Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae.

PubMed

Seth-Smith, Helena M B; Fookes, Maria C; Okoro, Chinyere K; Baker, Stephen; Harris, Simon R; Scott, Paul; Pickard, Derek; Quail, Michael A; Churcher, Carol; Sanders, Mandy; Harmse, Johan; Dougan, Gordon; Parkhill, Julian; Thomson, Nicholas R

2012-03-01

Integrative and conjugative elements (ICEs) are self-mobile genetic elements found in the genomes of some bacteria. These elements may confer a fitness advantage upon their host bacteria through the cargo genes that they carry. Salmonella pathogenicity island 7 (SPI-7), found within some pathogenic strains of Salmonella enterica, possesses features indicative of an ICE and carries genes implicated in virulence. We aimed to identify and fully analyze ICEs related to SPI-7 within the genus Salmonella and other Enterobacteriaceae. We report the sequence of two novel SPI-7-like elements, found within strains of Salmonella bongori, which share 97% nucleotide identity over conserved regions with SPI-7 and with each other. Although SPI-7 within Salmonella enterica serovar Typhi appears to be fixed within the chromosome, we present evidence that these novel elements are capable of excision and self-mobility. Phylogenetic analyses show that these Salmonella mobile elements share an ancestor which existed approximately 3.6 to 15.8 million years ago. Additionally, we identified more distantly related ICEs, with distinct cargo regions, within other strains of Salmonella as well as within Citrobacter, Erwinia, Escherichia, Photorhabdus, and Yersinia species. In total, we report on a collection of 17 SPI-7 related ICEs within enterobacterial species, of which six are novel. Using comparative and mutational studies, we have defined a core of 27 genes essential for conjugation. We present a growing family of SPI-7-related ICEs whose mobility, abundance, and cargo variability indicate that these elements may have had a large impact on the evolution of the Enterobacteriaceae.

Tn5253 family integrative and conjugative elements carrying mef(I) and catQ determinants in Streptococcus pneumoniae and Streptococcus pyogenes.

PubMed

Mingoia, Marina; Morici, Eleonora; Morroni, Gianluca; Giovanetti, Eleonora; Del Grosso, Maria; Pantosti, Annalisa; Varaldo, Pietro E

2014-10-01

The linkage between the macrolide efflux gene mef(I) and the chloramphenicol inactivation gene catQ was first described in Streptococcus pneumoniae (strain Spn529), where the two genes are located in a module designated IQ element. Subsequently, two different defective IQ elements were detected in Streptococcus pyogenes (strains Spy029 and Spy005). The genetic elements carrying the three IQ elements were characterized, and all were found to be Tn5253 family integrative and conjugative elements (ICEs). The ICE from S. pneumoniae (ICESpn529IQ) was sequenced, whereas the ICEs from S. pyogenes (ICESpy029IQ and ICESpy005IQ, the first Tn5253-like ICEs reported in this species) were characterized by PCR mapping, partial sequencing, and restriction analysis. ICESpn529IQ and ICESpy029IQ were found to share the intSp 23FST81 integrase gene and an identical Tn916 fragment, whereas ICESpy005IQ has int5252 and lacks Tn916. All three ICEs were found to lack the linearized pC194 plasmid that is usually associated with Tn5253-like ICEs, and all displayed a single copy of a toxin-antitoxin operon that is typically contained in the direct repeats flanking the excisable pC194 region when this region is present. Two different insertion sites of the IQ elements were detected, one in ICESpn529IQ and ICESpy029IQ, and another in ICESpy005IQ. The chromosomal integration of the three ICEs was site specific, depending on the integrase (intSp 23FST81 or int5252). Only ICESpy005IQ was excised in circular form and transferred by conjugation. By transformation, mef(I) and catQ were cotransferred at a high frequency from S. pyogenes Spy005 and at very low frequencies from S. pneumoniae Spn529 and S. pyogenes Spy029. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Redefinition and unification of the SXT/R391 family of integrative and conjugative elements.

PubMed

Bioteau, Audrey; Durand, Romain; Burrus, Vincent

2018-04-13

Integrative and conjugative elements (ICEs) of the SXT/R391 family are key drivers of the spread of antibiotic resistance in Vibrio cholerae , the infectious agent of cholera, and other pathogenic bacteria. The SXT/R391 family of ICEs was defined based on the conservation of a core set of 52 genes and site-specific integration into the 5' end of the chromosomal gene prfC Hence, the integrase gene int has been intensively used as a marker to detect SXT/R391 ICEs in clinical isolates. ICEs sharing most core genes but differing by their integration site and integrase gene have been recently reported and excluded from the SXT/R391 family. Here we explored the prevalence and diversity of atypical ICEs in Genbank databases and their relationship with typical SXT/R391 ICEs. We found atypical ICEs in V. cholerae isolates that predate the emergence and expansion of typical SXT/R391 ICEs in the mid-1980s in seventh pandemic toxigenic V. cholerae O1 and O139 strains. Our analyses revealed that while atypical ICEs are not associated with antibiotic resistance genes, they often carry cation efflux pumps suggesting heavy metal resistance. Atypical ICEs constitute a polyphyletic group likely because of occasional recombination events with typical ICEs. Furthermore, we show that the alternative integration and excision genes of atypical ICEs remain under the control of SetCD, the main activator of the conjugative functions of SXT/R391 ICEs. Together these observations indicate that substitution of the integration/excision module and change of specificity of integration do not preclude atypical ICEs from inclusion into the SXT/R391 family. Importance Vibrio cholerae is the causative agent of cholera, an acute intestinal infection that remains to this day a world public health threat. Integrative and conjugative elements (ICEs) of the SXT/R391 family have played a major role in spreading antimicrobial resistance in seventh pandemic V. cholerae but also in several species of Enterobacteriaceae Most epidemiological surveys use the integrase gene as a marker to screen for SXT/R391 ICEs in clinical or environmental strains. With the recent reports of closely related elements that encode an alternative integrase gene, it became urgent to investigate whether ICEs that have been left out of the family are a liability for the accuracy of such screenings. In this study based on comparative genomics, we broaden the SXT/R391 family of ICEs to include atypical ICEs that are often associated with heavy metal resistance. Copyright © 2018 American Society for Microbiology.

A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity.

PubMed

Fischer, Wolfgang; Breithaupt, Ute; Kern, Beate; Smith, Stella I; Spicher, Carolin; Haas, Rainer

2014-04-27

The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to changing environmental conditions during long-term colonization. This variability is reflected by the fact that almost each infected individual is colonized by a genetically unique strain. Strain-specific genes are dispersed throughout the genome, but clusters of genes organized as genomic islands may also collectively be present or absent. We have comparatively analysed such clusters, which are commonly termed plasticity zones, in a high number of H. pylori strains of varying geographical origin. We show that these regions contain fixed gene sets, rather than being true regions of genome plasticity, but two different types and several subtypes with partly diverging gene content can be distinguished. Their genetic diversity is incongruent with variations in the rest of the genome, suggesting that they are subject to horizontal gene transfer within H. pylori populations. We identified 40 distinct integration sites in 45 genome sequences, with a conserved heptanucleotide motif that seems to be the minimal requirement for integration. The significant number of possible integration sites, together with the requirement for a short conserved integration motif and the high level of gene conservation, indicates that these elements are best described as integrating conjugative elements (ICEs) with an intermediate integration site specificity.

A combined finite element-boundary integral formulation for solution of two-dimensional scattering problems via CGFFT. [Conjugate Gradient Fast Fourier Transformation

NASA Technical Reports Server (NTRS)

Collins, Jeffery D.; Volakis, John L.; Jin, Jian-Ming

1990-01-01

A new technique is presented for computing the scattering by 2-D structures of arbitrary composition. The proposed solution approach combines the usual finite element method with the boundary-integral equation to formulate a discrete system. This is subsequently solved via the conjugate gradient (CG) algorithm. A particular characteristic of the method is the use of rectangular boundaries to enclose the scatterer. Several of the resulting boundary integrals are therefore convolutions and may be evaluated via the fast Fourier transform (FFT) in the implementation of the CG algorithm. The solution approach offers the principal advantage of having O(N) memory demand and employs a 1-D FFT versus a 2-D FFT as required with a traditional implementation of the CGFFT algorithm. The speed of the proposed solution method is compared with that of the traditional CGFFT algorithm, and results for rectangular bodies are given and shown to be in excellent agreement with the moment method.

The Tcp conjugation system of Clostridium perfringens.

PubMed

Wisniewski, Jessica A; Rood, Julian I

2017-05-01

The Gram-positive pathogen Clostridium perfringens possesses a family of large conjugative plasmids that is typified by the tetracycline resistance plasmid pCW3. Since these plasmids may carry antibiotic resistance genes or genes encoding extracellular or sporulation-associated toxins, the conjugative transfer of these plasmids appears to be important for the epidemiology of C. perfringens-mediated diseases. Sequence analysis of members of this plasmid family identified a highly conserved 35kb region that encodes proteins with various functions, including plasmid replication and partitioning. The tcp conjugation locus also was identified in this region, initially based on low-level amino acid sequence identity to conjugation proteins from the integrative conjugative element Tn916. Genetic studies confirmed that the tcp locus is required for conjugative transfer and combined with biochemical and structural analyses have led to the development of a functional model of the Tcp conjugation apparatus. This review summarises our current understanding of the Tcp conjugation system, which is now one of the best-characterized conjugation systems in Gram-positive bacteria. Copyright © 2017 Elsevier Inc. All rights reserved.

The hidden life of integrative and conjugative elements

PubMed Central

Delavat, François; Miyazaki, Ryo; Carraro, Nicolas; Pradervand, Nicolas

2017-01-01

Abstract Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE–host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE ‘fitness’). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells. PMID:28369623

Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer

PubMed Central

Lorenzo-Diaz, Fabian; Fernández-Lopez, Cris; Douarre, Pierre-Emmanuel; Baez-Ortega, Adrian; Flores, Carlos; Glaser, Philippe

2016-01-01

Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3′-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A–J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOBV1. Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs. PMID:27707895

Streptococcal group B integrative and mobilizable element IMESag-rpsI encodes a functional relaxase involved in its transfer.

PubMed

Lorenzo-Diaz, Fabian; Fernández-Lopez, Cris; Douarre, Pierre-Emmanuel; Baez-Ortega, Adrian; Flores, Carlos; Glaser, Philippe; Espinosa, Manuel

2016-10-01

Streptococcus agalactiae or Group B Streptococcus (GBS) are opportunistic bacteria that can cause lethal sepsis in children and immuno-compromised patients. Their genome is a reservoir of mobile genetic elements that can be horizontally transferred. Among them, integrative and conjugative elements (ICEs) and the smaller integrative and mobilizable elements (IMEs) primarily reside in the bacterial chromosome, yet have the ability to be transferred between cells by conjugation. ICEs and IMEs are therefore a source of genetic variability that participates in the spread of antibiotic resistance. Although IMEs seem to be the most prevalent class of elements transferable by conjugation, they are poorly known. Here, we have studied a GBS-IME, termed IMESag-rpsI, which is widely distributed in GBS despite not carrying any apparent virulence trait. Analyses of 240 whole genomes showed that IMESag-rpsI is present in approximately 47% of the genomes, has a roughly constant size (approx. 9 kb) and is always integrated at a single location, the 3'-end of the gene encoding the ribosomal protein S9 (rpsI). Based on their genetic variation, several IMESag-rpsI types were defined (A-J) and classified in clonal complexes (CCs). CC1 was the most populated by IMESag-rpsI (more than 95%), mostly of type-A (71%). One CC1 strain (S. agalactiae HRC) was deep-sequenced to understand the rationale underlying type-A IMESag-rpsI enrichment in GBS. Thirteen open reading frames were identified, one of them encoding a protein (MobSag) belonging to the broadly distributed family of relaxases MOB V1 Protein MobSag was purified and, by a newly developed method, shown to cleave DNA at a specific dinucleotide. The S. agalactiae HRC-IMESag-rpsI is able to excise from the chromosome, as shown by the presence of circular intermediates, and it harbours a fully functional mobilization module. Further, the mobSag gene encoded by this mobile element is able to promote plasmid transfer among pneumococcal strains, suggesting that MobSag facilitates the spread of IMESag-rpsI and that this spread would explain the presence of the same IMESag-rpsI type in GBS strains belonging to different CCs. © 2016 The Authors.

Characterisation of a novel integrative and conjugative element ICESsD9 carrying erm(B) and tet(O) resistance determinants in Streptococcus suis, and the distribution of ICESsD9-like elements in clinical isolates.

PubMed

Huang, Kaisong; Song, Yajing; Zhang, Qiang; Zhang, Anding; Jin, Meilin

2016-12-01

This study identified a novel integrative and conjugative element (ICESsD9) carrying erm(B) and tet(O) resistance determinants in Streptococcus suis D9 and determined its prevalence in clinical isolates. Comparative genome analysis was performed using Mauve and Artemis Comparison Tool visualisation programs. Inverse PCR was utilised to detect its circular intermediate. The transfer capacity of ICESsD9 was evaluated by mating assays using S. suis A7 and Enterococcus faecalis JH2-2 as recipients. A genome walking approach was employed to analyse the characteristics of integration sites in transconjugants. A total of 118 clinical S. suis isolates were tested by PCR mapping assays to detect ICESsD9-like elements. MLST was performed on isolates containing ICESsD9 variants to determine their clonal relatedness. This 55 683-bp element can actively excise from the chromosome. Additionally, it was capable of transferring both into S. suis and E. faecalis with frequencies of 1.2×10 -4 and 5.8×10 -6 per donor, respectively. When investigating integration site features, it was found that ICESsD9 can enter S. suis and E. faecalis chromosomes by different sites, generating 15-bp and 3-bp direct repeat sequences, respectively. Twelve isolates mainly belonging to sequence types ST1, ST7 and ST28 were confirmed to harbour ICESsD9-like elements. In conclusion, this study provides the first description of an ICE in S. suis that is capable of transferring both into S. suis and E. faecalis. The presence of different ICESsD9 variants in clinical isolates suggests already wide dissemination of this family element in S. suis in China. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa

PubMed Central

Scott, Martin; Worden, Paul; Huntington, Peter; Hudson, Bernard; Karagiannis, Thomas; Charles, Ian G.; Djordjevic, Steven P.

2016-01-01

Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn6162 and Tn6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn6163 in GI2 carries a blaGES-5–aacA4–gcuE15–aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antibiotic resistance phenotypes in P. aeruginosa. PMID:26962050

Horizontal Gene Transfers in Mycoplasmas (Mollicutes).

PubMed

Citti, C; Dordet-Frisoni, E; Nouvel, L X; Kuo, C H; Baranowski, E

2018-04-12

The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT. While sharing common traits with other bacterial ICEs, such as their chromosomal integration and the use of a type IV secretion system to mediate horizontal dissemination, mycoplasma ICEs (MICEs) revealed unique features: their chromosomal integration is totally random and driven by a DDE recombinase related to the Mutator-like superfamily. Mycoplasma conjugation is not restricted to ICE transmission, but also involves the transfer of large chromosomal fragments that generates progenies with mosaic genomes, nearly every position of chromosome being mobile. Mycoplasmas have thus developed efficient ways to gain access to a considerable reservoir of genetic resources distributed among a vast number of species expanding the concept of minimal cell to the broader context of flowing information.

Interactions between inner membrane proteins in donor and recipient cells limit conjugal DNA transfer.

PubMed

Marrero, Joeli; Waldor, Matthew K

2005-06-01

Conjugation enables horizontal transmission of DNA among bacteria, thereby facilitating the rapid spread of genes such as those conferring resistance to antibiotics. Cell-cell contact is required for conjugative DNA transfer but does not ensure its success. The presence of certain plasmids in potential recipient cells inhibits redundant transfer of these plasmids from competent donors despite contact between donor and recipient cells. Here, we used two closely related integrating conjugative elements (ICEs), SXT and R391, to identify genes that inhibit redundant conjugative transfer. Cells containing SXT exclude transfer of a second copy of SXT but not R391 and vice versa. The specific exclusion of SXT and R391 is dependent upon variants of TraG and Eex, ICE-encoded inner membrane proteins in donor and recipient cells, respectively. We identified short sequences within each variant that determine the exquisite specificity of self-recognition; these data suggest that direct interactions between TraG and Eex mediate exclusion.

A new mosaic integrative and conjugative element from Streptococcus agalactiae carrying resistance genes for chloramphenicol (catQ) and macrolides [mef(I) and erm(TR)].

PubMed

Morici, Eleonora; Simoni, Serena; Brenciani, Andrea; Giovanetti, Eleonora; Varaldo, Pietro E; Mingoia, Marina

2017-01-01

To investigate the genetic basis of catQ-mediated chloramphenicol resistance in Streptococcus agalactiae. Two clinical strains of catQ-positive chloramphenicol-resistant S. agalactiae (Sag236 and Sag403) were recently isolated, typed (MLST, PFGE pulsotypes, capsular types) and their antibiotic resistances investigated by phenotypic and genotypic approaches. Several molecular methods (PCR mapping, restriction assays, Southern blotting, sequencing and sequence analysis, conjugal transfer assays) were used to determine the genetic context of catQ and characterize a genetic element detected in the isolates. Sag236 and Sag403 shared the same ST (ST19), but exhibited a different capsular type (III and V, respectively) and pulsotype. Both harboured the macrolide resistance genes mef(I) and erm(TR) and the tetracycline resistance gene tet(M). Accordingly, they were resistant to chloramphenicol, erythromycin and tetracycline. catQ and mef(I) were associated in an IQ module that was indistinguishable in Sag236 and Sag403. In mating assays, chloramphenicol and erythromycin resistance proved transferable, at low frequency, only from Sag236. Transconjugants carried not only catQ and mef(I), but also erm(TR), suggesting a linkage of the three resistance genes in a mobile element, which, though seemingly non-mobile, was also detected in Sag403. The new element (designated ICESag236, ∼110 kb) results from recombination of two integrative and conjugative elements (ICEs) originally described in different streptococcal species: S. agalactiae ICESagTR7, carrying erm(TR); and Streptococcus pneumoniae ICESpn529IQ, carrying the prototype IQ module. These findings strengthen the notion that widespread streptococcal ICEs may form mosaics that enhance their diversity and spread, broaden their host range and carry new cargo genes. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements.

PubMed

Li, Xiaobin; Xie, Yingzhou; Liu, Meng; Tai, Cui; Sun, Jingyong; Deng, Zixin; Ou, Hong-Yu

2018-05-04

oriTfinder is a web server that facilitates the rapid identification of the origin of transfer site (oriT) of a conjugative plasmid or chromosome-borne integrative and conjugative element. The utilized back-end database oriTDB was built upon more than one thousand known oriT regions of bacterial mobile genetic elements (MGEs) as well as the known MGE-encoding relaxases and type IV coupling proteins (T4CP). With a combination of similarity searches for the oriTDB-archived oriT nucleotide sequences and the co-localization of the flanking relaxase homologous genes, the oriTfinder can predict the oriT region with high accuracy in the DNA sequence of a bacterial plasmid or chromosome in minutes. The server also detects the other transfer-related modules, including the potential relaxase gene, T4CP gene and the type IV secretion system gene cluster, and the putative genes coding for virulence factors and acquired antibiotic resistance determinants. oriTfinder may contribute to meeting the increasing demands of re-annotations for bacterial conjugative, mobilizable or non-transferable elements and aid in the rapid risk accession of disease-relevant trait dissemination in pathogenic bacteria of interest. oriTfinder is freely available to all users without any login requirement at http://bioinfo-mml.sjtu.edu.cn/oriTfinder.

SXT/R391 integrative and conjugative elements in Proteus species reveal abundant genetic diversity and multidrug resistance

PubMed Central

Li, Xinyue; Du, Yu; Du, Pengcheng; Dai, Hang; Fang, Yujie; Li, Zhenpeng; Lv, Na; Zhu, Baoli; Kan, Biao; Wang, Duochun

2016-01-01

SXT/R391 integrative and conjugative elements (ICEs) are self-transmissible mobile genetic elements that are found in most members of Enterobacteriaceae. Here, we determined fifteen SXT/R391 ICEs carried by Proteus isolates from food (4.2%) and diarrhoea patients (17.3%). BLASTn searches against GenBank showed that the fifteen SXT/R391 ICEs were closely related to that from different Enterobacteriaceae species, including Proteus mirabilis. Using core gene phylogenetic analysis, the fifteen SXT/R391 ICEs were grouped into six distinct clusters, including a dominant cluster and three clusters that have not been previously reported in Proteus isolates. The SXT/R391 ICEs shared a common structure with a set of conserved genes, five hotspots and two variable regions, which contained more foreign genes, including drug-resistance genes. Notably, a class A β-lactamase gene was identified in nine SXT/R391 ICEs. Collectively, the ICE-carrying isolates carried resistance genes for 20 tested drugs. Six isolates were resistant to chloramphenicol, kanamycin, streptomycin, trimethoprim-sulfamethoxazole, sulfisoxazole and tetracycline, which are drug resistances commonly encoded by ICEs. Our results demonstrate abundant genetic diversity and multidrug resistance of the SXT/R391 ICEs carried by Proteus isolates, which may have significance for public health. It is therefore necessary to continuously monitor the antimicrobial resistance and related mobile elements among Proteus isolates. PMID:27892525

Combinatorial events of insertion sequences and ICE in Gram-negative bacteria.

