being treated once, twice, or thrice with LPS, intratracheally. Elastase activity was visualized using two elastase-specific synthetic substrates, to which a methoxynaphthylamine (MNA) group had been bound covalently. Liberated MNA, when made insoluble by coupling with 5-nitrosalicylaldehyde, fluoresces strongly. The authors observed that the interval between start of incubation and appearance of fluorescence and the intensity of fluorescence correlated with the number of LPS administrations. Fluorescence was observed to be located in or in close vicinity to alveolar walls. No fluorescence was observed in sections of untreated hamsters. Liberation of MNA from synthetic substrates was delayed strongly by the addition of a recombinant secretory leukocyte proteinase inhibitor or a substituted cephalosporin neutrophil elastase inhibitor. The authors conclude that LPS-mediated PMN influx into the lung is accompanied by release of elastase from these cells and speculate that this PMN-elastase is involved in the development of LPS-mediated emphysema. Images Figure 1 Figure 2 Figure 3 PMID:1632460

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

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

Remote parallel rendering for high-resolution tiled display walls

KAUST Repository

Nachbaur, Daniel; Dumusc, Raphael; Bilgili, Ahmet; Hernando, Juan; Eilemann, Stefan

2014-01-01

© 2014 IEEE. We present a complete, robust and simple to use hardware and software stack delivering remote parallel rendering of complex geometrical and volumetric models to high resolution tiled display walls in a production environment. We describe the setup and configuration, present preliminary benchmarks showing interactive framerates, and describe our contributions for a seamless integration of all the software components.

Remote parallel rendering for high-resolution tiled display walls

KAUST Repository

Nachbaur, Daniel

2014-11-01

© 2014 IEEE. We present a complete, robust and simple to use hardware and software stack delivering remote parallel rendering of complex geometrical and volumetric models to high resolution tiled display walls in a production environment. We describe the setup and configuration, present preliminary benchmarks showing interactive framerates, and describe our contributions for a seamless integration of all the software components.

Synthetic cannabis and acute ischemic stroke.

Science.gov (United States)

Bernson-Leung, Miya E; Leung, Lester Y; Kumar, Sandeep

2014-01-01

An association between marijuana use and stroke has been previously reported. However, the health risks of newer synthetic cannabinoid compounds are less well known. We describe 2 cases that introduce a previously unreported association between synthetic cannabis use and ischemic stroke in young adults. A 22-year-old woman presented with dysarthria, left hemiplegia, and left hemianesthesia within hours of first use of synthetic cannabis. She was healthy and without identified stroke risk factors other than oral contraceptive use and a patent foramen ovale without venous thromboses. A 26-year-old woman presented with nonfluent aphasia, left facial droop, and left hemianesthesia approximately 12 hours after first use of synthetic cannabis. Her other stroke risk factors included migraine with aura, oral contraceptive use, smoking, and a family history of superficial thrombophlebitis. Both women were found to have acute, large-territory infarctions of the right middle cerebral artery. Our 2 cases had risk factors for ischemic stroke but were otherwise young and healthy and the onset of their deficits occurred within hours after first-time exposure to synthetic cannabis. Synthetic cannabis use is an important consideration in the investigation of stroke in young adults. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

Synthetic Aziridines in Medicinal Chemistry: A Mini-Review.

Science.gov (United States)

Singh, Girija S

2016-01-01

Azaheterocyclic compounds are well-known to have diverse types of biological activity. Among them, azacyclopropanes, commonly referred as aziridines, occupy a prominent place in synthetic organic and medicinal chemistry due to its occurrence in natural resources, complexity involved in synthesis due to ring-strain, building blocks in organic synthesis, and its biological properties. Several novel compounds containing aziridine ring have been designed and synthesized recently by medicinal chemists for evaluating their biological profile. A number of compounds are reported as cysteine protease inhibitors, antibacterial, antifungal, anticancer, antileishmanial, and antimalarial agents. This review article summarizes the biological activity of such compounds. The preparation of such compounds is also described.

Landslide rehabilitation with geo synthetics in open coal mine Oslomej

International Nuclear Information System (INIS)

Dimitrievski, Ljupcho; Ilievska, Frosina; Ilievski, Darko

2004-01-01

In November 2002 stability is violated and landslides are registered in open coal mine Oslomej, Republic of Macedonia. Around the profile IV existing open irrigation channel was interrupted and landslide was extended to the regional way R421 Kicevo - Oslomej. The landslide was classified like big and dangerous, including danger for disruption of the regional road and pipeline Studencica - Oslomej for supplying of thermal power plant Oslomej with technical water. According to the proposed solution, main project design for landslide rehabilitation was prepared with using geo synthetics Stabilenka 200/45. In fill is local soil material which had been placed and compacted in layers, it had formed a composite construction. Stabilenka acts as a reinforcement due to its ability to absorb tensile forces. With the design solution two retaining walls of reinforced soil and complete drainage system of geo composite materials had been constructed This paper deals with details of the design and the construction. (Author)

Characteristics and fabrication of Geiger-Mueller counters with thin walls made of treated magnesium - Note about the use of araldite

International Nuclear Information System (INIS)

Charbonnel, A.