PubMed

Toleman, Mark A; Walsh, Timothy R

2011-09-01

The emergence of antibiotic and antimicrobial resistance in Gram-negative bacteria is incremental and linked to genetic elements that function in a so-called 'one-ended transposition' manner, including ISEcp1, ISCR elements and Tn3-like transposons. The power of these elements lies in their inability to consistently recognize one of their own terminal sequences, while recognizing more genetically distant surrogate sequences. This has the effect of mobilizing the DNA sequence found adjacent to their initial location. In general, resistance in Gram-negatives is closely linked to a few one-off events. These include the capture of the class 1 integron by a Tn5090-like transposon; the formation of the 3' conserved segment (3'-CS); and the fusion of the ISCR1 element to the 3'-CS. The structures formed by these rare events have been massively amplified and disseminated in Gram-negative bacteria, but hitherto, are rarely found in Gram-positives. Such events dominate current resistance gene acquisition and are instrumental in the construction of large resistance gene islands on chromosomes and plasmids. Similar combinatorial events appear to have occurred between conjugative plasmids and phages constructing hybrid elements called integrative and conjugative elements or conjugative transposons. These elements are beginning to be closely linked to some of the more powerful resistance mechanisms such as the extended spectrum β-lactamases, metallo- and AmpC type β-lactamases. Antibiotic resistance in Gram-negative bacteria is dominated by unusual combinatorial mistakes of Insertion sequences and gene fusions which have been selected and amplified by antibiotic pressure enabling the formation of extended resistance islands. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

The rhizome of the multidrug-resistant Enterobacter aerogenes genome reveals how new "killer bugs" are created because of a sympatric lifestyle.

PubMed

Diene, Seydina M; Merhej, Vicky; Henry, Mireille; El Filali, Adil; Roux, Véronique; Robert, Catherine; Azza, Saïd; Gavory, Frederick; Barbe, Valérie; La Scola, Bernard; Raoult, Didier; Rolain, Jean-Marc

2013-02-01

Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepancies of this bacterium and show that its core genome originates from another genus, Klebsiella. Atypical characteristics of this bacterium (i.e., motility, presence of ornithine decarboxylase, and lack of urease activity) are attributed to genomic mosaicism, by acquisition of additional genes, such as the complete 60,582 bp flagellar assembly operon acquired "en bloc" from the genus Serratia. The genealogic tree of the 162,202 bp multidrug-resistant conjugative plasmid shows that it is a chimera of transposons and integrative conjugative elements from various bacterial origins, resembling a rhizome. Moreover, we demonstrate biologically that a G53S mutation in the pmrA gene results in colistin resistance. E. aerogenes has a large RNA population comprising 8 rRNA operons and 87 cognate tRNAs that have the ability to translate transferred genes that use different codons, as exemplified by the significantly different codon usage between genes from the core genome and the "mobilome." On the basis of our findings, the evolution of this bacterium to become a "killer bug" with new genomic repertoires was from three criteria that are "opportunity, power, and usage" to indicate a sympatric lifestyle: "opportunity" to meet other bacteria and exchange foreign sequences since this bacteria was similar to sympatric bacteria; "power" to integrate these foreign sequences such as the acquisition of several mobile genetic elements (plasmids, integrative conjugative element, prophages, transposons, flagellar assembly system, etc.) found in his genome; and "usage" to have the ability to translate these sequences including those from rare codons to serve as a translator of foreign languages.

Macrolide resistance gene erm(TR) and erm(TR)-carrying genetic elements in Streptococcus agalactiae: characterization of ICESagTR7, a new composite element containing IMESp2907.

PubMed

Mingoia, Marina; Morici, Eleonora; Marini, Emanuela; Brenciani, Andrea; Giovanetti, Eleonora; Varaldo, Pietro E

2016-03-01

The objective of this study was to investigate macrolide-resistant Streptococcus agalactiae isolates harbouring erm(TR), an erm(A) gene subclass, with emphasis on their erm(TR)-carrying genetic elements. Four erm(TR)-carrying elements have been described to date: three closely related (ICE10750-RD.2, Tn1806 and ICESp1108) in Streptococcus pyogenes, Streptococcus pneumoniae and S. pyogenes, respectively; and one completely different (IMESp2907, embedded in ICESp2906 to form ICESp2905) in S. pyogenes. Seventeen macrolide-resistant erm(TR)-positive S. agalactiae isolates were phenotypically and genotypically characterized. Their erm(TR)-carrying elements were explored by analysing the distinctive recombination genes of known erm(TR)-carrying integrative and conjugative elements (ICEs) and by PCR mapping. The new genetic context and organization of IMESp2907 in S. agalactiae were explored using several experimental procedures and in silico analyses. Five isolates harboured ICE10750-RD.2/Tn1806, five isolates harboured ICESp1108 and five isolates bore unknown erm(TR)-carrying elements. The remaining two isolates, exhibiting identical serotypes and pulsotypes, harboured IMESp2907 in a new genetic environment, which was further investigated in one of the two isolates, SagTR7. IMESp2907 was circularizable in S. agalactiae, as described in S. pyogenes. The new IMESp2907 junctions were identified based on its site-specific integration; the att sites were almost identical to those in S. pyogenes. In strain SagTR7, erm(TR)-carrying IMESp2907 was embedded in an erm(TR)-less internal element related to ICE10750-RD.2/Tn1806, which, in turn, was embedded in an ICESde3396-like element. The resulting whole ICE, ICESagTR7 (∼129 kb), was integrated into the chromosome downstream of the rplL gene, and was excisable in circular form and transferable by conjugation. This is the first study exploring erm(TR)-carrying genetic elements in S. agalactiae. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ICESag37, a Novel Integrative and Conjugative Element Carrying Antimicrobial Resistance Genes and Potential Virulence Factors in Streptococcus agalactiae.

PubMed

Zhou, Kaixin; Xie, Lianyan; Han, Lizhong; Guo, Xiaokui; Wang, Yong; Sun, Jingyong

2017-01-01

ICE Sag37 , a novel integrative and conjugative element carrying multidrug resistance and potential virulence factors, was characterized in a clinical isolate of Streptococcus agalactiae . Two clinical strains of S. agalactiae , Sag37 and Sag158, were isolated from blood samples of new-borns with bacteremia. Sag37 was highly resistant to erythromycin and tetracycline, and susceptible to levofloxacin and penicillin, while Sag158 was resistant to tetracycline and levofloxacin, and susceptible to erythromycin. Transfer experiments were performed and selection was carried out with suitable antibiotic concentrations. Through mating experiments, the erythromycin resistance gene was found to be transferable from Sag37 to Sag158. Sma I-PFGE revealed a new Sma I fragment, confirming the transfer of the fragment containing the erythromycin resistance gene. Whole genome sequencing and sequence analysis revealed a mobile element, ICE Sag37 , which was characterized using several molecular methods and in silico analyses. ICE Sag37 was excised to generate a covalent circular intermediate, which was transferable to S. agalactiae . Inverse PCR was performed to detect the circular form. A serine family integrase mediated its chromosomal integration into rumA , which is a known hotspot for the integration of streptococcal ICEs. The integration site was confirmed using PCR. ICE Sag37 carried genes for resistance to multiple antibiotics, including erythromycin [ erm(B) ], tetracycline [ tet(O) ], and aminoglycosides [ aadE, aphA , and ant(6) ]. Potential virulence factors, including a two-component signal transduction system ( nisK/nisR ), were also observed in ICE Sag37 . S1-PFGE analysis ruled out the existence of plasmids. ICE Sag37 is the first ICE Sa2603 family-like element identified in S. agalactiae carrying both resistance and potential virulence determinants. It might act as a vehicle for the dissemination of multidrug resistance and pathogenicity among S. agalactiae .

Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing corynebacteria after intergeneric conjugation.

PubMed

Mateos, L M; Schäfer, A; Kalinowski, J; Martin, J F; Pühler, A

1996-10-01

Conjugative transfer of mobilizable derivatives of the Escherichia coli narrow-host-range plasmids pBR322, pBR325, pACYC177, and pACYC184 from E. coli to species of the gram-positive genera Corynebacterium and Brevibacterium resulted in the integration of the plasmids into the genomes of the recipient bacteria. Transconjugants appeared at low frequencies and reproducibly with a delay of 2 to 3 days compared with matings with replicative vectors. Southern analysis of corynebacterial transconjugants and nucleotide sequences from insertion sites revealed that integration occurs at different locations and that different parts of the vector are involved in the process. Integration is not dependent on indigenous insertion sequence elements but results from recombination between very short homologous DNA segments (8 to 12 bp) present in the vector and in the host DNA. In the majority of the cases (90%), integration led to cointegrate formation, and in some cases, deletions or rearrangements occurred during the recombination event. Insertions were found to be quite stable even in the absence of selective pressure.

Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing corynebacteria after intergeneric conjugation.

PubMed Central

Mateos, L M; Schäfer, A; Kalinowski, J; Martin, J F; Pühler, A

1996-01-01

Conjugative transfer of mobilizable derivatives of the Escherichia coli narrow-host-range plasmids pBR322, pBR325, pACYC177, and pACYC184 from E. coli to species of the gram-positive genera Corynebacterium and Brevibacterium resulted in the integration of the plasmids into the genomes of the recipient bacteria. Transconjugants appeared at low frequencies and reproducibly with a delay of 2 to 3 days compared with matings with replicative vectors. Southern analysis of corynebacterial transconjugants and nucleotide sequences from insertion sites revealed that integration occurs at different locations and that different parts of the vector are involved in the process. Integration is not dependent on indigenous insertion sequence elements but results from recombination between very short homologous DNA segments (8 to 12 bp) present in the vector and in the host DNA. In the majority of the cases (90%), integration led to cointegrate formation, and in some cases, deletions or rearrangements occurred during the recombination event. Insertions were found to be quite stable even in the absence of selective pressure. PMID:8824624

Efficient conjugate gradient algorithms for computation of the manipulator forward dynamics

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheid, Robert E.

1989-01-01

The applicability of conjugate gradient algorithms for computation of the manipulator forward dynamics is investigated. The redundancies in the previously proposed conjugate gradient algorithm are analyzed. A new version is developed which, by avoiding these redundancies, achieves a significantly greater efficiency. A preconditioned conjugate gradient algorithm is also presented. A diagonal matrix whose elements are the diagonal elements of the inertia matrix is proposed as the preconditioner. In order to increase the computational efficiency, an algorithm is developed which exploits the synergism between the computation of the diagonal elements of the inertia matrix and that required by the conjugate gradient algorithm.

Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes

USDA-ARS?s Scientific Manuscript database

Background: Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system ...

WARP3D-Release 10.8: Dynamic Nonlinear Analysis of Solids using a Preconditioned Conjugate Gradient Software Architecture

NASA Technical Reports Server (NTRS)

Koppenhoefer, Kyle C.; Gullerud, Arne S.; Ruggieri, Claudio; Dodds, Robert H., Jr.; Healy, Brian E.

1998-01-01

This report describes theoretical background material and commands necessary to use the WARP3D finite element code. WARP3D is under continuing development as a research code for the solution of very large-scale, 3-D solid models subjected to static and dynamic loads. Specific features in the code oriented toward the investigation of ductile fracture in metals include a robust finite strain formulation, a general J-integral computation facility (with inertia, face loading), an element extinction facility to model crack growth, nonlinear material models including viscoplastic effects, and the Gurson-Tver-gaard dilatant plasticity model for void growth. The nonlinear, dynamic equilibrium equations are solved using an incremental-iterative, implicit formulation with full Newton iterations to eliminate residual nodal forces. The history integration of the nonlinear equations of motion is accomplished with Newmarks Beta method. A central feature of WARP3D involves the use of a linear-preconditioned conjugate gradient (LPCG) solver implemented in an element-by-element format to replace a conventional direct linear equation solver. This software architecture dramatically reduces both the memory requirements and CPU time for very large, nonlinear solid models since formation of the assembled (dynamic) stiffness matrix is avoided. Analyses thus exhibit the numerical stability for large time (load) steps provided by the implicit formulation coupled with the low memory requirements characteristic of an explicit code. In addition to the much lower memory requirements of the LPCG solver, the CPU time required for solution of the linear equations during each Newton iteration is generally one-half or less of the CPU time required for a traditional direct solver. All other computational aspects of the code (element stiffnesses, element strains, stress updating, element internal forces) are implemented in the element-by- element, blocked architecture. This greatly improves vectorization of the code on uni-processor hardware and enables straightforward parallel-vector processing of element blocks on multi-processor hardware.

Staphylococci on ICE: Overlooked agents of horizontal gene transfer.

PubMed

Sansevere, Emily A; Robinson, D Ashley

2017-01-01

Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus , which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn 916 was capable of transfer from Enterococcus to Staphylococcus . However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn 916 that includes the Tn 5801 subfamily, and ICE 6013 that includes at least 7 subfamilies. Both Tn 5801 and ICE 6013 commonly occur in clinical strains of S. aureus . Tn 5801 is the most studied of the Tn 916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli , inhibits restriction barriers to incoming DNA. ICE 6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS 30 -like transposase as its recombinase, providing some versatility in integration sites. ICE 6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn 5801 . Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.

Conjugated Gammadion Chiral Metamaterial with Uniaxial Optical Activity and Negative Refractive Index

DTIC Science & Technology

2011-01-10

in Fig. 4, we discuss a procedure of transmutation from the simple -particle chiral element to the conjugated gammadion chiral metamaterial. The...the transmutation from the simple -particle chiral element to the conjugated gammadion chiral metamaterial. The procedure shows how the magnetic or

Iterative methods for elliptic finite element equations on general meshes

NASA Technical Reports Server (NTRS)

Nicolaides, R. A.; Choudhury, Shenaz

1986-01-01

Iterative methods for arbitrary mesh discretizations of elliptic partial differential equations are surveyed. The methods discussed are preconditioned conjugate gradients, algebraic multigrid, deflated conjugate gradients, an element-by-element techniques, and domain decomposition. Computational results are included.

Homology among tet determinants in conjugative elements of streptococci.

PubMed Central

Smith, M D; Hazum, S; Guild, W R

1981-01-01

A mutation to tetracycline sensitivity in a resistant strain of Streptococcus pneumoniae was shown by several criteria to be due to a point mutation in the conjugative omega (cat-tet) element found in the chromosomes of strains derived from BM6001, a clinical strain resistant to tetracycline and chloramphenicol. Strains carrying the mutation were transformed back to tetracycline resistance with the high efficiency of a point marker by donor deoxyribonucleic acids from its ancestral strain and from nine other clinical isolates of pneumococcus and by deoxyribonucleic acids from group D Streptococcus faecalis and group B Streptococcus agalactiae strains that also carry conjugative tet elements in their chromosomes. It was not transformed to resistance by tet plasmid deoxyribonucleic acids from either gram-negative or gram-positive species, except for one that carried transposon Tn916, the conjugative tet element present in the chromosomes of some S. faecalis strains. The results showed that the tet determinants in conjugative elements of several streptococcal species share a high degree of deoxyribonucleic acid sequence homology and suggested that they differ from other tet genes. PMID:6270063

Pathogens of Bovine Respiratory Disease in North American Feedlots Conferring Multidrug Resistance via Integrative Conjugative Elements

PubMed Central

Klima, Cassidy L.; Zaheer, Rahat; Cook, Shaun R.; Booker, Calvin W.; Hendrick, Steve

2014-01-01

In this study, we determined the prevalence of bovine respiratory disease (BRD)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. Nasopharyngeal swab and lung tissue samples from 68 BRD mortalities in Alberta, Canada (n = 42), Texas (n = 6), and Nebraska (n = 20) were screened using PCR for bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus, bovine herpesvirus 1, parainfluenza type 3 virus, Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Excepting bovine herpesvirus 1, all agents were detected. M. haemolytica (91%) and BVDV (69%) were the most prevalent, with cooccurrence in 63% of the cattle. Isolates of M. haemolytica (n = 55), P. multocida (n = 8), and H. somni (n = 10) from lungs were also collected. Among M. haemolytica isolates, a clonal subpopulation (n = 8) was obtained from a Nebraskan feedlot. All three bacterial pathogens exhibited a high rate of antimicrobial resistance, with 45% exhibiting resistance to three or more antimicrobials. M. haemolytica (n = 18), P. multocida (n = 3), and H. somni (n = 3) from Texas and Nebraska possessed integrative conjugative elements (ICE) that conferred resistance for up to seven different antimicrobial classes. ICE were shown to be transferred via conjugation from P. multocida to Escherichia coli and from M. haemolytica and H. somni to P. multocida. ICE-mediated multidrug-resistant profiles of bacterial BRD pathogens could be a major detriment to many of the therapeutic antimicrobial strategies currently used to control BRD. PMID:24478472

Pathogens of bovine respiratory disease in North American feedlots conferring multidrug resistance via integrative conjugative elements.

PubMed

Klima, Cassidy L; Zaheer, Rahat; Cook, Shaun R; Booker, Calvin W; Hendrick, Steve; Alexander, Trevor W; McAllister, Tim A

2014-02-01

In this study, we determined the prevalence of bovine respiratory disease (BRD)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. Nasopharyngeal swab and lung tissue samples from 68 BRD mortalities in Alberta, Canada (n = 42), Texas (n = 6), and Nebraska (n = 20) were screened using PCR for bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus, bovine herpesvirus 1, parainfluenza type 3 virus, Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Excepting bovine herpesvirus 1, all agents were detected. M. haemolytica (91%) and BVDV (69%) were the most prevalent, with cooccurrence in 63% of the cattle. Isolates of M. haemolytica (n = 55), P. multocida (n = 8), and H. somni (n = 10) from lungs were also collected. Among M. haemolytica isolates, a clonal subpopulation (n = 8) was obtained from a Nebraskan feedlot. All three bacterial pathogens exhibited a high rate of antimicrobial resistance, with 45% exhibiting resistance to three or more antimicrobials. M. haemolytica (n = 18), P. multocida (n = 3), and H. somni (n = 3) from Texas and Nebraska possessed integrative conjugative elements (ICE) that conferred resistance for up to seven different antimicrobial classes. ICE were shown to be transferred via conjugation from P. multocida to Escherichia coli and from M. haemolytica and H. somni to P. multocida. ICE-mediated multidrug-resistant profiles of bacterial BRD pathogens could be a major detriment to many of the therapeutic antimicrobial strategies currently used to control BRD.

The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties

PubMed Central

Gaillard, Muriel; Vallaeys, Tatiana; Vorhölter, Frank Jörg; Minoia, Marco; Werlen, Christoph; Sentchilo, Vladimir; Pühler, Alfred; van der Meer, Jan Roelof

2006-01-01

Pseudomonas sp. strain B13 is a bacterium known to degrade chloroaromatic compounds. The properties to use 3- and 4-chlorocatechol are determined by a self-transferable DNA element, the clc element, which normally resides at two locations in the cell's chromosome. Here we report the complete nucleotide sequence of the clc element, demonstrating the unique catabolic properties while showing its relatedness to genomic islands and integrative and conjugative elements rather than to other known catabolic plasmids. As far as catabolic functions, the clc element harbored, in addition to the genes for chlorocatechol degradation, a complete functional operon for 2-aminophenol degradation and genes for a putative aromatic compound transport protein and for a multicomponent aromatic ring dioxygenase similar to anthranilate hydroxylase. The genes for catabolic functions were inducible under various conditions, suggesting a network of catabolic pathway induction. For about half of the open reading frames (ORFs) on the clc element, no clear functional prediction could be given, although some indications were found for functions that were similar to plasmid conjugation. The region in which these ORFs were situated displayed a high overall conservation of nucleotide sequence and gene order to genomic regions in other recently completed bacterial genomes or to other genomic islands. Most notably, except for two discrete regions, the clc element was almost 100% identical over the whole length to a chromosomal region in Burkholderia xenovorans LB400. This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties. PMID:16484212

Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013

PubMed Central

Hernández-Monroy, Irma; López-Martínez, Irma; Ortiz-Alcántara, Joanna; González-Durán, Elizabeth; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ramírez-González, José Ernesto

2014-01-01

We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXφ and RS1φ. PMID:25359919

Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation.

PubMed

Chuzeville, Sarah; Dramsi, Shaynoor; Madec, Jean-Yves; Haenni, Marisa; Payot, Sophie

2015-11-01

Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen I/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mutans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515_tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL_2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

PubMed Central

Guérillot, Romain; Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael; Glaser, Philippe

2014-01-01

Transposable elements (TEs) are major components of both prokaryotic and eukaryotic genomes and play a significant role in their evolution. In this study, we have identified new prokaryotic DDE transposase families related to the eukaryotic Mutator-like transposases. These genes were retrieved by cascade PSI-Blast using as initial query the transposase of the streptococcal integrative and conjugative element (ICE) TnGBS2. By combining secondary structure predictions and protein sequence alignments, we predicted the DDE catalytic triad and the DNA-binding domain recognizing the terminal inverted repeats. Furthermore, we systematically characterized the organization and the insertion specificity of the TEs relying on these prokaryotic Mutator-like transposases (p-MULT) for their mobility. Strikingly, two distant TE families target their integration upstream σA dependent promoters. This allowed us to identify a transposase sequence signature associated with this unique insertion specificity and to show that the dissymmetry between the two inverted repeats is responsible for the orientation of the insertion. Surprisingly, while DDE transposases are generally associated with small and simple transposons such as insertion sequences (ISs), p-MULT encoding TEs show an unprecedented diversity with several families of IS, transposons, and ICEs ranging in size from 1.1 to 52 kb. PMID:24418649

Parallel processors and nonlinear structural dynamics algorithms and software

NASA Technical Reports Server (NTRS)

Belytschko, Ted

1990-01-01

Techniques are discussed for the implementation and improvement of vectorization and concurrency in nonlinear explicit structural finite element codes. In explicit integration methods, the computation of the element internal force vector consumes the bulk of the computer time. The program can be efficiently vectorized by subdividing the elements into blocks and executing all computations in vector mode. The structuring of elements into blocks also provides a convenient way to implement concurrency by creating tasks which can be assigned to available processors for evaluation. The techniques were implemented in a 3-D nonlinear program with one-point quadrature shell elements. Concurrency and vectorization were first implemented in a single time step version of the program. Techniques were developed to minimize processor idle time and to select the optimal vector length. A comparison of run times between the program executed in scalar, serial mode and the fully vectorized code executed concurrently using eight processors shows speed-ups of over 25. Conjugate gradient methods for solving nonlinear algebraic equations are also readily adapted to a parallel environment. A new technique for improving convergence properties of conjugate gradients in nonlinear problems is developed in conjunction with other techniques such as diagonal scaling. A significant reduction in the number of iterations required for convergence is shown for a statically loaded rigid bar suspended by three equally spaced springs.

The mosaic accessory gene structures of the SXT/R391-like integrative and conjugative elements derived from Vibrio spp. isolated from aquatic products and environment in the Yangtze River estuary, China

PubMed Central

2013-01-01

Background The emergence, resurgence and spread of human food-borne pathogenic Vibrios are one of the major contributors to disease burden and mortality particularly in developing countries with disputable sanitary conditions. Previous research on pathogenic Vibrio cholerae and Vibrio parahaemolitycus derived from clinical samples has proposed links between acquisition of virulence and multiple drug resistance traits and intercellular transmissibility of mobile genetic elements in the environment. To date, very few information is available on environmental Vibrio isolates. In this study, we characterized eleven Vibrio strains bearing the SXT/R391-like integrative and conjugative elements (ICEs) derived from aquatic products and environment in the Yangtze River Estuary, China. Results The eleven Vibrio strains were isolated in 2010 to 2011, and taxonomically identified, which included six Vibrio cholerae, three Vibrio parahaemolyticus, one Vibrio alginolyticus and one Vibrio natriegens. Most of the strains displayed strong resistance phenotypes to ampicillin, mercury and chromium. The majority of their ICEs, which belong to S and R exclusion system groups, contain ICEs-chromosome junction sequences and highly conserved core-genes required for ICE transfer. However, comparative sequence analysis uncovered interesting diversity in their mosaic accessory gene structures, which carry many novel genes that have not been described in any known ICEs to date. In addition, antibiotic resistance was transmitted by ICEVchChn6 and ICEVpaChn1 from V. cholerae, V. parahaemolyticus to E. coli MG1655 via conjugation, respectively. Our data also revealed that the ICEs characterized in this study are phylogenetically distant from most of the SXT/R391 ICEs reported previously, which may represent a novel cluster likely shaped by the ecological environment in the Yangtze River Estuary, China. Conclusions This study constitutes the first investigation of ICEs-positive Vibrio spp. in the Yangze River Estuary, China. The newly identified ICEs were characterized with mosaic accessory gene structures and many novel genes. The results demonstrated self-transmissibility of antibiotic resistance mediated by two of the ICEs from V. cholerae, V. parahaemolyticus to E. coli via conjugation, respectively. Our results also revealed that the ICEs examined in this study may represent a novel cluster in the SXT/R391 family. PMID:24074349

Evolution and comparative genomics of pAQU-like conjugative plasmids in Vibrio species.

PubMed

Li, Ruichao; Ye, Lianwei; Wong, Marcus Ho Yin; Zheng, Zhiwei; Chan, Edward Wai Chi; Chen, Sheng

2017-09-01

To investigate a set of MDR conjugative plasmids found in Vibrio species and characterize the underlying evolution process. pAQU-type plasmids from Vibrio species were sequenced using both Illumina and PacBio platforms. Bioinformatics tools were utilized to analyse the typical MDR regions and core genes in the plasmids. The nine pAQU-type plasmids ranged from ∼160 to 206 kb in size and were found to harbour as many as 111 core genes encoding conjugative, replication and maintenance functions. Eight plasmids were found to carry a typical MDR region, which contained various accessory and resistance genes, including ISCR1-blaPER-1-bearing complex class 1 integrons, ISCR2-floR, ISCR2-tet(D)-tetR-ISCR2, qnrVC6, a Tn10-like structure and others associated with mobile elements. Comparison between a plasmid without resistance genes and different MDR plasmids showed that integration of different mobile elements, such as IS26, ISCR1, ISCR2, IS10 and IS6100, into the plasmid backbone was the key mechanism by which foreign resistance genes were acquired during the evolution process. This study identified pAQU-type plasmids as emerging MDR conjugative plasmids among important pathogens from different origins in Asia. These findings suggest that aquatic bacteria constitute a major reservoir of resistance genes, which may be transmissible to other human pathogens during food production and processing. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genome analysis of a clinical isolate of Shewanella sp. uncovered an active hybrid integrative and conjugative element carrying an integron platform inserted in a novel genomic locus.

PubMed

Parmeciano Di Noto, Gisela; Jara, Eugenio; Iriarte, Andrés; Centrón, Daniela; Quiroga, Cecilia

2016-08-01

Shewanella spp. are currently considered to be emerging pathogens that can code for a blaOXA carbapenemase in their chromosome. Complete genome analysis of the clinical isolate Shewanella sp. Sh95 revealed that this strain is a novel species, which shares a lineage with marine isolates. Characterization of its resistome showed that it codes for genes drfA15, qacH and blaOXA-48. We propose that Shewanella sp. Sh95 acts as reservoir of blaOXA-48. Moreover, analysis of mobilome showed that it contains a novel integrative and conjugative element (ICE), named ICESh95. Comparative analysis between the close relatives ICESpuPO1 from Shewanella sp. W3-18-1 and ICE SXTMO10 from Vibrio cholerae showed that ICESh95 encompassed two new regions, a type III restriction modification system and a multidrug resistance integron. The integron platform contained a novel arrangement formed by gene cassettes drfA15 and qacH, and a class C-attC group II intron. Furthermore, insertion of ICESh95 occurred at a unique target site, which correlated with the presence of a different xis/int module. Mobility of ICESh95 was assessed and demonstrated its ability to self-transfer with high efficiency to different species of bacteria. Our results show that ICESh95 is a self-transmissible, mobile element, which can contribute to the dissemination of antimicrobial resistance; this is clearly a threat when natural bacteria from water ecosystems, such as Shewanella, act as vectors in its propagation.

Chromosomal transfers in mycoplasmas: when minimal genomes go mobile.

PubMed

Dordet-Frisoni, Emilie; Sagné, Eveline; Baranowski, Eric; Breton, Marc; Nouvel, Laurent Xavier; Blanchard, Alain; Marenda, Marc Serge; Tardy, Florence; Sirand-Pugnet, Pascal; Citti, Christine

2014-11-25

Horizontal gene transfer (HGT) is a main driving force of bacterial evolution and innovation. This phenomenon was long thought to be marginal in mycoplasmas, a large group of self-replicating bacteria characterized by minute genomes as a result of successive gene losses during evolution. Recent comparative genomic analyses challenged this paradigm, but the occurrence of chromosomal exchanges had never been formally addressed in mycoplasmas. Here, we demonstrated the conjugal transfer of large chromosomal regions within and among ruminant mycoplasma species, with the incorporation of the incoming DNA occurring by homologous recombination into the recipient chromosome. By combining classical mating experiments with high-throughput next-generation sequencing, we documented the transfer of almost every position of the mycoplasma chromosome. Mycoplasma conjugation relies on the occurrence of an integrative conjugative element (ICE) in at least one parent cell. While ICE propagates horizontally from ICE-positive to ICE-negative cells, chromosomal transfers (CTs) occurred in the opposite direction, from ICE-negative to ICE-positive cells, independently of ICE movement. These findings challenged the classical mechanisms proposed for other bacteria in which conjugative CTs are driven by conjugative elements, bringing into the spotlight a new means for rapid mycoplasma innovation. Overall, they radically change our current views concerning the evolution of mycoplasmas, with particularly far-reaching implications given that over 50 species are human or animal pathogens. Horizontal gene transfers (HGT) shape bacterial genomes and are key contributors to microbial diversity and innovation. One main mechanism involves conjugation, a process that allows the simultaneous transfer of significant amounts of DNA upon cell-to-cell contact. Recognizing and deciphering conjugal mechanisms are thus essential in understanding the impact of gene flux on bacterial evolution. We addressed this issue in mycoplasmas, the smallest and simplest self-replicating bacteria. In these organisms, HGT was long thought to be marginal. We showed here that nearly every position of the Mycoplasma agalactiae chromosome could be transferred via conjugation, using an unconventional mechanism. The transfer involved DNA blocks containing up to 80 genes that were incorporated into the host chromosome by homologous recombination. These findings radically change our views concerning mycoplasma evolution and adaptation with particularly far-reaching implications given that over 50 species are human or animal pathogens. Copyright © 2014 Dordet-Frisoni et al.

The novel conjugative transposon tn1207.3 carries the macrolide efflux gene mef(A) in Streptococcus pyogenes.

PubMed

Santagati, Maria; Iannelli, Francesco; Cascone, Carmela; Campanile, Floriana; Oggioni, Marco R; Stefani, Stefania; Pozzi, Gianni

2003-01-01

The macrolide efflux gene mef(A) of the Streptococcus pyogenes clinical strain 2812A was found to be carried by a 52-kb chromosomal genetic element that could be transferred by conjugation to the chromosome of other streptococcal species. The characteristics of this genetic element are typical of conjugative transposons and was named Tn1207.3. The size of Tn1207.3 was established by pulsed-field gel electrophoresis (PFGE), and DNA sequencing analysis showed that the 7,244 bp at the left end of Tn1207.3 were identical to those of the pneumococcal Tn1207.1 element. Tn1207.3-like genetic elements were found to be inserted at a single specific chromosomal site in 12 different clinical isolates S. pyogenes exhibiting the M phenotype of resistance to macrolides and carrying the mef(A) gene. Tn1207.3 was transferred from S. pyogenes 2812A to Streptococcus pneumoniae, and sequence analysis carried out on six independent transconjugants showed that insertion of Tn1207.3 in the pneumococcal genome always occurred at a single specific site as in Tn1207.1. Using MF2, a representative S. pneumoniae transconjugant, as a donor, Tn1207.3 was transferred again by conjugation to S. pyogenes and Streptococcus gordonii. The previously described nonconjugative element Tn1207.1 of S. pneumoniae appears to be a defective element, part of a longer conjugative transposon that carries mef(A) and is found in clinical isolates of S. pyogenes.

Genome Sequence of Vibrio cholerae Strain O1 Ogawa El Tor, Isolated in Mexico, 2013.

PubMed

Díaz-Quiñonez, José Alberto; Hernández-Monroy, Irma; López-Martínez, Irma; Ortiz-Alcántara, Joanna; González-Durán, Elizabeth; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ramírez-González, José Ernesto

2014-10-30

We present the draft genome sequence of Vibrio cholerae InDRE 3140 recovered in 2013 during a cholera outbreak in Mexico. The genome showed the Vibrio 7th pandemic islands VSP1 and VSP2, the pathogenic islands VPI-1 and VPI-2, the integrative and conjugative element SXT/R391 (ICE-SXT), and both prophages CTXφ and RS1φ. Copyright © 2014 Díaz-Quiñonez et al.

Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element.

PubMed

Mann, Rachel A; Blom, Jochen; Bühlmann, Andreas; Plummer, Kim M; Beer, Steven V; Luck, Joanne E; Goesmann, Alexander; Frey, Jürg E; Rodoni, Brendan C; Duffy, Brion; Smits, Theo H M

2012-08-01

The Hrp pathogenicity island (hrpPAI) of Erwinia amylovora not only encodes a type III secretion system (T3SS) and other genes required for pathogenesis on host plants, but also includes the so-called island transfer (IT) region, a region that originates from an integrative conjugative element (ICE). Comparative genomic analysis of the IT regions of two Spiraeoideae- and three Rubus-infecting strains revealed that the regions in Spiraeoideae-infecting strains were syntenic and highly conserved in length and genetic information, but that the IT regions of the Rubus-infecting strains varied in gene content and length, showing a mosaic structure. None of the ICEs in E. amylovora strains were complete, as conserved ICE genes and the left border were missing, probably due to reductive genome evolution. Comparison of the hrpPAI region of E. amylovora strains to syntenic regions from other Erwinia spp. indicates that the hrpPAI and the IT regions are the result of several insertion and deletion events that have occurred within the ICE. It also suggests that the T3SS was present in a common ancestor of the pathoadapted Erwinia spp. and that insertion and deletion events in the IT region occurred during speciation. Copyright © 2012 Elsevier B.V. All rights reserved.

Worldwide Occurrence of Integrative Conjugative Element Encoding Multidrug Resistance Determinants in Epidemic Vibrio cholerae O1

PubMed Central

Marin, Michel A.; Fonseca, Erica L.; Andrade, Bruno N.; Cabral, Adriana C.; Vicente, Ana Carolina P.

2014-01-01

In the last decades, there has been an increase of cholera epidemics caused by multidrug resistant strains. Particularly, the integrative and conjugative element (ICE) seems to play a major role in the emergence of multidrug resistant Vibrio cholerae. This study fully characterized, by whole genome sequencing, new ICEs carried by multidrug resistant V. cholerae O1 strains from Nigeria (2010) (ICEVchNig1) and Nepal (1994) (ICEVchNep1). The gene content and gene order of these two ICEs are the same, and identical to ICEVchInd5, ICEVchBan5 and ICEVchHai1 previously identified in multidrug resistant V. cholerae O1. This ICE is characterized by dfrA1, sul2, strAB and floR antimicrobial resistance genes, and by unique gene content in HS4 and HS5 ICE regions. Screening for ICEs, in publicly available V. cholerae genomes, revealed the occurrence and widespread distribution of this ICE among V. cholerae O1. Metagenomic analysis found segments of this ICE in marine environments far from the direct influence of the cholera epidemic. Therefore, this study revealed the epidemiology of a spatio-temporal prevalent ICE in V. cholerae O1. Its occurrence and dispersion in V. cholerae O1 strains from different continents throughout more than two decades can be indicative of its role in the fitness of the current pandemic lineage. PMID:25265418

A combined finite element and boundary integral formulation for solution via CGFFT of 2-dimensional scattering problems

NASA Technical Reports Server (NTRS)

Collins, Jeffery D.; Volakis, John L.

1989-01-01

A new technique is presented for computing the scattering by 2-D structures of arbitrary composition. The proposed solution approach combines the usual finite element method with the boundary integral equation to formulate a discrete system. This is subsequently solved via the conjugate gradient (CG) algorithm. A particular characteristic of the method is the use of rectangular boundaries to enclose the scatterer. Several of the resulting boundary integrals are therefore convolutions and may be evaluated via the fast Fourier transform (FFT) in the implementation of the CG algorithm. The solution approach offers the principle advantage of having O(N) memory demand and employs a 1-D FFT versus a 2-D FFT as required with a traditional implementation of the CGFFT algorithm. The speed of the proposed solution method is compared with that of the traditional CGFFT algorithm, and results for rectangular bodies are given and shown to be in excellent agreement with the moment method.

Microfluidic bioassay system based on microarrays of hydrogel sensing elements entrapping quantum dot-enzyme conjugates.

PubMed

Jang, Eunji; Kim, Sinyoung; Koh, Won-Gun

2012-01-15

This paper presents a simple method to fabricate a microfluidic biosensor that is able to detect substrates for H(2)O(2)-generating oxidase. The biosensor consists of three components (quantum dot-enzyme conjugates, hydrogel microstructures, and a set of microchannels) that were hierarchically integrated into a microfluidic device. The quantum dot (QD)-enzyme conjugates were entrapped within the poly(ethylene glycol) (PEG)-based hydrogel microstructures that were fabricated within the microchannels by a photopatterning process. Glucose oxidase (GOX) and alcohol oxidase (AOX) were chosen as the model oxidase enzymes, conjugated to carboxyl-terminated CdSe/ZnS QDs, and entrapped within the hydrogel microstructures, which resulted in a fluorescent hydrogel microarray that was responsive to glucose or alcohol. The hydrogel-entrapped GOX and AOX were able to perform enzyme-catalyzed oxidation of glucose and alcohol, respectively, to produce H(2)O(2), which subsequently quenched the fluorescence of the conjugated QDs. The fluorescence intensity of the hydrogel microstructures decreased as the glucose and alcohol concentrations increased, and the detection limits of this system were found to be 50 μM of glucose and 70 μM of alcohol. Because each microchannel was able to carry out different assays independently, the simultaneous detection of glucose and alcohol was possible using our novel microfluidic device composed of multiple microchannels. Copyright © 2011 Elsevier B.V. All rights reserved.

Scattering and radiation analysis of three-dimensional cavity arrays via a hybrid finite element method

NASA Technical Reports Server (NTRS)

Jin, Jian-Ming; Volakis, John L.

1992-01-01

A hybrid numerical technique is presented for a characterization of the scattering and radiation properties of three-dimensional cavity arrays recessed in a ground plane. The technique combines the finite element and boundary integral methods and invokes Floquet's representation to formulate a system of equations for the fields at the apertures and those inside the cavities. The system is solved via the conjugate gradient method in conjunction with the Fast Fourier Transform (FFT) thus achieving an O(N) storage requirement. By virtue of the finite element method, the proposed technique is applicable to periodic arrays comprised of cavities having arbitrary shape and filled with inhomogeneous dielectrics. Several numerical results are presented, along with new measured data, which demonstrate the validity, efficiency, and capability of the technique.

Site-Specific Integration of Foreign DNA into Minimal Bacterial and Human Target Sequences Mediated by a Conjugative Relaxase

PubMed Central

Agúndez, Leticia; González-Prieto, Coral; Machón, Cristina; Llosa, Matxalen

2012-01-01

Background Bacterial conjugation is a mechanism for horizontal DNA transfer between bacteria which requires cell to cell contact, usually mediated by self-transmissible plasmids. A protein known as relaxase is responsible for the processing of DNA during bacterial conjugation. TrwC, the relaxase of conjugative plasmid R388, is also able to catalyze site-specific integration of the transferred DNA into a copy of its target, the origin of transfer (oriT), present in a recipient plasmid. This reaction confers TrwC a high biotechnological potential as a tool for genomic engineering. Methodology/Principal Findings We have characterized this reaction by conjugal mobilization of a suicide plasmid to a recipient cell with an oriT-containing plasmid, selecting for the cointegrates. Proteins TrwA and IHF enhanced integration frequency. TrwC could also catalyze integration when it is expressed from the recipient cell. Both Y18 and Y26 catalytic tyrosil residues were essential to perform the reaction, while TrwC DNA helicase activity was dispensable. The target DNA could be reduced to 17 bp encompassing TrwC nicking and binding sites. Two human genomic sequences resembling the 17 bp segment were accepted as targets for TrwC-mediated site-specific integration. TrwC could also integrate the incoming DNA molecule into an oriT copy present in the recipient chromosome. Conclusions/Significance The results support a model for TrwC-mediated site-specific integration. This reaction may allow R388 to integrate into the genome of non-permissive hosts upon conjugative transfer. Also, the ability to act on target sequences present in the human genome underscores the biotechnological potential of conjugative relaxase TrwC as a site-specific integrase for genomic modification of human cells. PMID:22292089

Physiological impact of transposable elements encoding DDE transposases in the environmental adaptation of Streptococcus agalactiae.

PubMed

Fléchard, Maud; Gilot, Philippe

2014-07-01

We have referenced and described Streptococcus agalactiae transposable elements encoding DDE transposases. These elements belonged to nine families of insertion sequences (ISs) and to a family of conjugative transposons (TnGBSs). An overview of the physiological impact of the insertion of all these elements is provided. DDE-transposable elements affect S. agalactiae in a number of aspects of its capability to adapt to various environments and modulate the expression of several virulence genes, the scpB-lmB genomic region and the genes involved in capsule expression and haemolysin transport being the targets of several different mobile elements. The referenced mobile elements modify S. agalactiae behaviour by transferring new gene(s) to its genome, by modifying the expression of neighbouring genes at the integration site or by promoting genomic rearrangements. Transposition of some of these elements occurs in vivo, suggesting that by dynamically regulating some adaptation and/or virulence genes, they improve the ability of S. agalactiae to reach different niches within its host and ensure the 'success' of the infectious process. © 2014 The Authors.

Functional conjugated pyridines via main-group element tuning.

PubMed

Stolar, Monika; Baumgartner, Thomas

2018-03-29

Pyridine-based materials have seen widespread attention for the development of n-type organic materials. In recent years, the incorporation of main-group elements has also explored significant advantages for the development and tunability of organic conjugated materials. The unique chemical and electronic structure of main-group elements has led to several enhancements in conventional organic materials. This Feature article highlights recent main-group based pyridine materials by discussing property enhancements and application in organic electronics.

A finite element conjugate gradient FFT method for scattering

NASA Technical Reports Server (NTRS)

Collins, Jeffery D.; Zapp, John; Hsa, Chang-Yu; Volakis, John L.

1990-01-01

An extension of a two dimensional formulation is presented for a three dimensional body of revolution. With the introduction of a Fourier expansion of the vector electric and magnetic fields, a coupled two dimensional system is generated and solved via the finite element method. An exact boundary condition is employed to terminate the mesh and the fast fourier transformation (FFT) is used to evaluate the boundary integrals for low O(n) memory demand when an iterative solution algorithm is used. By virtue of the finite element method, the algorithm is applicable to structures of arbitrary material composition. Several improvements to the two dimensional algorithm are also described. These include: (1) modifications for terminating the mesh at circular boundaries without distorting the convolutionality of the boundary integrals; (2) the development of nonproprietary mesh generation routines for two dimensional applications; (3) the development of preprocessors for interfacing SDRC IDEAS with the main algorithm; and (4) the development of post-processing algorithms based on the public domain package GRAFIC to generate two and three dimensional gray level and color field maps.

MHOST: An efficient finite element program for inelastic analysis of solids and structures

NASA Technical Reports Server (NTRS)

Nakazawa, S.

1988-01-01

An efficient finite element program for 3-D inelastic analysis of gas turbine hot section components was constructed and validated. A novel mixed iterative solution strategy is derived from the augmented Hu-Washizu variational principle in order to nodally interpolate coordinates, displacements, deformation, strains, stresses and material properties. A series of increasingly sophisticated material models incorporated in MHOST include elasticity, secant plasticity, infinitesimal and finite deformation plasticity, creep and unified viscoplastic constitutive model proposed by Walker. A library of high performance elements is built into this computer program utilizing the concepts of selective reduced integrations and independent strain interpolations. A family of efficient solution algorithms is implemented in MHOST for linear and nonlinear equation solution including the classical Newton-Raphson, modified, quasi and secant Newton methods with optional line search and the conjugate gradient method.

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island

PubMed Central

Ling, Jun; Wang, Hui; Wu, Ping; Li, Tao; Tang, Yu; Naseer, Nawar; Zheng, Huiming; Masson-Boivin, Catherine; Zhong, Zengtao

2016-01-01

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICEAc) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICEAc-located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity. PMID:27849579

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island.