1949-03-01

This report describes, first, the advantage of magnesium for the manufacturing of Geiger-Mueller counters: suitable for machining and polishing, but strong reactivity with the counter atmosphere in the case of magnesium-rich alloys. Thus, the inside wall of the counter (cylinder of 20 mm diameter and 6 cm length) requires a non-reactive protective coating with excellent sealing properties. The synthetic resin 'araldite' fulfills all these conditions. The second part of the report describes the different steps of the fabrication of magnesium wall counters: lathe work, machining down and chemical polishing of hulls, assembly, tight sealing, pumping, filling-up and control tests. The average service life of these counters is of about 4 months. A note about the use and properties (hardening, mechanical properties, resistance..) of araldite is given in appendix. (J.S.)

Finite element limit loads for non-idealized through-wall cracks in thick-walled pipe

International Nuclear Information System (INIS)

Shim, Do-Jun; Han, Tae-Song; Huh, Nam-Su

2013-01-01

Highlights: • The lower bound bulging factor of thin-walled pipe can be used for thick-walled pipe. • The limit loads are proposed for thick-walled, transition through-wall cracked pipe. • The correction factors are proposed for estimating limit loads of transition cracks. • The limit loads of short transition cracks are similar to those of idealized cracks. - Abstract: The present paper provides plastic limit loads for non-idealized through-wall cracks in thick-walled pipe. These solutions are based on detailed 3-dimensional finite element (FE) analyses which can be used for structural integrity assessment of nuclear piping. To cover a practical range of interest, the geometric variables and loading conditions affecting the plastic limit loads of thick-walled pipe with non-idealized through-wall cracks were systematically varied. In terms of crack orientation, both circumferential and axial through-wall cracks were considered. As for loading conditions, axial tension, global bending, and internal pressure were considered for circumferential cracks, whereas only internal pressure was considered for axial cracks. Furthermore, the values of geometric factor representing shape characteristics of non-idealized through-wall cracks were also systematically varied. In order to provide confidence in the present FE analyses results, plastic limit loads of un-cracked, thick-walled pipe resulting from the present FE analyses were compared with the theoretical solutions. Finally, correction factors to the idealized through-wall crack solutions were developed to determine the plastic limit loads of non-idealized through-wall cracks in thick-walled pipe

Towards a synthetic osteo-odonto-keratoprosthesis.

Science.gov (United States)

Viitala, Reeta; Franklin, Valerie; Green, David; Liu, Christopher; Lloyd, Andrew; Tighe, Brian

2009-01-01

Osteo-odonto-keratoprostheses (OOKP) is a unique form of keratoprosthesis involving surgical removal of a tooth root and surrounding bone from the patient which are then used to construct an osteo-odonto lamina into which an optical cylinder is cemented. The OOKP procedure is successful and capable of withstanding the very hostile ocular environments found in severe Stevens-Johnson syndrome, pemphigoid, chemical burns, trachoma and multiple corneal graft failure. The existing procedure is complex and time consuming in terms of operative time, and additionally involves sacrifice of the oral structures. This paper discusses the rational search for a "synthetic" analogue of the dental lamina, capable of mimicking those features of the natural system that are responsible for the success of OOKP. In this study the degradation of selected commercial and natural bioceramics was tested in vitro using a purpose-designed resorption assay. Degradation rate was compared with tooth and bone, which are currently used in OOKP lamina. At normal physiological pH the degradation of bioceramics was equivalent to tooth and bone; however, at pH 6.5-5.0, associated with infectious and inflamed tissues, the bioceramics degrade more rapidly. At lower pH the degradation rate decreased in the following order: calcium carbonate corals>biphasic calcium phosphates>hydroxyapatite. Porosity did not significantly influence these degradation rates. Such degradation is likely to compromise the stability and viability of the synthetic OOKP. Consequently more chemically stable materials are required that are optimized for the surrounding ocular environment.

Dynamic modeling and response of soil-wall systems

International Nuclear Information System (INIS)

Veletsos, A.S.; Younan, A.H.