PubMed

Ling, Jun; Wang, Hui; Wu, Ping; Li, Tao; Tang, Yu; Naseer, Nawar; Zheng, Huiming; Masson-Boivin, Catherine; Zhong, Zengtao; Zhu, Jun

2016-11-29

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICE Ac ) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICE Ac -located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.

Identification of potent orally active factor Xa inhibitors based on conjugation strategy and application of predictable fragment recommender system.

PubMed

Ishihara, Tsukasa; Koga, Yuji; Iwatsuki, Yoshiyuki; Hirayama, Fukushi

2015-01-15

Anticoagulant agents have emerged as a promising class of therapeutic drugs for the treatment and prevention of arterial and venous thrombosis. We investigated a series of novel orally active factor Xa inhibitors designed using our previously reported conjugation strategy to boost oral anticoagulant effect. Structural optimization of anthranilamide derivative 3 as a lead compound with installation of phenolic hydroxyl group and extensive exploration of the P1 binding element led to the identification of 5-chloro-N-(5-chloro-2-pyridyl)-3-hydroxy-2-{[4-(4-methyl-1,4-diazepan-1-yl)benzoyl]amino}benzamide (33, AS1468240) as a potent factor Xa inhibitor with significant oral anticoagulant activity. We also reported a newly developed Free-Wilson-like fragment recommender system based on the integration of R-group decomposition with collaborative filtering for the structural optimization process. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Schellenberg, Matthew J; Appel, C Denise; Adhikari, Sanjay

The topoisomerase II (topo II) DNA incision-and-ligation cycle can be poisoned (for example following treatment with cancer chemotherapeutics) to generate cytotoxic DNA double-strand breaks (DSBs) with topo II covalently conjugated to DNA. Tyrosyl-DNA phosphodiesterase 2 (Tdp2) protects genomic integrity by reversing 5'-phosphotyrosyl–linked topo II–DNA adducts. Here, X-ray structures of mouse Tdp2–DNA complexes reveal that Tdp2 β–2-helix–β DNA damage–binding 'grasp', helical 'cap' and DNA lesion–binding elements fuse to form an elongated protein-DNA conjugate substrate-interaction groove. The Tdp2 DNA-binding surface is highly tailored for engagement of 5'-adducted single-stranded DNA ends and restricts nonspecific endonucleolytic or exonucleolytic processing. Structural, mutational and functional analysesmore » support a single–metal ion catalytic mechanism for the exonuclease-endonuclease-phosphatase (EEP) nuclease superfamily and establish a molecular framework for targeted small-molecule blockade of Tdp2-mediated resistance to anticancer topoisomerase drugs.« less

An Advanced One-Dimensional Finite Element Model for Incompressible Thermally Expandable Flow

DOE PAGES

Hu, Rui

2017-03-27

Here, this paper provides an overview of a new one-dimensional finite element flow model for incompressible but thermally expandable flow. The flow model was developed for use in system analysis tools for whole-plant safety analysis of sodium fast reactors. Although the pressure-based formulation was implemented, the use of integral equations in the conservative form ensured the conservation laws of the fluid. A stabilization scheme based on streamline-upwind/Petrov-Galerkin and pressure-stabilizing/Petrov-Galerkin formulations is also introduced. The flow model and its implementation have been verified by many test problems, including density wave propagation, steep gradient problems, discharging between tanks, and the conjugate heatmore » transfer in a heat exchanger.« less

An Advanced One-Dimensional Finite Element Model for Incompressible Thermally Expandable Flow

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

Hu, Rui

Here, this paper provides an overview of a new one-dimensional finite element flow model for incompressible but thermally expandable flow. The flow model was developed for use in system analysis tools for whole-plant safety analysis of sodium fast reactors. Although the pressure-based formulation was implemented, the use of integral equations in the conservative form ensured the conservation laws of the fluid. A stabilization scheme based on streamline-upwind/Petrov-Galerkin and pressure-stabilizing/Petrov-Galerkin formulations is also introduced. The flow model and its implementation have been verified by many test problems, including density wave propagation, steep gradient problems, discharging between tanks, and the conjugate heatmore » transfer in a heat exchanger.« less

Finite elements and the method of conjugate gradients on a concurrent processor

NASA Technical Reports Server (NTRS)

Lyzenga, G. A.; Raefsky, A.; Hager, G. H.

1985-01-01

An algorithm for the iterative solution of finite element problems on a concurrent processor is presented. The method of conjugate gradients is used to solve the system of matrix equations, which is distributed among the processors of a MIMD computer according to an element-based spatial decomposition. This algorithm is implemented in a two-dimensional elastostatics program on the Caltech Hypercube concurrent processor. The results of tests on up to 32 processors show nearly linear concurrent speedup, with efficiencies over 90 percent for sufficiently large problems.

Finite elements and the method of conjugate gradients on a concurrent processor

NASA Technical Reports Server (NTRS)

Lyzenga, G. A.; Raefsky, A.; Hager, B. H.

1984-01-01

An algorithm for the iterative solution of finite element problems on a concurrent processor is presented. The method of conjugate gradients is used to solve the system of matrix equations, which is distributed among the processors of a MIMD computer according to an element-based spatial decomposition. This algorithm is implemented in a two-dimensional elastostatics program on the Caltech Hypercube concurrent processor. The results of tests on up to 32 processors show nearly linear concurrent speedup, with efficiencies over 90% for sufficiently large problems.

A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens.

PubMed

Cameron, Andrew; Klima, Cassidy L; Ha, Reuben; Gruninger, Robert J; Zaheer, Rahat; McAllister, Tim A

2018-01-01

A novel variant of the AAD(3″) class of aminoglycoside-modifying enzymes was discovered in fatal bovine respiratory disease-associated pathogens Pasteurella multocida and Histophilus somni . The aadA31 gene encodes a spectinomycin/streptomycin adenylyltransferase and was located in a variant of the integrative and conjugative element ICE Mh1 , a mobile genetic element transmissible among members of the family Pasteurellaceae . The gene was also detected in Mannheimia haemolytica from a case of porcine pneumonia and in Moraxella bovoculi from a case of keratoconjunctivitis. IMPORTANCE Aminoglycosides are important antimicrobials used worldwide for prophylaxis and/or therapy in multiple production animal species. The emergence of new resistance genes jeopardizes current pathogen detection and treatment methods. The risk of resistance gene transfer to other animal and human pathogens is elevated when resistance genes are carried by mobile genetic elements. This study identified a new variant of a spectinomycin/streptomycin resistance gene harbored in a self-transmissible mobile element. The gene was also present in four different bovine pathogen species.

A Novel aadA Aminoglycoside Resistance Gene in Bovine and Porcine Pathogens

PubMed Central

Cameron, Andrew; Klima, Cassidy L.; Ha, Reuben; Gruninger, Robert J.; Zaheer, Rahat

2018-01-01

ABSTRACT A novel variant of the AAD(3″) class of aminoglycoside-modifying enzymes was discovered in fatal bovine respiratory disease-associated pathogens Pasteurella multocida and Histophilus somni. The aadA31 gene encodes a spectinomycin/streptomycin adenylyltransferase and was located in a variant of the integrative and conjugative element ICEMh1, a mobile genetic element transmissible among members of the family Pasteurellaceae. The gene was also detected in Mannheimia haemolytica from a case of porcine pneumonia and in Moraxella bovoculi from a case of keratoconjunctivitis. IMPORTANCE Aminoglycosides are important antimicrobials used worldwide for prophylaxis and/or therapy in multiple production animal species. The emergence of new resistance genes jeopardizes current pathogen detection and treatment methods. The risk of resistance gene transfer to other animal and human pathogens is elevated when resistance genes are carried by mobile genetic elements. This study identified a new variant of a spectinomycin/streptomycin resistance gene harbored in a self-transmissible mobile element. The gene was also present in four different bovine pathogen species. PMID:29507894

Surface conforming thermal/pressure seal. [tail assemblies of space shuttle orbiters

NASA Technical Reports Server (NTRS)

Stevens, M. L. (Inventor)

1981-01-01

An assembly is disclosed for sealing a variable gap between the surface of element and a second element in movable relation to it. A seal housing is attached to the second element for movement therewith and has a sealing surface. At least one elongated seal member carried by the housing has first and second conjugate sealing surfaces. The first sealing surface is for rubbing and sealing engagement with the first element surface and the second sealing surface is for sliding and sealing engagement with the housing sealing surface. A biasing assembly may be carried by the housing for biasing the first and second conjugate sealing surfaces of the sealing member toward sealing engagement with the first element surface and housing sealing surface, respectively.

Integrated circuits based on conjugated polymer monolayer

DOE PAGES

Li, Mengmeng; Mangalore, Deepthi Kamath; Zhao, Jingbo; ...

2018-01-31

It is still a great challenge to fabricate conjugated polymer monolayer field-effect transistors (PoM-FETs) due to intricate crystallization and film formation of conjugated polymers. Here we demonstrate PoM-FETs based on a single monolayer of a conjugated polymer. The resulting PoM-FETs are highly reproducible and exhibit charge carrier mobilities reaching 3 cm 2 V -1 s -1. The high performance is attributed to the strong interactions of the polymer chains present already in solution leading to pronounced edge-on packing and well-defined microstructure in the monolayer. The high reproducibility enables the integration of discrete unipolar PoM-FETs into inverters and ring oscillators. Realmore » logic functionality has been demonstrated by constructing a 15-bit code generator in which hundreds of self-assembled PoM-FETs are addressed simultaneously. Lastly, our results provide the state-of-the-art example of integrated circuits based on a conjugated polymer monolayer, opening prospective pathways for bottom-up organic electronics.« less

Integrated circuits based on conjugated polymer monolayer

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

Li, Mengmeng; Mangalore, Deepthi Kamath; Zhao, Jingbo

It is still a great challenge to fabricate conjugated polymer monolayer field-effect transistors (PoM-FETs) due to intricate crystallization and film formation of conjugated polymers. Here we demonstrate PoM-FETs based on a single monolayer of a conjugated polymer. The resulting PoM-FETs are highly reproducible and exhibit charge carrier mobilities reaching 3 cm 2 V -1 s -1. The high performance is attributed to the strong interactions of the polymer chains present already in solution leading to pronounced edge-on packing and well-defined microstructure in the monolayer. The high reproducibility enables the integration of discrete unipolar PoM-FETs into inverters and ring oscillators. Realmore » logic functionality has been demonstrated by constructing a 15-bit code generator in which hundreds of self-assembled PoM-FETs are addressed simultaneously. Lastly, our results provide the state-of-the-art example of integrated circuits based on a conjugated polymer monolayer, opening prospective pathways for bottom-up organic electronics.« less

Integrated circuits based on conjugated polymer monolayer.

PubMed

Li, Mengmeng; Mangalore, Deepthi Kamath; Zhao, Jingbo; Carpenter, Joshua H; Yan, Hongping; Ade, Harald; Yan, He; Müllen, Klaus; Blom, Paul W M; Pisula, Wojciech; de Leeuw, Dago M; Asadi, Kamal

2018-01-31

It is still a great challenge to fabricate conjugated polymer monolayer field-effect transistors (PoM-FETs) due to intricate crystallization and film formation of conjugated polymers. Here we demonstrate PoM-FETs based on a single monolayer of a conjugated polymer. The resulting PoM-FETs are highly reproducible and exhibit charge carrier mobilities reaching 3 cm 2  V -1  s -1 . The high performance is attributed to the strong interactions of the polymer chains present already in solution leading to pronounced edge-on packing and well-defined microstructure in the monolayer. The high reproducibility enables the integration of discrete unipolar PoM-FETs into inverters and ring oscillators. Real logic functionality has been demonstrated by constructing a 15-bit code generator in which hundreds of self-assembled PoM-FETs are addressed simultaneously. Our results provide the state-of-the-art example of integrated circuits based on a conjugated polymer monolayer, opening prospective pathways for bottom-up organic electronics.

VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria.

PubMed

Li, Jun; Tai, Cui; Deng, Zixin; Zhong, Weihong; He, Yongqun; Ou, Hong-Yu

2017-01-10

VRprofile is a Web server that facilitates rapid investigation of virulence and antibiotic resistance genes, as well as extends these trait transfer-related genetic contexts, in newly sequenced pathogenic bacterial genomes. The used backend database MobilomeDB was firstly built on sets of known gene cluster loci of bacterial type III/IV/VI/VII secretion systems and mobile genetic elements, including integrative and conjugative elements, prophages, class I integrons, IS elements and pathogenicity/antibiotic resistance islands. VRprofile is thus able to co-localize the homologs of these conserved gene clusters using HMMer or BLASTp searches. With the integration of the homologous gene cluster search module with a sequence composition module, VRprofile has exhibited better performance for island-like region predictions than the other widely used methods. In addition, VRprofile also provides an integrated Web interface for aligning and visualizing identified gene clusters with MobilomeDB-archived gene clusters, or a variety set of bacterial genomes. VRprofile might contribute to meet the increasing demands of re-annotations of bacterial variable regions, and aid in the real-time definitions of disease-relevant gene clusters in pathogenic bacteria of interest. VRprofile is freely available at http://bioinfo-mml.sjtu.edu.cn/VRprofile. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements.

PubMed

Delahay, Robin M; Croxall, Nicola J; Stephens, Amberley D

2018-01-01

The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island ( cag PAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4 . All three islands are implicated as virulence factors, although whereas the cag PAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population. To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement. Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes.

Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism

PubMed Central

Huang, Kaisong; Zhang, Qiang; Song, Yajing; Zhang, Zhewen; Zhang, Anding; Xiao, Jingfa

2016-01-01

Spectinomycin is an aminocyclitol antibiotic used clinically to treat a variety of infections in animals. Here, we characterized drug resistance prevalence in clinical Streptococcus suis isolates and discovered a novel resistance mechanism in which the s5 mutation (Gly26Asp) results in high spectinomycin resistance. Additionally, a novel integrative and conjugative element encompassing a multidrug resistance spw_like-aadE-lnu(B)-lsa(E) cluster and a cadmium resistance operon were identified, suggesting a possible cause for the wide dissemination of spectinomycin resistance in S. suis. PMID:27458226

Complete genetic analysis of plasmids carrying mcr-1 and other resistance genes in an Escherichia coli isolate of animal origin.

PubMed

Li, Ruichao; Xie, Miaomiao; Lv, Jingzhang; Wai-Chi Chan, Edward; Chen, Sheng

2017-03-01

To investigate the genetic features of three plasmids recovered from an MCR-1 and ESBL-producing Escherichia coli strain, HYEC7, and characterize the transmission mechanism of mcr-1 . The genetic profiles of three plasmids were determined by PCR, S1-PFGE, Southern hybridization and WGS analysis. The ability of the mcr-1 -bearing plasmid to undergo conjugation was also assessed. The mcr-1 -bearing transposon Tn 6330 was characterized by PCR and DNA sequencing. Complete sequences of three plasmids were obtained. A non-conjugative phage P7-like plasmid, pHYEC7- mcr1 , was found to harbour the mcr-1 -bearing transposon Tn 6330 , which could be excised from the plasmid by generating a circular intermediate harbouring mcr-1 and the IS Apl1 element. The insertion of the circular intermediate into another plasmid, pHYEC7-IncHI2, could form pHNSHP45-2, the original IncHI2-type mcr-1 -carrying plasmid that was reported. The third plasmid, pHYEC7-110, harboured two replicons, IncX1 and IncFIB, and comprised multiple antimicrobial resistance mobile elements, some of which were shared by pHYEC7-IncHI2. The Tn 6330 element located in the phage-like plasmid pHYEC7- mcr1 could be excised from the plasmid and formed a circular intermediate that could be integrated into plasmids containing the IS Apl1 element. This phenomenon indicated that Tn 6330 is a key element responsible for widespread dissemination of mcr-1 among various types of plasmids and bacterial chromosomes. The dissemination rate of such an element may be further enhanced upon translocation into phage-like vectors, which may also be transmitted via transduction events. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Using Multifunctional Peptide Conjugated Au Nanorods for Monitoring β-amyloid Aggregation and Chemo-Photothermal Treatment of Alzheimer's Disease.

PubMed

Li, Meng; Guan, Yijia; Zhao, Andong; Ren, Jinsong; Qu, Xiaogang

2017-01-01

Development of sensitive detectors of Aβ aggregates and effective inhibitors of Aβ aggregation are of diagnostic importance and therapeutic implications for Alzheimer's disease (AD) treatment. Herein, a novel strategy has been presented by self-assembly of peptide conjugated Au nanorods (AuP) as multifunctional Aβ fibrillization detectors and inhibitors. Our design combines the unique high NIR absorption property of AuNRs with two known Aβ inhibitors, Aβ15-20 and polyoxometalates (POMs). The synthesized AuP can effectively inhibit Aβ aggregation and dissociate amyloid deposits with NIR irradiation both in buffer and in mice cerebrospinal fluid (CSF), and protect cells from Aβ-related toxicity upon NIR irradiation. In addition, with the shape and size-dependent optical properties, the nanorods can also act as effective diagnostic probes to sensitively detect the Aβ aggregates. This is the first report to integrate 3 segments, an Aβ-targeting element, a reporter and inhibitors, in one drug delivery system for AD treatment.

Using Multifunctional Peptide Conjugated Au Nanorods for Monitoring β-amyloid Aggregation and Chemo-Photothermal Treatment of Alzheimer's Disease

PubMed Central

Li, Meng; Guan, Yijia; Zhao, Andong; Ren, Jinsong; Qu, Xiaogang

2017-01-01

Development of sensitive detectors of Aβ aggregates and effective inhibitors of Aβ aggregation are of diagnostic importance and therapeutic implications for Alzheimer's disease (AD) treatment. Herein, a novel strategy has been presented by self-assembly of peptide conjugated Au nanorods (AuP) as multifunctional Aβ fibrillization detectors and inhibitors. Our design combines the unique high NIR absorption property of AuNRs with two known Aβ inhibitors, Aβ15-20 and polyoxometalates (POMs). The synthesized AuP can effectively inhibit Aβ aggregation and dissociate amyloid deposits with NIR irradiation both in buffer and in mice cerebrospinal fluid (CSF), and protect cells from Aβ-related toxicity upon NIR irradiation. In addition, with the shape and size-dependent optical properties, the nanorods can also act as effective diagnostic probes to sensitively detect the Aβ aggregates. This is the first report to integrate 3 segments, an Aβ-targeting element, a reporter and inhibitors, in one drug delivery system for AD treatment. PMID:28839459

Unusual genome complexity in Lactobacillus salivarius JCM1046.

PubMed

Raftis, Emma J; Forde, Brian M; Claesson, Marcus J; O'Toole, Paul W

2014-09-08

Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable and is often mediated by plasmids or integrative and conjugative elements. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. Linear plasmids are less common in lactobacilli and show a very limited distribution in L. salivarius. Here we present experimental evidence that supports an unusually complex multireplicon genome structure in the porcine isolate L. salivarius JCM1046. JCM1046 harbours a 1.83 Mb chromosome, and four plasmids which constitute 20% of the genome. In addition to the known 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated the topology of three additional replicons, the circular pMP1046B (129 kb), a linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative transposon. pMP1046B harbours both plasmid-associated replication genes and paralogues of chromosomally encoded housekeeping and information-processing related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited sequence homology or gene synteny with other L. salivarius plasmids, and its putative replication-associated protein is homologous to the RepA/E proteins found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046 harbours a single copy of an integrated conjugative transposon (Tn6224) which appears to be functionally intact and includes the tetracycline resistance gene tetM. Experimental validation of sequence assemblies and plasmid topology resolved the complex genome architecture of L. salivarius JCM1046. A high-coverage draft genome sequence would not have elucidated the genome complexity in this strain. Given the expanding use of L. salivarius as a probiotic, it is important to determine the genotypic and phenotypic organization of L. salivarius strains. The identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications.

Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes.

PubMed

Marini, Emanuela; Palmieri, Claudio; Magi, Gloria; Facinelli, Bruna

2015-07-09

Integrative conjugative elements (ICEs) are mobile genetic elements that reside in the chromosome but retain the ability to undergo excision and to transfer by conjugation. Genes involved in drug resistance, virulence, or niche adaptation are often found among backbone genes as cargo DNA. We recently characterized in Streptococcus suis an ICE (ICESsu32457) carrying resistance genes [tet(O/W/32/O), tet(40), erm(B), aphA, and aadE] in the 15K unstable genetic element, which is flanked by two ∼1.3kb direct repeats. Remarkably, ∼1.3-kb sequences are conserved in ICESa2603 of Streptococcus agalactiae 2603V/R, which carry heavy metal resistance genes cadC/cadA and mer. In matings between S. suis 32457 (donor) and S. agalactiae 2603V/R (recipient), transconjugants were obtained. PCR experiments, PFGE, and sequence analysis of transconjugants demonstrated a tandem array between ICESsu32457 and ICESa2603. Matings between tandem array-containing S. agalactiae 2603V/R (donor) and Streptococcus pyogenes RF12 (recipient) yielded a single transconjugant containing a hybrid ICE, here named ICESa2603/ICESsu32457. The hybrid formed by recombination of the left ∼1.3-kb sequence of ICESsu32457 and the ∼1.3-kb sequence of ICESa2603. Interestingly, the hybrid ICE was transferable between S. pyogenes strains, thus demonstrating that it behaves as a conventional ICE. These findings suggest that both tandem arrays and hybrid ICEs may contribute to the evolution of antibiotic resistance in streptococci, creating novel mobile elements capable of disseminating new combinations of antibiotic resistance genes. Copyright © 2015 Elsevier B.V. All rights reserved.

An integrated multiple-analyte pharmacokinetic model to characterize trastuzumab emtansine (T-DM1) clearance pathways and to evaluate reduced pharmacokinetic sampling in patients with HER2-positive metastatic breast cancer.

PubMed

Lu, Dan; Joshi, Amita; Wang, Bei; Olsen, Steve; Yi, Joo-Hee; Krop, Ian E; Burris, Howard A; Girish, Sandhya

2013-08-01

Trastuzumab emtansine (T-DM1) is an antibody-drug conjugate recently approved by the US Food and Drug Administration for the treatment of human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer previously treated with trastuzumab and taxane chemotherapy. It comprises the microtubule inhibitory cytotoxic agent DM1 conjugated to the HER2-targeted humanized monoclonal antibody trastuzumab via a stable linker. To characterize the pharmacokinetics of T-DM1 in patients with metastatic breast cancer, concentrations of multiple analytes were quantified, including serum concentrations of T-DM1 conjugate and total trastuzumab (the sum of conjugated and unconjugated trastuzumab), as well as plasma concentrations of DM1. The clearance of T-DM1 conjugate is approximately 2 to 3 times faster than its parent antibody, trastuzumab. However, the clearance pathways accounting for this faster clearance rate are unclear. An integrated population pharmacokinetic model that simultaneously fits the pharmacokinetics of T-DM1 conjugate and total trastuzumab can help to elucidate the clearance pathways of T-DM1. The model can also be used to predict total trastuzumab pharmacokinetic profiles based on T-DM1 conjugate pharmacokinetic data and sparse total trastuzumab pharmacokinetic data, thereby reducing the frequency of pharmacokinetic sampling. T-DM1 conjugate and total trastuzumab serum concentration data, including baseline trastuzumab concentrations prior to T-DM1 treatment, from phase I and II studies were used to develop this integrated population pharmacokinetic model. Based on a hypothetical T-DM1 catabolism scheme, two-compartment models for T-DM1 conjugate and trastuzumab were integrated by assuming a one-step deconjugation clearance from T-DM1 conjugate to trastuzumab. The ability of the model to predict the total trastuzumab pharmacokinetic profile based on T-DM1 conjugate pharmacokinetics and various sampling schemes of total trastuzumab pharmacokinetics was assessed to evaluate total trastuzumab sampling schemes. The final model reflects a simplified catabolism scheme of T-DM1, suggesting that T-DM1 clearance pathways include both deconjugation and proteolytic degradation. The model fits T-DM1 conjugate and total trastuzumab pharmacokinetic data simultaneously. The deconjugation clearance of T-DM1 was estimated to be ~0.4 L/day. Proteolytic degradation clearances for T-DM1 and trastuzumab were similar (~0.3 L/day). This model accurately predicts total trastuzumab pharmacokinetic profiles based on T-DM1 conjugate pharmacokinetic data and sparse total trastuzumab pharmacokinetic data sampled at preinfusion and end of infusion in cycle 1, and in one additional steady state cycle. This semi-mechanistic integrated model links T-DM1 conjugate and total trastuzumab pharmacokinetic data, and supports the inclusion of both proteolytic degradation and deconjugation as clearance pathways in the hypothetical T-DM1 catabolism scheme. The model attributes a faster T-DM1 conjugate clearance versus that of trastuzumab to the presence of a deconjugation process and suggests a similar proteolytic clearance of T-DM1 and trastuzumab. Based on the model and T-DM1 conjugate pharmacokinetic data, a sparse pharmacokinetic sampling scheme for total trastuzumab provides an entire pharmacokinetic profile with similar predictive accuracy to that of a dense pharmacokinetic sampling scheme.

Acquisition and evolution of SXT-R391 integrative conjugative elements in the seventh-pandemic Vibrio cholerae lineage.

PubMed

Spagnoletti, Matteo; Ceccarelli, Daniela; Rieux, Adrien; Fondi, Marco; Taviani, Elisa; Fani, Renato; Colombo, Mauro M; Colwell, Rita R; Balloux, François

2014-08-19

SXT-R391 Integrative conjugative elements (ICEs) are self-transmissible mobile genetic elements able to confer multidrug resistance and other adaptive features to bacterial hosts, including Vibrio cholerae, the causative agent of cholera. ICEs are arranged in a mosaic genetic structure composed of a conserved backbone interspersed with variable DNA clusters located in conserved hot spots. In this study, we investigated ICE acquisition and subsequent microevolution in pandemic V. cholerae. Ninety-six ICEs were retrieved from publicly available sequence databases from V. cholerae clinical strains and were compared to a set of reference ICEs. Comparative genomics highlighted the existence of five main ICE groups with a distinct genetic makeup, exemplified by ICEVchInd5, ICEVchMoz10, SXT, ICEVchInd6, and ICEVchBan11. ICEVchInd5 (the most frequent element, represented by 70 of 96 elements analyzed) displayed no sequence rearrangements and was characterized by 46 single nucleotide polymorphisms (SNPs). SNP analysis revealed that recent inter-ICE homologous recombination between ICEVchInd5 and other ICEs circulating in gammaproteobacteria generated ICEVchMoz10, ICEVchInd6, and ICEVchBan11. Bayesian phylogenetic analyses indicated that ICEVchInd5 and SXT were independently acquired by the current pandemic V. cholerae O1 and O139 lineages, respectively, within a period of only a few years. SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V. cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V. cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V. cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria. Copyright © 2014 Spagnoletti et al.

Characterization of a Streptococcus suis tet(O/W/32/O)-carrying element transferable to major streptococcal pathogens.

PubMed

Palmieri, Claudio; Magi, Gloria; Mingoia, Marina; Bagnarelli, Patrizia; Ripa, Sandro; Varaldo, Pietro E; Facinelli, Bruna

2012-09-01

Mosaic tetracycline resistance determinants are a recently discovered class of hybrids of ribosomal protection tet genes. They may show different patterns of mosaicism, but their final size has remained unaltered. Initially thought to be confined to a small group of anaerobic bacteria, mosaic tet genes were then found to be widespread. In the genus Streptococcus, a mosaic tet gene [tet(O/W/32/O)] was first discovered in Streptococcus suis, an emerging drug-resistant pig and human pathogen. In this study, we report the molecular characterization of a tet(O/W/32/O) gene-carrying mobile element from an S. suis isolate. tet(O/W/32/O) was detected, in tandem with tet(40), in a circular 14,741-bp genetic element (39.1% G+C; 17 open reading frames [ORFs] identified). The novel element, which we designated 15K, also carried the macrolide resistance determinant erm(B) and an aminoglycoside resistance four-gene cluster including aadE (streptomycin) and aphA (kanamycin). 15K appeared to be an unstable genetic element that, in the absence of recombinases, is capable of undergoing spontaneous excision under standard growth conditions. In the integrated form, 15K was found inside a 54,879-bp integrative and conjugative element (ICE) (50.5% G+C; 55 ORFs), which we designated ICESsu32457. An ∼1.3-kb segment that apparently served as the att site for excision of the unstable 15K element was identified. The novel ICE was transferable at high frequency to recipients from pathogenic Streptococcus species (S. suis, Streptococcus pyogenes, Streptococcus pneumoniae, and Streptococcus agalactiae), suggesting that the multiresistance 15K element can successfully spread within streptococcal populations.

An Integrated Solution for Performing Thermo-fluid Conjugate Analysis

NASA Technical Reports Server (NTRS)

Kornberg, Oren

2009-01-01

A method has been developed which integrates a fluid flow analyzer and a thermal analyzer to produce both steady state and transient results of 1-D, 2-D, and 3-D analysis models. The Generalized Fluid System Simulation Program (GFSSP) is a one dimensional, general purpose fluid analysis code which computes pressures and flow distributions in complex fluid networks. The MSC Systems Improved Numerical Differencing Analyzer (MSC.SINDA) is a one dimensional general purpose thermal analyzer that solves network representations of thermal systems. Both GFSSP and MSC.SINDA have graphical user interfaces which are used to build the respective model and prepare it for analysis. The SINDA/GFSSP Conjugate Integrator (SGCI) is a formbase graphical integration program used to set input parameters for the conjugate analyses and run the models. The contents of this paper describes SGCI and its thermo-fluids conjugate analysis techniques and capabilities by presenting results from some example models including the cryogenic chill down of a copper pipe, a bar between two walls in a fluid stream, and a solid plate creating a phase change in a flowing fluid.

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

Wannamaker, Philip E.

We have developed an algorithm for the inversion of magnetotelluric (MT) data to a 3D earth resistivity model based upon the finite element method. Hexahedral edge finite elements are implemented to accommodate discontinuities in the electric field across resistivity boundaries, and to accurately simulate topographic variations. All matrices are reduced and solved using direct solution modules which avoids ill-conditioning endemic to iterative solvers such as conjugate gradients, principally PARDISO for the finite element system and PLASMA for the parameter step estimate. Large model parameterizations can be handled by transforming the Gauss-Newton estimator to data-space form. Accuracy of the forward problemmore » and jacobians has been checked by comparison to integral equations results and by limiting asymptotes. Inverse accuracy and performance has been verified against the public Dublin Secret Test Model 2 and the well-known Mount St Helens 3D MT data set. This algorithm we believe is the most capable yet for forming 3D images of earth resistivity structure and their implications for geothermal fluids and pathways.« less

Characterization of the Porphyromonas gingivalis conjugative transposon CTnPg1: determination of the integration site and the genes essential for conjugal transfer.

PubMed

Naito, Mariko; Sato, Keiko; Shoji, Mikio; Yukitake, Hideharu; Ogura, Yoshitoshi; Hayashi, Tetsuya; Nakayama, Koji

2011-07-01

In our previous study, extensive genomic rearrangements were found in two strains of the Gram-negative anaerobic bacterium Porphyromonas (Por.) gingivalis, and most of these rearrangements were associated with mobile genetic elements such as insertion sequences and conjugative transposons (CTns). CTnPg1, identified in Por. gingivalis strain ATCC 33277, was the first complete CTn reported for the genus Porphyromonas. In the present study, we found that CTnPg1 can be transferred from strain ATCC 33277 to another Por. gingivalis strain, W83, at a frequency of 10(-7) to 10(-6). The excision of CTnPg1 from the chromosome in a donor cell depends on an integrase (Int; PGN_0094) encoded in CTnPg1, whereas CTnPg1 excision is independent of PGN_0084 (a DNA topoisomerase I homologue; Exc) encoded within CTnPg1 and recA (PGN_1057) on the donor chromosome. Intriguingly, however, the transfer of CTnPg1 between Por. gingivalis strains requires RecA function in the recipient. Sequencing analysis of CTnPg1-integrated sites on the chromosomes of transconjugants revealed that the consensus attachment (att) sequence is a 13 bp sequence, TTTTCNNNNAAAA. We further report that CTnPg1 is able to transfer to two other bacterial species, Bacteroides thetaiotaomicron and Prevotella oralis. In addition, CTnPg1-like CTns are located in the genomes of other oral anaerobic bacteria, Porphyromonas endodontalis, Prevotella buccae and Prevotella intermedia, with the same consensus att sequence. These results suggest that CTns in the CTnPg1 family are widely distributed among oral anaerobic Gram-negative bacteria found in humans and play important roles in horizontal gene transfer among these bacteria.

A feasibility study of a 3-D finite element solution scheme for aeroengine duct acoustics

NASA Technical Reports Server (NTRS)

Abrahamson, A. L.

1980-01-01

The advantage from development of a 3-D model of aeroengine duct acoustics is the ability to analyze axial and circumferential liner segmentation simultaneously. The feasibility of a 3-D duct acoustics model was investigated using Galerkin or least squares element formulations combined with Gaussian elimination, successive over-relaxation, or conjugate gradient solution algorithms on conventional scalar computers and on a vector machine. A least squares element formulation combined with a conjugate gradient solver on a CDC Star vector computer initially appeared to have great promise, but severe difficulties were encountered with matrix ill-conditioning. These difficulties in conditioning rendered this technique impractical for realistic problems.

Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism.

PubMed

Huang, Kaisong; Zhang, Qiang; Song, Yajing; Zhang, Zhewen; Zhang, Anding; Xiao, Jingfa; Jin, Meilin

2016-10-01

Spectinomycin is an aminocyclitol antibiotic used clinically to treat a variety of infections in animals. Here, we characterized drug resistance prevalence in clinical Streptococcus suis isolates and discovered a novel resistance mechanism in which the s5 mutation (Gly26Asp) results in high spectinomycin resistance. Additionally, a novel integrative and conjugative element encompassing a multidrug resistance spw_like-aadE-lnu(B)-lsa(E) cluster and a cadmium resistance operon were identified, suggesting a possible cause for the wide dissemination of spectinomycin resistance in S. suis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The marriage of metallacycle transfer chemistry with Suzuki-Miyaura cross-coupling to give main group element-containing conjugated polymers.

PubMed

He, Gang; Kang, Le; Torres Delgado, William; Shynkaruk, Olena; Ferguson, Michael J; McDonald, Robert; Rivard, Eric

2013-04-10

A versatile and general synthetic route for the synthesis of conjugated main group element-based polymers, previously inaccessible by conventional means, is reported. These polymers contain five-membered chalcogenophene rings based on S, Se, and Te, and we demonstrate that optoelectronic properties can be readily tuned via controlled atom substitution chemistry. In addition, regioregular hybrid thiophene-selenophene-tellurophene and selenophene-fluorene copolymers were synthesized to provide a further illustration of the scope of the presented metallacycle transfer/cross-coupling polymerization method.

Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.

PubMed

López-Pérez, Mario; Ramon-Marco, Nieves; Rodriguez-Valera, Francisco

2017-01-05

To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time. We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold. We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity.

Toward High Performance Photovoltaic Cells based on Conjugated Polymers

DTIC Science & Technology

2016-12-26

AFRL-AFOSR-JP-TR-2016-0103 Toward High Performance Photovoltaic Cells based on Conjugated Polymers Kung-Hwa Wei National Chiao Tung University Final...Conjugated Polymers 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-15-1-4113 5c.  PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) Kung-Hwa Wei 5d.  PROJECT...gap polymer with good packing order as the active layer for a single-junction photovoltaic device. The light absorptions for the small molecule and the

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements

PubMed Central

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-01-01

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading. PMID:25686154

pTC Plasmids from Sulfolobus Species in the Geothermal Area of Tengchong, China: Genomic Conservation and Naturally-Occurring Variations as a Result of Transposition by Mobile Genetic Elements.

PubMed

Xiang, Xiaoyu; Huang, Xiaoxing; Wang, Haina; Huang, Li

2015-02-12

Plasmids occur frequently in Archaea. A novel plasmid (denoted pTC1) containing typical conjugation functions has been isolated from Sulfolobus tengchongensis RT8-4, a strain obtained from a hot spring in Tengchong, China, and characterized. The plasmid is a circular double-stranded DNA molecule of 20,417 bp. Among a total of 26 predicted pTC1 ORFs, 23 have homologues in other known Sulfolobus conjugative plasmids (CPs). pTC1 resembles other Sulfolobus CPs in genome architecture, and is most highly conserved in the genomic region encoding conjugation functions. However, attempts to demonstrate experimentally the capacity of the plasmid for conjugational transfer were unsuccessful. A survey revealed that pTC1 and its closely related plasmid variants were widespread in the geothermal area of Tengchong. Variations of the plasmids at the target sites for transposition by an insertion sequence (IS) and a miniature inverted-repeat transposable element (MITE) were readily detected. The IS was efficiently inserted into the pTC1 genome, and the inserted sequence was inactivated and degraded more frequently in an imprecise manner than in a precise manner. These results suggest that the host organism has evolved a strategy to maintain a balance between the insertion and elimination of mobile genetic elements to permit genomic plasticity while inhibiting their fast spreading.

Numerical Simulations of Single Flow Element in a Nuclear Thermal Thrust Chamber

NASA Technical Reports Server (NTRS)

Cheng, Gary; Ito, Yasushi; Ross, Doug; Chen, Yen-Sen; Wang, Ten-See

2007-01-01

The objective of this effort is to develop an efficient and accurate computational methodology to predict both detailed and global thermo-fluid environments of a single now element in a hypothetical solid-core nuclear thermal thrust chamber assembly, Several numerical and multi-physics thermo-fluid models, such as chemical reactions, turbulence, conjugate heat transfer, porosity, and power generation, were incorporated into an unstructured-grid, pressure-based computational fluid dynamics solver. The numerical simulations of a single now element provide a detailed thermo-fluid environment for thermal stress estimation and insight for possible occurrence of mid-section corrosion. In addition, detailed conjugate heat transfer simulations were employed to develop the porosity models for efficient pressure drop and thermal load calculations.

Preliminary result of the solar multi-conjugate adaptive optics for 1m new vacuum solar telescope

NASA Astrophysics Data System (ADS)

Zhang, Lanqiang; Kong, Lin; Bao, Hua; Zhu, Lei; Rao, Xuejun; Rao, Changhui

2016-07-01

Solar observation with high resolution in large field of view (FoV) is required for some solar active regions with the typical sizes of 1' to 3'. Conventional adaptive optics (AO) could not satisfy this demand because of the atmospheric anisoplanatism. Through compensating the turbulence in different heights, multi-conjugate adaptive optics (MCAO) has been proved to obtain a larger corrected FoV. A MCAO experimental system including a conventional 151-element AO system and a 37-element MCAO part is being developed. The MCAO part contains a 37-element deformable mirror conjugated into the 2km to 5km height and a multi-direction Shack-Hartmann wavefront sensor (MD-SHWFS) with 7×7 subaperture array and 60 arcsec FoV, the frame rate of the MD-SHWFS is up to 840Hz. Three-dimensional (3-D) wavefront sensing utilizing atmospheric tomography had been validated by solar observation. Based on these results, a ground layer adaptive optics (GLAO) experimental system including a 151-element deformable mirror and the MD-SHWFS has been built at the 1m New Vacuum Solar Telescope (NVST). In this paper, the MCAO experimental system will be introduced. The preliminary experimental results of three-dimensional wavefront sensing and GLAO on the NVST of Full-shine Lake Solar Observatory are presented.

Discovery of a conjugative megaplasmid in Bifidobacterium breve.

PubMed

Bottacini, Francesca; O'Connell Motherway, Mary; Casey, Eoghan; McDonnell, Brian; Mahony, Jennifer; Ventura, Marco; van Sinderen, Douwe

2015-01-01

Bifidobacterium breve is a common and sometimes very abundant inhabitant of the human gut. Genome sequencing of B. breve JCM 7017 revealed the presence of an extrachromosomal element, designated pMP7017 consisting of >190 kb, thus representing the first reported bifidobacterial megaplasmid. In silico characterization of this element revealed several genomic features supporting a stable establishment of the megaplasmid in its host, illustrated by predicted CRISPR-Cas functions that are known to protect the host against intrusion of foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer apparatus and, consistent with this notion, we demonstrate here the conjugal transfer of pMP7017 to representative strains of B. breve and B. longum subsp. longum. We also demonstrate the presence of a megaplasmid with homology to pMP7017 in three B. longum subsp. longum strains. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Discovery of a Conjugative Megaplasmid in Bifidobacterium breve

PubMed Central

Bottacini, Francesca; O'Connell Motherway, Mary; Casey, Eoghan; McDonnell, Brian; Mahony, Jennifer; Ventura, Marco

2014-01-01

Bifidobacterium breve is a common and sometimes very abundant inhabitant of the human gut. Genome sequencing of B. breve JCM 7017 revealed the presence of an extrachromosomal element, designated pMP7017 consisting of >190 kb, thus representing the first reported bifidobacterial megaplasmid. In silico characterization of this element revealed several genomic features supporting a stable establishment of the megaplasmid in its host, illustrated by predicted CRISPR-Cas functions that are known to protect the host against intrusion of foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer apparatus and, consistent with this notion, we demonstrate here the conjugal transfer of pMP7017 to representative strains of B. breve and B. longum subsp. longum. We also demonstrate the presence of a megaplasmid with homology to pMP7017 in three B. longum subsp. longum strains. PMID:25326305

On a concurrent element-by-element preconditioned conjugate gradient algorithm for multiple load cases

NASA Technical Reports Server (NTRS)

Watson, Brian; Kamat, M. P.

1990-01-01

Element-by-element preconditioned conjugate gradient (EBE-PCG) algorithms have been advocated for use in parallel/vector processing environments as being superior to the conventional LDL(exp T) decomposition algorithm for single load cases. Although there may be some advantages in using such algorithms for a single load case, when it comes to situations involving multiple load cases, the LDL(exp T) decomposition algorithm would appear to be decidedly more cost-effective. The authors have outlined an EBE-PCG algorithm suitable for multiple load cases and compared its effectiveness to the highly efficient LDL(exp T) decomposition scheme. The proposed algorithm offers almost no advantages over the LDL(exp T) algorithm for the linear problems investigated on the Alliant FX/8. However, there may be some merit in the algorithm in solving nonlinear problems with load incrementation, but that remains to be investigated.

An M-step preconditioned conjugate gradient method for parallel computation

NASA Technical Reports Server (NTRS)

Adams, L.

1983-01-01

This paper describes a preconditioned conjugate gradient method that can be effectively implemented on both vector machines and parallel arrays to solve sparse symmetric and positive definite systems of linear equations. The implementation on the CYBER 203/205 and on the Finite Element Machine is discussed and results obtained using the method on these machines are given.

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

Chen, Haixia; Zhang, Jing

We propose a scheme for continuous-variable quantum cloning of coherent states with phase-conjugate input modes using linear optics. The quantum cloning machine yields M identical optimal clones from N replicas of a coherent state and N replicas of its phase conjugate. This scheme can be straightforwardly implemented with the setups accessible at present since its optical implementation only employs simple linear optical elements and homodyne detection. Compared with the original scheme for continuous-variable quantum cloning with phase-conjugate input modes proposed by Cerf and Iblisdir [Phys. Rev. Lett. 87, 247903 (2001)], which utilized a nondegenerate optical parametric amplifier, our scheme losesmore » the output of phase-conjugate clones and is regarded as irreversible quantum cloning.« less

Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance.