1993-10-01

The study reported herein is the third in a series of investigations motivated by need to gain improved understanding of the responses to earthquakes of deeply embedded and underground tanks storing radioactive wastes, and to develop rational but simple methods of analysis and design for such systems. Following a brief review of the errors that may result from the use of a popular model for evaluating the dynamic soil forces induced in a base-excited rigid wall retaining an elastic stratum, the sources of the errors are identified and a modification is proposed which defines correctly the action of the system. In the proposed modification, the stratum is modeled by a series of elastically supported, semi-infinite horizontal bars with distributed mass instead of massless springs. The concepts involved are introduced by reference to a system composed of a fixed-based wall and a homogeneous elastic stratum, and are then applied to the analysis of more complex soil-wall systems. Both harmonic and transient excitations are considered, and comprehensive numerical solutions are presented which elucidate the actions involved and the effects and relative importance of the relevant parameters

Interaction and modulation of two antagonistic cell wall enzymes of mycobacteria.

Directory of Open Access Journals (Sweden)

Erik C Hett

2010-07-01

Full Text Available Bacterial cell growth and division require coordinated cell wall hydrolysis and synthesis, allowing for the removal and expansion of cell wall material. Without proper coordination, unchecked hydrolysis can result in cell lysis. How these opposing activities are simultaneously regulated is poorly understood. In Mycobacterium tuberculosis, the resuscitation-promoting factor B (RpfB, a lytic transglycosylase, interacts and synergizes with Rpf-interacting protein A (RipA, an endopeptidase, to hydrolyze peptidoglycan. However, it remains unclear what governs this synergy and how it is coordinated with cell wall synthesis. Here we identify the bifunctional peptidoglycan-synthesizing enzyme, penicillin binding protein 1 (PBP1, as a RipA-interacting protein. PBP1, like RipA, localizes both at the poles and septa of dividing cells. Depletion of the ponA1 gene, encoding PBP1 in M. smegmatis, results in a severe growth defect and abnormally shaped cells, indicating that PBP1 is necessary for viability and cell wall stability. Finally, PBP1 inhibits the synergistic hydrolysis of peptidoglycan by the RipA-RpfB complex in vitro. These data reveal a post-translational mechanism for regulating cell wall hydrolysis and synthesis through protein-protein interactions between enzymes with antagonistic functions.

Vibration improved the fluidity of aluminum alloys in thin wall ...

African Journals Online (AJOL)

Misrun is a term used to describe the incomplete filling of the mould cavity. It is a major defect in the investment casting process when used to produce turbine blades, impellers and impulse blades for turbo pumps which have complex profiles, thin walls and sharp edges. From the casting engineering point of view, poor ...

The effect of adiabatic and conducting wall boundary conditions on LES of a thermal mixing tee

International Nuclear Information System (INIS)

Howard, Richard J.A.; Pasutto, Thomas

2009-01-01

In this paper preliminary LES simulations are carried out of the FATHERINO mixing T junction experiment. In this experiment 80degC hot water enters a lateral steel pipe which has a diameter of D=0.054m, at a speed of 1.04m/s and meets 5degC cold water which enters a perpendicular steel pipe branch that also has a diameter D=0.054m but this time at a lower speed of 0.26m/s. The modelling of the steel pipe walls is tested by comparing adiabatic and 1D conducting wall boundary conditions. The numerical grid used contains approximately 440,000 hexahedral elements. The near wall refinement is not sufficient to resolve the near wall boundary layer (y + approx. = 32) and a standard logarithmic boundary condition is used. A method known as the synthetic eddy method is used to generate the turbulent flow at the pipe inlets. Three different LES models are used (Smagorinsky, dynamic Smagorinsky and wale) to resolve the subgrid turbulent motion beyond the wall grid. An additional test is carried out where no subgrid model is used with only the wall modelling being applied. The results show that the wale model generates much less resolved turbulence than the other cases and this model shows virtually no difference between the two methods of wall thermal modelling. The dynamic Smagorinsky model shows that, downstream of the mixing T, the lower wall remains at a lower temperature for longer when the adiabatic boundary condition is applied. The Smagorinsky model is found to produce the highest level of resolved temperature fluctuation. For this model the 1D thermal modelling approach increases the unsteadiness of both the velocity and temperature fields at the onset of the mixing and in the middle of the pipe downstream of the T junction. However near the lower wall the 1D thermal modelling approach tends to reduce the unsteadiness. The case with no subgrid modelling shows higher levels of turbulence kinetic energy but lower levels of temperature fluctuation than the cases with

A morphospace for synthetic organs and organoids: the possible and the actual.