PubMed

Davies, Mark R; Holden, Matthew T; Coupland, Paul; Chen, Jonathan H K; Venturini, Carola; Barnett, Timothy C; Zakour, Nouri L Ben; Tse, Herman; Dougan, Gordon; Yuen, Kwok-Yung; Walker, Mark J

2015-01-01

A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1-6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two mobile genetic elements that were closely associated with emm12 outbreak isolates: the integrative and conjugative element ICE-emm12, encoding genes for tetracycline and macrolide resistance, and prophage ΦHKU.vir, encoding the superantigens SSA and SpeC, as well as the DNase Spd1 (ref. 4). Here we sequenced the genomes of 141 emm12 isolates, including 132 isolated in Hong Kong between 2005 and 2011. We found that the introduction of several ICE-emm12 variants, ΦHKU.vir and a new prophage, ΦHKU.ssa, occurred in three distinct emm12 lineages late in the twentieth century. Acquisition of ssa and transposable elements encoding multidrug resistance genes triggered the expansion of scarlet fever-associated emm12 lineages in Hong Kong. The occurrence of multidrug-resistant ssa-harboring scarlet fever strains should prompt heightened surveillance within China and abroad for the dissemination of these mobile genetic elements.

Exploiting the co-reliance of tumours upon transport of amino acids and lactate: Gln and Tyr conjugates of MCT1 inhibitors.

PubMed

Nair, Reji N; Mishra, Jitendra K; Li, Fangzheng; Tortosa, Mariola; Yang, Chunying; Doherty, Joanne R; Cameron, Michael; Cleveland, John L; Roush, William R; Bannister, Thomas D

2016-05-01

Glutamine and tyrosine-based amino acid conjugates of monocarboxylate transporter types 1 and 2 inhibitors (MCT1/2) were designed, synthesized and evaluated for their potency in blocking the proliferation of a human B lymphoma cell line that expresses the transporters Asct2, LAT1 and MCT1. Appropriate placement of an amino acid transporter recognition element was shown to augment anti-tumour efficacy vs. Raji cells. Amino acid conjugation also improves the pharmacodynamic properties of experimental MCT1/2 inhibitors.

Tuning the properties of conjugated polyelectrolytes and application in a biosensor platform

DOEpatents

Chen, Liaohai

2004-05-18

The present invention provides a method of detecting a biological agent including contacting a sample with a sensor including a polymer system capable of having an alterable measurable property from the group of luminescence, anisotropy, redox potential and uv/vis absorption, the polymer system including an ionic conjugated polymer and an electronically inert polyelectrolyte having a biological agent recognition element bound thereto, the electronically inert polyelectrolyte adapted for undergoing a conformational structural change upon exposure to a biological agent having affinity for binding to the recognition element bound to the electronically inert polyelectrolyte, and, detecting the detectable change in the alterable measurable property. A chemical moiety being the reaction product of (i) a polyelectrolyte monomer and (ii) a biological agent recognition element-substituted polyelectrolyte monomer is also provided.

Studies on transposable elements in yeast. I. ROAM mutations causing increased expression of yeast genes: their activation by signals directed toward conjugation functions and their formation by insertion of Tyl repetitive elements

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

Errede, B.; Cardillo, T.S.; Wever, G.

1981-01-01

Mechanisms available to eukaryotic organisms for the coordinate regulation of gene expression are being examined by genetic and biochemical characterization of an unusual mutation, CYC7-H2, which causes over-production of iso-2-cytochrome c in the yeast Saccharomyces cerevisiae. The CYC7-H2 mutation causes overproduction in haploid strains but only a 1- to 40-fold overproduction in MATa/MAT..cap alpha.. diploid strains. This regulation of overproduction has been characterized as a response to signals controlling conjugation in yeast. Furthermore, the abnormal controlling region has been identified as an insertion of a transposable and reiterated Ty1 element adjacent to the structural gene. Therefore, we suggest that Ty1more » elements or portions of Ty1 elements occur adjacent to some of the genes required for conjugation and that they normally function to control expression of this process. The suggested role of reiterated sequences may represent a general mechanism of coordinate regulation in eukaryotes. The CYC7-H2 mutation is closely related to other regulatory mutations occurring at the cargA, cargB and DUR1,2 loci. Similar to the CYC7-H2 mutation, the mutations designated cargA/sup +/O/sup h/, cargB/sup +/O/sup h/, and durO/sup h/ cause constitutive production of their respective gene products at much lower levels of MATa/MAT..cap alpha.. diploid strains than in the corresponding haploid strains. A consistent relationship between conjugation competence and the level of overproduction in all four mutants has been established. Observations characterizing the regulation of overproduction in the CYC7-H2 mutant are presented with the additional and parallel observations for the O/sup h/ mutants. Together these results provide a demonstration of the specificity and equivalence of regulatory control exhibited by ROAM mutants.« less

Targeting FR-expressing cells in ovarian cancer with Fab-functionalized nanoparticles: a full study to provide the proof of principle from in vitro to in vivo

NASA Astrophysics Data System (ADS)

Quarta, Alessandra; Bernareggi, Davide; Benigni, Fabio; Luison, Elena; Nano, Giuseppe; Nitti, Simone; Cesta, Maria Candida; di Ciccio, Luciano; Canevari, Silvana; Pellegrino, Teresa; Figini, Mariangela

2015-01-01

Efficient targeting in tumor therapies is still an open issue: systemic biodistribution and poor specific accumulation of drugs weaken efficacy of treatments. Engineered nanoparticles are expected to bring benefits by allowing specific delivery of drug to the tumor or acting themselves as localized therapeutic agents. In this study we have targeted epithelial ovarian cancer with inorganic nanoparticles conjugated to a human antibody fragment against the folate receptor over-expressed on cancer cells. The conjugation approach is generally applicable. Indeed several types of nanoparticles (either magnetic or fluorescent) were engineered with the fragment, and their biological activity was preserved as demonstrated by biochemical methods in vitro. In vivo studies with mice bearing orthotopic and subcutaneous tumors were performed. Elemental and histological analyses showed that the conjugated magnetic nanoparticles accumulated specifically and were retained at tumor sites longer than the non-conjugated nanoparticles.Efficient targeting in tumor therapies is still an open issue: systemic biodistribution and poor specific accumulation of drugs weaken efficacy of treatments. Engineered nanoparticles are expected to bring benefits by allowing specific delivery of drug to the tumor or acting themselves as localized therapeutic agents. In this study we have targeted epithelial ovarian cancer with inorganic nanoparticles conjugated to a human antibody fragment against the folate receptor over-expressed on cancer cells. The conjugation approach is generally applicable. Indeed several types of nanoparticles (either magnetic or fluorescent) were engineered with the fragment, and their biological activity was preserved as demonstrated by biochemical methods in vitro. In vivo studies with mice bearing orthotopic and subcutaneous tumors were performed. Elemental and histological analyses showed that the conjugated magnetic nanoparticles accumulated specifically and were retained at tumor sites longer than the non-conjugated nanoparticles. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr04426f

Integration of replication-defective R68.45-like plasmids into the Pseudomonas aeruginosa chromosome.

PubMed

Reimmann, C; Rella, M; Haas, D

1988-06-01

R68.45 and other similar broad-host-range (IncP) plasmids carrying a tandem repeat of the 2.1 kb insertion element IS21 mobilize the chromosome of many different Gram-negative bacteria. To analyse the structure of R68.45-chromosome cointegrates, whose involvement in the mobilization process had been postulated previously, we selected for the stable integration of R68.45-like plasmids into the Pseudomonas aeruginosa chromosome. Two plasmids were chosen: pME28, a transfer-deficient, mobilizable RP1 derivative with an inactive replication control (trfA) gene, and pME487, an R68.45 derivative with a trfA(ts) mutation causing temperature-sensitive replication. Chromosomally integrated pME28 and pME487 were found to be flanked by single IS21 elements. This structure is in agreement with a 'cut-and-paste' mode of R68.45 transposition. pME28 and pME487 showed a low specificity of insertion but rarely (less than 0.1%) induced auxotrophic mutations. Hfr (high-frequency-of-recombination) donors of P. aeruginosa could be obtained by chromosomal integration of pME487 or pME28; in the latter case, the transfer functions lacking from pME28 had to be provided in trans on an autonomous plasmid. Hfr donors gave higher conjugational linkage and transferred longer stretches of the P. aeruginosa chromosome than did R68.45 donors. This suggests that the integration of R68.45 into the donor chromosome is short-lived in P. aeruginosa.

Single domain antibody-quantum dot conjugates for ricin detection by both fluoroimmunoassay and surface plasmon resonance.

PubMed

Anderson, George P; Glaven, Richard H; Algar, W Russ; Susumu, Kimihiro; Stewart, Michael H; Medintz, Igor L; Goldman, Ellen R

2013-07-05

The combination of stable biorecognition elements and robust quantum dots (QDs) has the potential to yield highly effective reporters for bioanalyses. Llama-derived single domain antibodies (sdAb) provide small thermostable recognition elements that can be easily manipulated using standard DNA methods. The sdAb was self-assembled on dihydrolipoic acid (DHLA) ligand-capped CdSe-ZnS core-shell QDs made in our laboratory through the polyhistidine tail of the protein, which coordinated to zinc ions on the QD surface. The sdAb-QD bioconjugates were then applied in both fluorometric and surface plasmon resonance (SPR) immunoassays for the detection of ricin, a potential biothreat agent. The sdAb-QD conjugates functioned in fluoroimmunoassays for the detection of ricin, providing equivalent limits of detection when compared to the same anti-ricin sdAb labeled with a conventional fluorophore. In addition, the DHLA-QD-sdAb conjugates were very effective reporter elements in SPR sandwich assays, providing more sensitive detection with a signal enhancement of ~10-fold over sdAb reporters and 2-4 fold over full sized antibody reporters. Commercially prepared streptavidin-modified polymer-coated QDs also amplified the SPR signal for the detection of ricin when applied to locations where biotinylated anti-ricin sdAb was bound to target; however, we observed a 4-fold greater amplification when using the DHLA-QD-sdAb conjugates in this format. Copyright © 2013. Published by Elsevier B.V.

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICE MfuInd1a and ICE MfuInd1b, and ICE MprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476 T and Marinomonas profundimaris Strain D104

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

Badhai, Jhasketan; Das, Subrata K.

The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476 T (ICE MfuInd1a and ICE MfuInd1b) and in Marinomonas profundimaris strain D104 (ICE MprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICE MfuInd1b andmore » ICE MprChn1 were inserted into the genome at 5'-end of an typical host prfC gene, while ICE MfuInd1a was inserted at 5'-end of an atypical hipA-like gene. Despite their coexistence, the ICE MfuInd1a and ICE MfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICE MfuInd1a, ICE MfuInd1b, and ICE MprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hot spot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICE MprChn1 from M. profundimaris. Lastly, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.« less

Characterization of Three Novel SXT/R391 Integrating Conjugative Elements ICE MfuInd1a and ICE MfuInd1b, and ICE MprChn1 Identified in the Genomes of Marinomonas fungiae JCM 18476 T and Marinomonas profundimaris Strain D104

DOE PAGES

Badhai, Jhasketan; Das, Subrata K.

2016-11-25

The genus Marinomonas comprises Gram negative bacteria which are widespread in the marine environment and there is no report on the genomic analysis of SXT/R391 ICEs derived from this group of bacteria. This study describes the genomic features of three new SXT/R391 integrating conjugating elements (ICEs) identified in the genome of Marinomonas fungiae JCM 18476 T (ICE MfuInd1a and ICE MfuInd1b) and in Marinomonas profundimaris strain D104 (ICE MprChn1). Structural organizations of the three ICEs were similar to the typical SXT/R391 family of ICEs and showed high degree of conservation in the core genes. Sequence analysis revealed ICE MfuInd1b andmore » ICE MprChn1 were inserted into the genome at 5'-end of an typical host prfC gene, while ICE MfuInd1a was inserted at 5'-end of an atypical hipA-like gene. Despite their coexistence, the ICE MfuInd1a and ICE MfuInd1b were not present in a tandem fashion in the genome of M. fungiae. Phylogenetic analyses revealed the three ICEs either evolved independently or high degrees of recombination events had masked their evolution from a common SXT ancestor. Further, we found that the typical entry exclusion mechanism mediated by the TraG/EeX protein pair was likely defective in preventing the conjugative transfer of a second copy of the same S (SXT) group ICE into the M. fungiae genome due to mutations. Our analysis showed the presence of 16, 25, and 27 variable genes in the hotspots of ICE MfuInd1a, ICE MfuInd1b, and ICE MprChn1, respectively, many of which were not reported earlier for SXT/R391 ICEs. Sequence analysis predicted these hot spot regions were shaped by acquisition of genes through homologous recombination between the SXT and R391 related ICEs or mobile genetic elements present in disparate marine bacteria. Multidrug resistance genes which are hallmark feature of SXT/R391 ICEs were not present in either of the two ICEs from M. fungiae but were present within a transposon cassette in the HS-1 of the ICE MprChn1 from M. profundimaris. Lastly, our data provided information on the genetic diversity and predicted functions encoded by variable genes present in the hotspot regions of these new ICEs.« less

Synthesis of galabiose-chitosan conjugate as potent inhibitor of Streptococcus suis adhesion.

PubMed

Xu, Yaozu; Fan, Hongjie; Lu, Chengping; Gao, George F; Li, Xuebing

2010-07-12

The aim of this work is to construct a safe and effective drug candidate against Streptococcus suis infection. A panel of chitosan-based polymer conjugates with branched galabiose (Galalpha1-4Gal) side chains was synthesized as inhibitors of S. suis adhesion. The synthesis was achieved by using an aldehyde-functionalized galabiose derivative to graft it onto chitosan amino groups. Structural compositions of the conjugates were verified by 1H NMR spectroscopy and CHN elemental analyses. Potent inhibitory activities of the conjugates against S. suis adhesion to human erythrocytes were determined at low nanomolar concentration by HAI assay. An SPR study revealed a high affinity binding (Kd=39.6 nM) of the conjugate with BSI-B4 lectin. By using biocompatible chitosan as the scaffold for presenting S. suis -specific galabiose units, as well as the concise route tailored for the conjugate syntheses, the present study provides a practical way for explorations of new anti- S. suis therapies.

9,10-Azaboraphenanthrene-containing small molecules and conjugated polymers: synthesis and their application in chemodosimeters for the ratiometric detection of fluoride ions.

PubMed

Zhang, Weidong; Li, Guoping; Xu, Letian; Zhuo, Yue; Wan, Wenming; Yan, Ni; He, Gang

2018-05-21

The introduction of main group elements into conjugated scaffolds is emerging as a key route to novel optoelectronic materials. Herein, an efficient and versatile way to synthesize polymerizable 9,10-azaboraphenanthrene ( BNP )-containing monomers by aromaticity-driven ring expansion reactions between highly antiaromatic borafluorene and azides is reported, and the corresponding conjugated small molecules and polymers are developed as well. The BNP -containing small molecules and conjugated polymers showed good air/moisture stability and notable fluorescence properties. Addition of fluoride ions to the BNP -based small molecules and polymers induced a rapid change in the emission color from blue to green/yellow, respectively, accompanied by strong intensity changes. The conjugated polymers showed better ratiometric sensing performance than small molecules due to the exciton migration along the conjugated chains. Further experiments showed that the sensing process is fully reversible. The films prepared by solution-deposition of BNP -based compounds in the presence of polycaprolactone also showed good ratiometric sensing for fluoride ions.

Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci.

PubMed

Mills, D A; McKay, L L; Dunny, G M

1996-06-01

Analysis of a region involved in the conjugative transfer of the lactococcal conjugative element pRS01 has revealed a bacteria] group II intron. Splicing of this lactococcal intron (designated Ll.ltrB) in vivo resulted in the ligation of two exon messages (ltrBE1 and ltrBE2) which encoded a putative conjugative relaxase essential for the transfer of pRS01. Like many group II introns, the Ll.ltrB intron possessed an open reading frame (ltrA) with homology to reverse transcriptases. Remarkably, sequence analysis of ltrA suggested a greater similarity to open reading frames encoded by eukaryotic mitochondrial group II introns than to those identified to date from other bacteria. Several insertional mutations within ltrA resulted in plasmids exhibiting a conjugative transfer-deficient phenotype. These results provide the first direct evidence for splicing of a prokaryotic group II intron in vivo and suggest that conjugative transfer is a mechanism for group II intron dissemination in bacteria.

Micronucleus-specific histone H1 is required for micronuclear chromosome integrity in Tetrahymena thermophila

PubMed Central

Qiao, Juxia; Xu, Jing; Bo, Tao

2017-01-01

Histone H1 molecules play a key role in establishing and maintaining higher order chromatin structures. They can bind to linker DNA entering and exiting the nucleosome and regulate transcriptional activity. Tetrahymena thermophila has two histone H1, namely, macronuclear histone H1 and micronuclear histone H1 (Mlh1). Mlh1 is specifically localized at micronuclei during growth and starvation stages. Moreover, Mlh1 is localized around micronuclei and forms a specific structure during the conjugation stage. It co-localizes partially with spindle apparatus during micronuclear meiosis. Analysis of MLH1 knock-out revealed that Mlh1 was required for the micronuclear integrity and development during conjugation stage. Overexpression of Mlh1 led to abnormal conjugation progression. RT-PCR analysis indicated that the expression level of HMGB3 increased in ΔMLH1 strains, while the expression level of MLH1 increased in ΔHMGB3 cells during conjugation. These results indicate that micronuclear integrity and sexual development require normal expression level of Mlh1 and that HmgB3 and Mlh1 may functionally compensate each other in regulating micronuclear structure in T. thermophila. PMID:29095884

M-step preconditioned conjugate gradient methods

NASA Technical Reports Server (NTRS)

Adams, L.

1983-01-01

Preconditioned conjugate gradient methods for solving sparse symmetric and positive finite systems of linear equations are described. Necessary and sufficient conditions are given for when these preconditioners can be used and an analysis of their effectiveness is given. Efficient computer implementations of these methods are discussed and results on the CYBER 203 and the Finite Element Machine under construction at NASA Langley Research Center are included.

Stability, Entrapment and Variant Formation of Salmonella Genomic Island 1

PubMed Central

Kiss, János; Nagy, Béla; Olasz, Ferenc

2012-01-01

Background The Salmonella genomic island 1 (SGI1) is a 42.4 kb integrative mobilizable element containing several antibiotic resistance determinants embedded in a complex integron segment In104. The numerous SGI1 variants identified so far, differ mainly in this segment and the explanations of their emergence were mostly based on comparative structure analyses. Here we provide experimental studies on the stability, entrapment and variant formation of this peculiar gene cluster originally found in S. Typhimurium. Methodology/Principal Findings Segregation and conjugation tests and various molecular techniques were used to detect the emerging SGI1 variants in Salmonella populations of 17 Salmonella enterica serovar Typhimurium DT104 isolates from Hungary. The SGI1s in these isolates proved to be fully competent in excision, conjugal transfer by the IncA/C helper plasmid R55, and integration into the E. coli chromosome. A trap vector has been constructed and successfully applied to capture the island on a plasmid. Monitoring of segregation of SGI1 indicated high stability of the island. SGI1-free segregants did not accumulate during long-term propagation, but several SGI1 variants could be obtained. Most of them appeared to be identical to SGI1-B and SGI1-C, but two new variants caused by deletions via a short-homology-dependent recombination process have also been detected. We have also noticed that the presence of the conjugation helper plasmid increased the formation of these deletion variants considerably. Conclusions/Significance Despite that excision of SGI1 from the chromosome was proven in SGI1+ Salmonella populations, its complete loss could not be observed. On the other hand, we demonstrated that several variants, among them two newly identified ones, arose with detectable frequencies in these populations in a short timescale and their formation was promoted by the helper plasmid. This reflects that IncA/C helper plasmids are not only involved in the horizontal spreading of SGI1, but may also contribute to its evolution. PMID:22384263

Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting

PubMed Central

Piazza, Carol Lyn; Smith, Dorie

2018-01-01

Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns. PMID:29905149

Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting.

PubMed

Qu, Guosheng; Piazza, Carol Lyn; Smith, Dorie; Belfort, Marlene

2018-06-15

Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis , inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns. © 2018, Qu et al.

CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes

PubMed Central

2013-01-01

Background Bacteria and archaea develop immunity against invading genomes by incorporating pieces of the invaders' sequences, called spacers, into a clustered regularly interspaced short palindromic repeats (CRISPR) locus between repeats, forming arrays of repeat-spacer units. When spacers are expressed, they direct CRISPR-associated (Cas) proteins to silence complementary invading DNA. In order to characterize the invaders of human microbiomes, we use spacers from CRISPR arrays that we had previously assembled from shotgun metagenomic datasets, and identify contigs that contain these spacers' targets. Results We discover 95,000 contigs that are putative invasive mobile genetic elements, some targeted by hundreds of CRISPR spacers. We find that oral sites in healthy human populations have a much greater variety of mobile genetic elements than stool samples. Mobile genetic elements carry genes encoding diverse functions: only 7% of the mobile genetic elements are similar to known phages or plasmids, although a much greater proportion contain phage- or plasmid-related genes. A small number of contigs share similarity with known integrative and conjugative elements, providing the first examples of CRISPR defenses against this class of element. We provide detailed analyses of a few large mobile genetic elements of various types, and a relative abundance analysis of mobile genetic elements and putative hosts, exploring the dynamic activities of mobile genetic elements in human microbiomes. A joint analysis of mobile genetic elements and CRISPRs shows that protospacer-adjacent motifs drive their interaction network; however, some CRISPR-Cas systems target mobile genetic elements lacking motifs. Conclusions We identify a large collection of invasive mobile genetic elements in human microbiomes, an important resource for further study of the interaction between the CRISPR-Cas immune system and invaders. PMID:23628424

Microwave phase conjugation using artificial nonlinear microwave surfaces

NASA Astrophysics Data System (ADS)

Chang, Yian

1997-09-01

A new technique is developed and demonstrated to simulate nonlinear materials in the microwave and millimeter wave regime. Such materials are required to extend nonlinear optical techniques into longer wavelength areas. Using an array of antenna coupled mixers as an artificial nonlinear surface, we have demonstrated two-dimensional free space microwave phase conjugation at 10 GHz. The basic concept is to replace the weak nonlinearity of electron distribution in a crystal with the strong nonlinear V-I response of a P-N junction. This demnstration uses a three-wave mixing method with the effective nonlinear susceptibility χ(2) provided by an artificial nonlinear surface. The pump signal at 2ω (20 GHz) can be injected to the mixing elements electrically or optically. Electrical injection was first used to prove the concept of artificial nonlinear surfaces. However, due to the loss and size of microwave components, electrical injection is not practical for an array of artificial nonlinear surfaces, as would be needed in a three-dimensional free space phase conjugation setup. Therefore optical injection was implemented to carry the 2ω microwave pump signal in phase to all mixing elements. In both cases, two-dimensional free space phase conjugation was observed by directly measuring the electric field amplitude and phase distribution. The electric field wavefronts exhibited retro-directivity and auto- correction characteristics of phase conjugation. This demonstration surface also shows a power gain of 10 dB, which is desired for potential communication applications.

Electromagnetic characterization of conformal antennas

NASA Technical Reports Server (NTRS)

Volakis, John L.; Kempel, Leo C.; Alexanian, Angelos; Jin, J. M.; Yu, C. L.; Woo, Alex C.

1992-01-01

The ultimate objective of this project is to develop a new technique which permits an accurate simulation of microstrip patch antennas or arrays with various feed, superstrate and/or substrate configurations residing in a recessed cavity whose aperture is planar, cylindrical or otherwise conformed to the substructure. The technique combines the finite element and boundary integral methods to formulate a system suitable for solution via the conjugate gradient method in conjunction with the fast Fourier transform. The final code is intended to compute both scattering and radiation patterns of the structure with an affordable memory demand. With upgraded capabilities, the four included papers examined the radar cross section (RCS), input impedance, gain, and resonant frequency of several rectangular configurations using different loading and substrate/superstrate configurations.

Properties of new Escherichia coli Hfr strains constructed by integration of pSC101-derived conjugative plasmids.

PubMed Central

François, V; Conter, A; Louarn, J M

1990-01-01

Conjugative temperature-sensitive plasmids were derived from pSC101. These plasmids are useful in genetic analysis for two reasons: (i) they render possible the construction of new Hfr lines by plasmid integration at predetermined chromosomal loci via Tn10 inverse transposition, and (ii) the Hfr characters are transducible via bacteriophage P1. We also showed that replication from pSC101 origin is deleterious for the plasmid-chromosome fusion. PMID:2155201

Discovery of a new family of relaxases in Firmicutes bacteria.

PubMed

Ramachandran, Gayetri; Miguel-Arribas, Andrés; Abia, David; Singh, Praveen K; Crespo, Isidro; Gago-Córdoba, César; Hao, Jian An; Luque-Ortega, Juan Roman; Alfonso, Carlos; Wu, Ling J; Boer, D Roeland; Meijer, Wilfried J J

2017-02-01

Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.

Discovery of a new family of relaxases in Firmicutes bacteria

PubMed Central

Singh, Praveen K.; Hao, Jian An; Luque-Ortega, Juan Roman; Wu, Ling J.; Boer, D. Roeland

2017-01-01

Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research. PMID:28207825

Molecular Approach to Conjugated Polymers with Biomimetic Properties.

PubMed

Baek, Paul; Voorhaar, Lenny; Barker, David; Travas-Sejdic, Jadranka

2018-06-13

The field of bioelectronics involves the fascinating interplay between biology and human-made electronics. Applications such as tissue engineering, biosensing, drug delivery, and wearable electronics require biomimetic materials that can translate the physiological and chemical processes of biological systems, such as organs, tissues. and cells, into electrical signals and vice versa. However, the difference in the physical nature of soft biological elements and rigid electronic materials calls for new conductive or electroactive materials with added biomimetic properties that can bridge the gap. Soft electronics that utilize organic materials, such as conjugated polymers, can bring many important features to bioelectronics. Among the many advantages of conjugated polymers, the ability to modulate the biocompatibility, solubility, functionality, and mechanical properties through side chain engineering can alleviate the issues of mechanical mismatch and provide better interface between the electronics and biological elements. Additionally, conjugated polymers, being both ionically and electrically conductive through reversible doping processes provide means for direct sensing and stimulation of biological processes in cells, tissues, and organs. In this Account, we focus on our recent progress in molecular engineering of conjugated polymers with tunable biomimetic properties, such as biocompatibility, responsiveness, stretchability, self-healing, and adhesion. Our approach is general and versatile, which is based on functionalization of conjugated polymers with long side chains, commonly polymeric or biomolecules. Applications for such materials are wide-ranging, where we have demonstrated conductive, stimuli-responsive antifouling, and cell adhesive biointerfaces that can respond to external stimuli such as temperature, salt concentration, and redox reactions, the processes that in turn modify and reversibly switch the surface properties. Furthermore, utilizing the advantageous chemical, physical, mechanical and functional properties of the grafts, we progressed into grafting of the long side chains onto conjugated polymers in solution, with the vision of synthesizing solution-processable conjugated graft copolymers with biomimetic functionalities. Examples of the developed materials to date include rubbery and adhesive photoluminescent plastics, biomolecule-functionalized electrospun biosensors, thermally and dually responsive photoluminescent conjugated polymers, and tunable self-healing, adhesive, and stretchable strain sensors, advanced functional biocidal polymers, and filtration membranes. As outlined in these examples, the applications of these biomimetic, conjugated polymers are still in the development stage toward truly printable, organic bioelectronic devices. However, in this Account, we advocate that molecular engineering of conjugated polymers is an attractive approach to a versatile class of organic electronics with both ionic and electrical conductivity as well as mechanical properties required for next-generation bioelectronics.

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Reversal of the contrast of optical radiation in round-trip amplifiers with a phase conjugation mirror

NASA Astrophysics Data System (ADS)

Afanas'ev, Anatolii A.; Samson, B. A.

1989-02-01

A description is given of a method for inversion of the contrast of optical radiation in a round-trip amplifier with a phase conjugation mirror and a phase nonreciprocal element. The system can be used to achieve high powers of contrast-reversed radiation because of compensation of phase distortions introduced by amplification.

Particle-in-a-box model of one-dimensional excitons in conjugated polymers

NASA Astrophysics Data System (ADS)

Pedersen, Thomas G.; Johansen, Per M.; Pedersen, Henrik C.

2000-04-01

A simple two-particle model of excitons in conjugated polymers is proposed as an alternative to usual highly computationally demanding quantum chemical methods. In the two-particle model, the exciton is described as an electron-hole pair interacting via Coulomb forces and confined to the polymer backbone by rigid walls. Furthermore, by integrating out the transverse part, the two-particle equation is reduced to one-dimensional form. It is demonstrated how essentially exact solutions are obtained in the cases of short and long conjugation length, respectively. From a linear combination of these cases an approximate solution for the general case is obtained. As an application of the model the influence of a static electric field on the electron-hole overlap integral and exciton energy is considered.

Preparation and in vitro characterization of pluronic-attached polyamidoamine dendrimers for drug delivery.

PubMed

Gu, Zhuojun; Wang, Meng; Fang, Qiongyan; Zheng, Huaiyu; Wu, Feiyue; Lin, Dai; Xu, Ying; Jin, Yi

2015-05-01

Polyamidoamine (PAMAM) dendrimers have attracted lots of interest as drug carriers. And little study about whether pluronic-attached PAMAM dendrimers could be potential drug delivery systems has been carried on. Pluronic F127 (PF127) attached PAMAM dendrimers were designed as novel drug carriers. Two conjugation ratios of PF127-attached PAMAM dendrimers were synthesized. (1)H nuclear magnetic resonance ((1)H-NMR), Fourier transform infrared spectrum (FTIR), element analysis and ninhydrin assay were used to characterize the conjugates. Size, zeta potential and critical micelle concentrations (CMC) were also detected. And DOX was incorporated into the hydrophobic interior of the conjugates. Studies on their drug loading and drug release were carried on. Furthermore, hemolysis and cytotoxicity assay were used to evaluate the toxicity of the conjugates. PF127 was successfully conjugated to the fifth generation PAMAM dendrimer at two molar ratios of 19% and 57% (PF127 to surface amine per PAMAM dendrimer molecular). The conjugates showed an increased size and a reduced zeta potential. And higher CMC values were obtained than pure PF127. Compared with unconjugated PAMAM dendrimer, PF127 conjugation significantly reduced the hemolytic toxicity and cytotoxicity of PAMAM dendrimer in vitro. The encapsulation results showed that the ability to encapsulate DOX by the conjugate of 19% conjugation ratio was better than that of 57% conjugation ratio. And the maximum is ∼12.87 DOX molecules per conjugate molecule. Moreover, the complexes showed a sustained release behavior compared to pure DOX. Findings from the in vitro study show that the PF127-attached PAMAM dendrimers may be potential carriers for drug delivery.

Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci.

PubMed

Huang, Jinhu; Ma, Jiale; Shang, Kexin; Hu, Xiao; Liang, Yuan; Li, Daiwei; Wu, Zuowei; Dai, Lei; Chen, Li; Wang, Liping

2016-01-01

Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis . Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species ( Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes , and S. suis ) revealed the existence of different groups of MGEs, including Tn5252, ICE Sp 1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICE Sa 2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICE Sa 2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.

Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci

PubMed Central

Huang, Jinhu; Ma, Jiale; Shang, Kexin; Hu, Xiao; Liang, Yuan; Li, Daiwei; Wu, Zuowei; Dai, Lei; Chen, Li; Wang, Liping

2016-01-01

Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs. PMID:27774436

Sensitivity calculations for iteratively solved problems

NASA Technical Reports Server (NTRS)

Haftka, R. T.

1985-01-01

The calculation of sensitivity derivatives of solutions of iteratively solved systems of algebraic equations is investigated. A modified finite difference procedure is presented which improves the accuracy of the calculated derivatives. The procedure is demonstrated for a simple algebraic example as well as an element-by-element preconditioned conjugate gradient iterative solution technique applied to truss examples.

Coherent perfect absorber and laser modes in purely imaginary metamaterials

NASA Astrophysics Data System (ADS)

Fu, Yangyang; Cao, Yanyan; Cummer, Steven A.; Xu, Yadong; Chen, Huanyang

2017-10-01

Conjugate metamaterials, in which the permittivity and the permeability are complex conjugates of each other, possess the elements of loss and gain simultaneously. By employing a conjugate metamaterial with a purely imaginary form, we propose a mechanism for realizing both coherent perfect absorber (CPA) and laser modes. Moreover, the general conditions for obtaining CPA and laser modes, including obtaining them simultaneously, are revealed by analyzing the wave scattering properties of a slab made of purely imaginary metamaterials (PIMs). Specifically, in a PIM slab with a subunity effective refractive index, the CPA mode can be simplified as a perfect absorption mode and the incident wave from one side could be perfectly absorbed.

Physico-chemical and immunological examination of the thermal stability of tetanus toxoid conjugate vaccines.

PubMed

Ho, Mei M; Mawas, Fatme; Bolgiano, Barbara; Lemercinier, Xavier; Crane, Dennis T; Huskisson, Rachel; Corbel, Michael J

2002-10-04

The thermal stability of meningococcal C (MenC)- and Haemophilus influenzae b (Hib)-tetanus toxoid (TT) conjugate vaccines was investigated using spectroscopic and chromatographic techniques and immunogenicity assays in animal models. In this stability study, both the bulk concentrate and final fills were incubated at -20, 4, 23, 37 or 55 degrees C for 5 weeks or subjected to cycles of freeze-thawing. The structural stability, hydrodynamic size and molecular integrity of the treated vaccines were monitored by circular dichroism (CD), fluorescence and nuclear magnetic resonance (NMR) spectroscopic techniques, size exclusion chromatography (FPLC-SEC), and high performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD). Only storage at 55 degrees C for 5 weeks caused some slight unfolding and modification in the tertiary structure of the carrier protein in the MenC-TT conjugate. Substantial loss of saccharide content from the MenC conjugates was observed at 37 and 55 degrees C. Unexpectedly, the experimental immunogenicity of MenC-TT vaccine adsorbed to Alhydrogel was significantly reduced only by repeated freeze-thawing, but not significantly decreased by thermal denaturation. Neither the molecular integrity nor the immunogenicity of the lyophilised Hib-TT vaccines was significantly affected by freeze-thawing or by storage at high temperature. In conclusion, the MenC- and Hib-TT conjugate vaccines were relatively stable when stored at higher temperatures, though when MenC-TT vaccine was adsorbed to Alhydrogel, it was more vulnerable to repeated freeze-thawing. When compared with CRM(197) conjugate vaccines studied previously using similar techniques, the tetanus toxoid conjugates were found to have higher relative thermal stability in that they retained immunogenicity following storage at elevated temperatures.

Energy Transfer between Conjugated Colloidal Ga2O3 and CdSe/CdS Core/Shell Nanocrystals for White Light Emitting Applications

PubMed Central

Stanish, Paul C.; Radovanovic, Pavle V.

2016-01-01

Developing solid state materials capable of generating homogeneous white light in an energy efficient and resource-sustainable way is central to the design of new and improved devices for various lighting applications. Most currently-used phosphors depend on strategically important rare earth elements, and rely on a multicomponent approach, which produces sub-optimal quality white light. Here, we report the design and preparation of a colloidal white-light emitting nanocrystal conjugate. This conjugate is obtained by linking colloidal Ga2O3 and II–VI nanocrystals in the solution phase with a short bifunctional organic molecule (thioglycolic acid). The two types of nanocrystals are electronically coupled by Förster resonance energy transfer owing to the short separation between Ga2O3 (energy donor) and core/shell CdSe/CdS (energy acceptor) nanocrystals, and the spectral overlap between the photoluminescence of the donor and the absorption of the acceptor. Using steady state and time-resolved photoluminescence spectroscopies, we quantified the contribution of the energy transfer to the photoluminescence spectral power distribution and the corresponding chromaticity of this nanocrystal conjugate. Quantitative understanding of this new system allows for tuning of the emission color and the design of quasi-single white light emitting inorganic phosphors without the use of rare-earth elements. PMID:28344289

Using two MEMS deformable mirrors in an adaptive optics test bed for multiconjugate correction

NASA Astrophysics Data System (ADS)

Andrews, Jonathan R.; Martinez, Ty; Teare, Scott W.; Restaino, Sergio R.; Wilcox, Christopher C.; Santiago, Freddie; Payne, Don M.

2010-02-01

Adaptive optics systems have advanced considerably over the past decade and have become common tools for optical engineers. The most recent advances in adaptive optics technology have lead to significant reductions in the cost of most of the key components. Most significantly, the cost of deformable elements and wavefront sensor components have dropped to the point where multiple deformable mirrors and Shack- Hartmann array based wavefront sensor cameras can be included in a single system. Matched with the appropriate hardware and software, formidable systems can be operating in nearly any sized research laboratory. The significant advancement of MEMS deformable mirrors has made them very popular for use as the active corrective element in multi-conjugate adaptive optics systems so that, in particular for astronomical applications, this allows correction in more than one plane. The NRL compact AO system and atmospheric simulation systems has now been expanded to support Multi Conjugate Adaptive Optics (MCAO), taking advantage of using the liquid crystal spatial light modulator (SLM) driven aberration generators in two conjugate planes that are well separated spatially. Thus, by using two SLM based aberration generators and two separate wavefront sensors, the system can measure and apply wavefront correction with two MEMS deformable mirrors. This paper describes the multi-conjugate adaptive optics system and the testing and calibration of the system and demonstrates preliminary results with this system.

Aptamer-conjugated nanoparticles for cancer cell detection.

PubMed

Medley, Colin D; Bamrungsap, Suwussa; Tan, Weihong; Smith, Joshua E

2011-02-01

Aptamer-conjugated nanoparticles (ACNPs) have been used for a variety of applications, particularly dual nanoparticles for magnetic extraction and fluorescent labeling. In this type of assay, silica-coated magnetic and fluorophore-doped silica nanoparticles are conjugated to highly selective aptamers to detect and extract targeted cells in a variety of matrixes. However, considerable improvements are required in order to increase the selectivity and sensitivity of this two-particle assay to be useful in a clinical setting. To accomplish this, several parameters were investigated, including nanoparticle size, conjugation chemistry, use of multiple aptamer sequences on the nanoparticles, and use of multiple nanoparticles with different aptamer sequences. After identifying the best-performing elements, the improvements made to this assay's conditional parameters were combined to illustrate the overall enhanced sensitivity and selectivity of the two-particle assay using an innovative multiple aptamer approach, signifying a critical feature in the advancement of this technique.

Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

NASA Technical Reports Server (NTRS)

Navon, I. M.

1984-01-01

A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus.

PubMed

Luo, Peng; He, Xiangyan; Wang, Yanhong; Liu, Qiuting; Hu, Chaoqun

2016-05-04

Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012-2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192 V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes. A sequence analysis showed that there were only 14 variable bases dispersed between ICEValE0601 and ICEValHN492. ICEValE0601 and ICEValHN492 were treated as the same ICE. ICEValA056-1, ICEValE0601 and ICEValHN492 integrate into the 5' end of the host's prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICEValE0601 or ICEValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEValA056-2, ICEValHN396 and ICEValHN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICEValA056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant transposase genes compared with other parts of their host genomes. A phylogenetic analysis indicated that transposase genes in these ICEs are highly diverse. ICEValA056-1, ICEValE0601 and ICEValHN492 are typical members of the SXT/R391 family. ICEValA056-2, ICEValHN396 and ICEValHN437 form a new atypical group belonging to the SXT/R391 family. In addition to the many genes found to be present in other ICEs, six ICEs contain a large number of unique genes or gene clusters that were not found in other ICEs. ICEs may serve as a carrier for transposable genetic elements (TEs) and largely facilitate the dissemination of TEs.

Conjugated Polymers in Bioelectronics.

PubMed

Inal, Sahika; Rivnay, Jonathan; Suiu, Andreea-Otilia; Malliaras, George G; McCulloch, Iain

2018-06-19

The emerging field of organic bioelectronics bridges the electronic world of organic-semiconductor-based devices with the soft, predominantly ionic world of biology. This crosstalk can occur in both directions. For example, a biochemical reaction may change the doping state of an organic material, generating an electronic readout. Conversely, an electronic signal from a device may stimulate a biological event. Cutting-edge research in this field results in the development of a broad variety of meaningful applications, from biosensors and drug delivery systems to health monitoring devices and brain-machine interfaces. Conjugated polymers share similarities in chemical "nature" with biological molecules and can be engineered on various forms, including hydrogels that have Young's moduli similar to those of soft tissues and are ionically conducting. The structure of organic materials can be tuned through synthetic chemistry, and their biological properties can be controlled using a variety of functionalization strategies. Finally, organic electronic materials can be integrated with a variety of mechanical supports, giving rise to devices with form factors that enable integration with biological systems. While these developments are innovative and promising, it is important to note that the field is still in its infancy, with many unknowns and immense scope for exploration and highly collaborative research. The first part of this Account details the unique properties that render conjugated polymers excellent biointerfacing materials. We then offer an overview of the most common conjugated polymers that have been used as active layers in various organic bioelectronics devices, highlighting the importance of developing new materials. These materials are the most popular ethylenedioxythiophene derivatives as well as conjugated polyelectrolytes and ion-free organic semiconductors functionalized for the biological interface. We then discuss several applications and operation principles of state-of-the-art bioelectronics devices. These devices include electrodes applied to sense/trigger electrophysiological activity of cells as well as electrolyte-gated field-effect and electrochemical transistors used for sensing of biochemical markers. Another prime application example of conjugated polymers is cell actuators. External modulation of the redox state of the underlying conjugated polymer films controls the adhesion behavior and viability of cells. These smart surfaces can be also designed in the form of three-dimensional architectures because of the processability of conjugated polymers. As such, cell-loaded scaffolds based on electroactive polymers enable integrated sensing or stimulation within the engineered tissue itself. A last application example is organic neuromorphic devices, an alternative computing architecture that takes inspiration from biology and, in particular, from the way the brain works. Leveraging ion redistribution inside a conjugated polymer upon application of an electrical field and its coupling with electronic charges, conjugated polymers can be engineered to act as artificial neurons or synapses with complex, history-dependent behavior. We conclude this Account by highlighting main factors that need to be considered for the design of a conjugated polymer for applications in bioelectronics-although there can be various figures of merit given the broad range of applications, as emphasized in this Account.

Conjugate-Gradient Algorithms For Dynamics Of Manipulators

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheid, Robert E.

1993-01-01

Algorithms for serial and parallel computation of forward dynamics of multiple-link robotic manipulators by conjugate-gradient method developed. Parallel algorithms have potential for speedup of computations on multiple linked, specialized processors implemented in very-large-scale integrated circuits. Such processors used to stimulate dynamics, possibly faster than in real time, for purposes of planning and control.

Conjugate Ground-Spacecraft Observations of VLF Chorus Elements

NASA Astrophysics Data System (ADS)

Demekhov, A. G.; Manninen, J.; Santolík, O.; Titova, E. E.

2017-12-01

We present results of simultaneous observations of VLF chorus elements at the ground-based station Kannuslehto in Northern Finland and on board Van Allen Probe A. Visual inspection and correlation analysis of the data reveal one-to-one correspondence of several (at least 12) chorus elements following each other in a sequence. Poynting flux calculated from electromagnetic fields measured by the Electric and Magnetic Field Instrument Suite and Integrated Science instrument on board Van Allen Probe A shows that the waves propagate at small angles to the geomagnetic field and oppositely to its direction, that is, from northern to southern geographic hemisphere. The spacecraft was located at L≃4.1 at a geomagnetic latitude of -12.4∘ close to the plasmapause and inside a localized density inhomogeneity with about 30% density increase and a transverse size of about 600 km. The time delay between the waves detected on the ground and on the spacecraft is about 1.3 s, with ground-based detection leading spacecraft detection. The measured time delay is consistent with the wave travel time of quasi-parallel whistler-mode waves for a realistic profile of the plasma density distribution along the field line. The results suggest that chorus discrete elements can preserve their spectral shape during a hop from the generation region to the ground followed by reflection from the ionosphere and return to the near-equatorial region.

Insights into the genomic plasticity of Pseudomonas putida KF715, a strain with unique biphenyl-utilizing activity and genome instability properties.

PubMed

Suenaga, Hikaru; Fujihara, Hidehiko; Kimura, Nobutada; Hirose, Jun; Watanabe, Takahito; Futagami, Taiki; Goto, Masatoshi; Shimodaira, Jun; Furukawa, Kensuke

2017-10-01

Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. putida strains. In this study, we first determined the complete nucleotide sequence of the KF715 genome. Next, to determine the underlying cause of genome plasticity in KF715, we compared the KF715 genome with the genomes of one KF715 defective mutant, two transconjugants, and several P. putida strains available from public databases. The gapless KF715 genome sequence revealed five replicons: one circular chromosome, and four plasmids. Southern blot analysis indicated that most of the KF715 cell population carries the bph-sal element on the chromosome whereas a small number carry it on a huge plasmid, pKF715A. Moreover, the bph-sal element is present stably on the plasmid and did not integrate into the chromosome of its transconjugants. Comparative genome analysis and experiments showed that a number of diverse putative genetic elements are present in KF715 and are likely involved in genome rearrangement. These data provide insights into the genetic plasticity and adaptability of microorganisms for survival in various ecological niches. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

The 2.5 Å Structure of the Enterococcus Conjugation Protein TraM resembles VirB8 Type IV Secretion Proteins*

PubMed Central

Goessweiner-Mohr, Nikolaus; Grumet, Lukas; Arends, Karsten; Pavkov-Keller, Tea; Gruber, Christian C.; Gruber, Karl; Birner-Gruenberger, Ruth; Kropec-Huebner, Andrea; Huebner, Johannes; Grohmann, Elisabeth; Keller, Walter

2013-01-01

Conjugative plasmid transfer is the most important means of spreading antibiotic resistance and virulence genes among bacteria and therefore presents a serious threat to human health. The process requires direct cell-cell contact made possible by a multiprotein complex that spans cellular membranes and serves as a channel for macromolecular secretion. Thus far, well studied conjugative type IV secretion systems (T4SS) are of Gram-negative (G−) origin. Although many medically relevant pathogens (e.g., enterococci, staphylococci, and streptococci) are Gram-positive (G+), their conjugation systems have received little attention. This study provides structural information for the transfer protein TraM of the G+ broad host range Enterococcus conjugative plasmid pIP501. Immunolocalization demonstrated that the protein localizes to the cell wall. We then used opsonophagocytosis as a novel tool to verify that TraM was exposed on the cell surface. In these assays, antibodies generated to TraM recruited macrophages and enabled killing of pIP501 harboring Enteroccocus faecalis cells. The crystal structure of the C-terminal, surface-exposed domain of TraM was determined to 2.5 Å resolution. The structure, molecular dynamics, and cross-linking studies indicated that a TraM trimer acts as the biological unit. Despite the absence of sequence-based similarity, TraM unexpectedly displayed a fold similar to the T4SS VirB8 proteins from Agrobacterium tumefaciens and Brucella suis (G−) and to the transfer protein TcpC from Clostridium perfringens plasmid pCW3 (G+). Based on the alignments of secondary structure elements of VirB8-like proteins from mobile genetic elements and chromosomally encoded T4SS from G+ and G− bacteria, we propose a new classification scheme of VirB8-like proteins. PMID:23188825

Integration of β-carotene molecules in small liposomes

NASA Astrophysics Data System (ADS)

Andreeva, Atanaska; Popova, Antoaneta

2010-11-01

The most typical feature of carotenoids is the long polyene chain with conjugated double bonds suggesting that they can serve as conductors of electrons, acting as ''molecular wires'', important elements in the molecular electronic devices. Carotenoids are essential components of photosynthetic systems, performing different functions as light harvesting, photoprotection and electron transfer. They act also as natural antioxidants. In addition they perform structural role stabilizing the three-dimensional organization of photosynthetic membranes. Carotenoids contribute to the stability of the lipid phase, preserving the membrane integrity under potentially harmful environmental conditions. Carotenoids can be easily integrated into model membranes, facilitating the investigation of their functional roles. In carotenoid-egg phosphatidylcholine (EPC) liposomes ß-carotene is randomly distributed in the hydrocarbon interior of the bilayer, without any preferred, well defined orientation and retains a substantial degree of mobility. Here we investigate the degree of integration of ß-carotene in small unilamellar EPC liposomes and the changes in ß-carotene absorption and Raman spectra due to the lipid-pigment interaction. All observed changes in ß-carotene absorption and Raman spectra may be regarded as a result of the lipid-pigment interactions leading to the polyene geometry distortion and increasing of the environment heterogenety in the liposomes as compared to the solutions.

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110

PubMed Central

2012-01-01

Background Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Results Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. Conclusions The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest. PMID:22443545

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.

PubMed

Schwientek, Patrick; Szczepanowski, Rafael; Rückert, Christian; Kalinowski, Jörn; Klein, Andreas; Selber, Klaus; Wehmeier, Udo F; Stoye, Jens; Pühler, Alfred

2012-03-23

Actinoplanes sp. SE50/110 is known as the wild type producer of the alpha-glucosidase inhibitor acarbose, a potent drug used worldwide in the treatment of type-2 diabetes mellitus. As the incidence of diabetes is rapidly rising worldwide, an ever increasing demand for diabetes drugs, such as acarbose, needs to be anticipated. Consequently, derived Actinoplanes strains with increased acarbose yields are being used in large scale industrial batch fermentation since 1990 and were continuously optimized by conventional mutagenesis and screening experiments. This strategy reached its limits and is generally superseded by modern genetic engineering approaches. As a prerequisite for targeted genetic modifications, the complete genome sequence of the organism has to be known. Here, we present the complete genome sequence of Actinoplanes sp. SE50/110 [GenBank:CP003170], the first publicly available genome of the genus Actinoplanes, comprising various producers of pharmaceutically and economically important secondary metabolites. The genome features a high mean G + C content of 71.32% and consists of one circular chromosome with a size of 9,239,851 bp hosting 8,270 predicted protein coding sequences. Phylogenetic analysis of the core genome revealed a rather distant relation to other sequenced species of the family Micromonosporaceae whereas Actinoplanes utahensis was found to be the closest species based on 16S rRNA gene sequence comparison. Besides the already published acarbose biosynthetic gene cluster sequence, several new non-ribosomal peptide synthetase-, polyketide synthase- and hybrid-clusters were identified on the Actinoplanes genome. Another key feature of the genome represents the discovery of a functional actinomycete integrative and conjugative element. The complete genome sequence of Actinoplanes sp. SE50/110 marks an important step towards the rational genetic optimization of the acarbose production. In this regard, the identified actinomycete integrative and conjugative element could play a central role by providing the basis for the development of a genetic transformation system for Actinoplanes sp. SE50/110 and other Actinoplanes spp. Furthermore, the identified non-ribosomal peptide synthetase- and polyketide synthase-clusters potentially encode new antibiotics and/or other bioactive compounds, which might be of pharmacologic interest.

Conjugated Polymer with Intrinsic Alkyne Units for Synergistically Enhanced Raman Imaging in Living Cells.

PubMed

Li, Shengliang; Chen, Tao; Wang, Yunxia; Liu, Libing; Lv, Fengting; Li, Zhiliang; Huang, Yanyi; Schanze, Kirk S; Wang, Shu

2017-10-16

Development of Raman-active materials with enhanced and distinctive Raman vibrations in the Raman-silent region (1800-2800 cm -1 ) is highly required for specific molecular imaging of living cells with high spatial resolution. Herein, water-soluble cationic conjugated polymers (CCPs), poly(phenylene ethynylene) (PPE) derivatives, are explored for use as alkyne-state-dependent Raman probes for living cell imaging due to synergetic enhancement effect of alkyne vibrations in Raman-silent region compared to alkyne-containing small molecules. The enhanced alkyne signals result from the integration of alkyne groups into the rigid backbone and the delocalized π-conjugated structure. PPE-based conjugated polymer nanoparticles (CPNs) were also prepared as Raman-responsive nanomaterials for distinct imaging application. This work opens a new way into the development of conjugated polymer materials for enhanced Raman imaging. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conjugation of Specifically Developed Antibodies for High- and Low-Molecular-Weight Glutenins with Fluorescent Quantum Dots as a Tool for Their Detection in Wheat Flour Dough.

PubMed

Bonilla, Jose C; Ryan, Valerie; Yazar, Gamze; Kokini, Jozef L; Bhunia, Arun K

2018-04-25

The importance of gluten proteins, gliadins and glutenins, is well-known in the quality of wheat products. To gain more specific information about the role of glutenins in wheat dough, the two major subunits of glutenin, high- and low-molecular-weight (HMW and LMW) glutenins, were extracted, isolated, and identified by mass spectrometry. Antibodies for HMW and LMW glutenins were developed using the proteomic information on the characterized glutenin subunits. The antibodies were found to be specific to each subunit by western immunoblots and were then conjugated to quantum dots (QDs) using site-click conjugation, a new method to keep antibody integrity. A fluorescence-link immunosorbent assay tested the successful QD conjugation. The QD-conjugated antibodies were applied to dough samples, where they recognized glutenin subunits and were visualized using a confocal laser scanning microscope.

A septal chromosome segregator protein evolved into a conjugative DNA-translocator protein

PubMed Central

Sepulveda, Edgardo; Vogelmann, Jutta

2011-01-01

Streptomycetes, Gram-positive soil bacteria well known for the production of antibiotics feature a unique conjugative DNA transfer system. In contrast to classical conjugation which is characterized by the secretion of a pilot protein covalently linked to a single-stranded DNA molecule, in Streptomyces a double-stranded DNA molecule is translocated during conjugative transfer. This transfer involves a single plasmid encoded protein, TraB. A detailed biochemical and biophysical characterization of TraB, revealed a close relationship to FtsK, mediating chromosome segregation during bacterial cell division. TraB translocates plasmid DNA by recognizing 8-bp direct repeats located in a specific plasmid region clt. Similar sequences accidentally also occur on chromosomes and have been shown to be bound by TraB. We suggest that TraB mobilizes chromosomal genes by the interaction with these chromosomal clt-like sequences not relying on the integration of the conjugative plasmid into the chromosome. PMID:22479692

A computational procedure for the dynamics of flexible beams within multibody systems. Ph.D. Thesis Final Technical Report

NASA Technical Reports Server (NTRS)

Downer, Janice Diane

1990-01-01

The dynamic analysis of three dimensional elastic beams which experience large rotational and large deformational motions are examined. The beam motion is modeled using an inertial reference for the translational displacements and a body-fixed reference for the rotational quantities. Finite strain rod theories are then defined in conjunction with the beam kinematic description which accounts for the effects of stretching, bending, torsion, and transverse shear deformations. A convected coordinate representation of the Cauchy stress tensor and a conjugate strain definition is introduced to model the beam deformation. To treat the beam dynamics, a two-stage modification of the central difference algorithm is presented to integrate the translational coordinates and the angular velocity vector. The angular orientation is then obtained from the application of an implicit integration algorithm to the Euler parameter/angular velocity kinematical relation. The combined developments of the objective internal force computation with the dynamic solution procedures result in the computational preservation of total energy for undamped systems. The present methodology is also extended to model the dynamics of deployment/retrieval of the flexible members. A moving spatial grid corresponding to the configuration of a deployed rigid beam is employed as a reference for the dynamic variables. A transient integration scheme which accurately accounts for the deforming spatial grid is derived from a space-time finite element discretization of a Hamiltonian variational statement. The computational results of this general deforming finite element beam formulation are compared to reported results for a planar inverse-spaghetti problem.

Conjugate field approaches for active array compensation

NASA Technical Reports Server (NTRS)

Acosta, R. J.

1989-01-01

Two approaches for calculating the compensating feed array complex excitations are namely, the indirect conjugate field matching (ICFM) and the direct conjugate field matching (DCFM) approach. In the ICFM approach the compensating feed array excitations are determined by considering the transmitting mode and the reciprocity principle. The DCF, in contrast calculates the array excitations by integrating directly the induced surface currents on the reflector under a receiving mode. DCFM allows the reflector to be illuminated by an incident plane wave with a tapered amplitude. The level of taper can effectively control the sidelobe level of the compensated antenna pattern. Both approaches are examined briefly.

Multiplexed protein detection using antibody-conjugated microbead arrays in a microfabricated electrophoretic device

PubMed Central

Barbee, Kristopher D.; Hsiao, Alexander P.; Roller, Eric E.; Huang, Xiaohua

2011-01-01

We report the development of a microfabricated electrophoretic device for assembling high-density arrays of antibody-conjugated microbeads for chip-based protein detection. The device consists of a flow cell formed between a gold-coated silicon chip with an array of microwells etched in a silicon dioxide film and a glass coverslip with a series of thin gold counter electrode lines. We have demonstrated that 0.4 and 1 μm beads conjugated with antibodies can be rapidly assembled into the microwells by applying a pulsed electric field across the chamber. By assembling step-wise a mixture of fluorescently labeled antibody-conjugated microbeads, we incorporated both spatial and fluorescence encoding strategies to demonstrate significant multiplexing capabilities. We have shown that these antibody-conjugated microbead arrays can be used to perform on-chip sandwich immunoassays to detect test antigens at concentrations as low as 40 pM (6 ng/mL). A finite element model was also developed to examine the electric field distribution within the device for different counter electrode configurations over a range of line pitches and chamber heights. This device will be useful for assembling high-density, encoded antibody arrays for multiplexed detection of proteins and other types of protein-conjugated microbeads for applications such as the analysis of protein-protein interactions. PMID:20820631

Iterative and multigrid methods in the finite element solution of incompressible and turbulent fluid flow

NASA Astrophysics Data System (ADS)

Lavery, N.; Taylor, C.

1999-07-01

Multigrid and iterative methods are used to reduce the solution time of the matrix equations which arise from the finite element (FE) discretisation of the time-independent equations of motion of the incompressible fluid in turbulent motion. Incompressible flow is solved by using the method of reduce interpolation for the pressure to satisfy the Brezzi-Babuska condition. The k-l model is used to complete the turbulence closure problem. The non-symmetric iterative matrix methods examined are the methods of least squares conjugate gradient (LSCG), biconjugate gradient (BCG), conjugate gradient squared (CGS), and the biconjugate gradient squared stabilised (BCGSTAB). The multigrid algorithm applied is based on the FAS algorithm of Brandt, and uses two and three levels of grids with a V-cycling schedule. These methods are all compared to the non-symmetric frontal solver. Copyright

Documentation of a numerical code for the simulation of variable density ground-water flow in three dimensions

USGS Publications Warehouse

Kuiper, L.K.

1985-01-01

A numerical code is documented for the simulation of variable density time dependent groundwater flow in three dimensions. The groundwater density, although variable with distance, is assumed to be constant in time. The Integrated Finite Difference grid elements in the code follow the geologic strata in the modeled area. If appropriate, the determination of hydraulic head in confining beds can be deleted to decrease computation time. The strongly implicit procedure (SIP), successive over-relaxation (SOR), and eight different preconditioned conjugate gradient (PCG) methods are used to solve the approximating equations. The use of the computer program that performs the calculations in the numerical code is emphasized. Detailed instructions are given for using the computer program, including input data formats. An example simulation and the Fortran listing of the program are included. (USGS)

Kalman filter based control for Adaptive Optics

NASA Astrophysics Data System (ADS)

Petit, Cyril; Quiros-Pacheco, Fernando; Conan, Jean-Marc; Kulcsár, Caroline; Raynaud, Henri-François; Fusco, Thierry

2004-12-01

Classical Adaptive Optics suffer from a limitation of the corrected Field Of View. This drawback has lead to the development of MultiConjugated Adaptive Optics. While the first MCAO experimental set-ups are presently under construction, little attention has been paid to the control loop. This is however a key element in the optimization process especially for MCAO systems. Different approaches have been proposed in recent articles for astronomical applications : simple integrator, Optimized Modal Gain Integrator and Kalman filtering. We study here Kalman filtering which seems a very promising solution. Following the work of Brice Leroux, we focus on a frequential characterization of kalman filters, computing a transfer matrix. The result brings much information about their behaviour and allows comparisons with classical controllers. It also appears that straightforward improvements of the system models can lead to static aberrations and vibrations filtering. Simulation results are proposed and analysed thanks to our frequential characterization. Related problems such as model errors, aliasing effect reduction or experimental implementation and testing of Kalman filter control loop on a simplified MCAO experimental set-up could be then discussed.

Versatile Cas9-Driven Subpopulation Selection Toolbox for Lactococcus lactis.

PubMed

van der Els, Simon; James, Jennelle K; Kleerebezem, Michiel; Bron, Peter A

2018-04-15

CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here, we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget, encoding the Streptocccus pyogenes Cas9 under the control of a constitutive promoter, was constructed, allowing plug and play introduction of short guide RNA (sgRNA) sequences to target specific genetic loci. Introduction of a pepN -targeting derivative of pLABTarget into L. lactis strain MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in a pepN deletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9-mediated double-strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of a pepN deletion subpopulation from its corresponding single-crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives in L. lactis Finally, pLABTarget, which contained sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages, and integrative conjugative elements (ICEs). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting in L. lactis , while the broad-host-range vector used suggests that this toolbox could readily be expanded to other Gram-positive bacteria. IMPORTANCE Mobile genetic elements in Lactococcus lactis and other lactic acid bacteria (LAB) play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 toward mobile genetic elements enabled their effective curing, which is of particular interest in the context of potentially problematic prophages present in a strain. Moreover, Cas9 targeting of other mobile genetic elements enables the deciphering of their contribution to dairy fermentation processes and further establishment of their importance for product characteristics. Copyright © 2018 American Society for Microbiology.

Detection of reactive metabolites using isotope-labeled glutathione trapping and simultaneous neutral loss and precursor ion scanning with ultra-high-pressure liquid chromatography triple quadruple mass spectrometry.

PubMed

Huang, Ke; Huang, Lingyi; van Breemen, Richard B

2015-04-07

Metabolic activation of drugs to electrophilic species is responsible for over 60% of black box warnings and drug withdrawals from the market place in the United States. Reactive metabolite trapping using glutathione (GSH) and analysis using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) or HPLC with high resolution mass spectrometry (mass defect filtering) have enabled screening for metabolic activation to become routine during drug development. However, current MS-based approaches cannot detect all GSH conjugates present in complex mixtures, especially those present in extracts of botanical dietary supplements. To overcome these limitations, a fast triple quadrupole mass spectrometer-based approach was developed that can detect positively and negatively charged GSH conjugates in a single analysis without the need for advanced knowledge of the elemental compositions of potential conjugates and while avoiding false positives. This approach utilized UHPLC instead of HPLC to shorten separation time and enhance sensitivity, incorporated stable-isotope labeled GSH to avoid false positives, and used fast polarity switching electrospray MS/MS to detect GSH conjugates that form positive and/or negative ions. The general new method was then used to test the licorice dietary supplement Glycyrrhiza glabra, which was found to form multiple GSH conjugates upon metabolic activation. Among the GSH conjugates found in the licorice assay were conjugates with isoliquiritigenin and glabridin, which is an irreversible inhibitor of cytochrome P450 enzymes.

Block copolymer modified surfaces for conjugation of biomacromolecules with control of quantity and activity.

PubMed

Li, Xin; Wang, Mengmeng; Wang, Lei; Shi, Xiujuan; Xu, Yajun; Song, Bo; Chen, Hong

2013-01-29

Polymer brush layers based on block copolymers of poly(oligo(ethylene glycol) methacrylate) (POEGMA) and poly(glycidyl methacrylate) (PGMA) were formed on silicon wafers by activators generated by electron transfer atom transfer radical polymerization (AGET ATRP). Different types of biomolecule can be conjugated to these brush layers by reaction of PGMA epoxide groups with amino groups in the biomolecule, while POEGMA, which resists nonspecific protein adsorption, provides an antifouling environment. Surfaces were characterized by water contact angle, ellipsometry, and Fourier transform infrared spectroscopy (FTIR) to confirm the modification reactions. Phase segregation of the copolymer blocks in the layers was observed by AFM. The effect of surface properties on protein conjugation was investigated using radiolabeling methods. It was shown that surfaces with POEGMA layers were protein resistant, while the quantity of protein conjugated to the diblock copolymer modified surfaces increased with increasing PGMA layer thickness. The activity of lysozyme conjugated on the surface could also be controlled by varying the thickness of the copolymer layer. When biotin was conjugated to the block copolymer grafts, the surface remained resistant to nonspecific protein adsorption but showed specific binding of avidin. These properties, that is, well-controlled quantity and activity of conjugated biomolecules and specificity of interaction with target biomolecules may be exploited for the improvement of signal-to-noise ratio in sensor applications. More generally, such surfaces may be useful as biological recognition elements of high specificity for functional biomaterials.

The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome.

PubMed

González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred; Llosa, Matxalen

2017-06-15

Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery. IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site-specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination. Copyright © 2017 American Society for Microbiology.

The Conjugative Relaxase TrwC Promotes Integration of Foreign DNA in the Human Genome

PubMed Central

González-Prieto, Coral; Gabriel, Richard; Dehio, Christoph; Schmidt, Manfred

2017-01-01

ABSTRACT Bacterial conjugation is a mechanism of horizontal DNA transfer. The relaxase TrwC of the conjugative plasmid R388 cleaves one strand of the transferred DNA at the oriT gene, covalently attaches to it, and leads the single-stranded DNA (ssDNA) into the recipient cell. In addition, TrwC catalyzes site-specific integration of the transferred DNA into its target sequence present in the genome of the recipient bacterium. Here, we report the analysis of the efficiency and specificity of the integrase activity of TrwC in human cells, using the type IV secretion system of the human pathogen Bartonella henselae to introduce relaxase-DNA complexes. Compared to Mob relaxase from plasmid pBGR1, we found that TrwC mediated a 10-fold increase in the rate of plasmid DNA transfer to human cells and a 100-fold increase in the rate of chromosomal integration of the transferred DNA. We used linear amplification-mediated PCR and plasmid rescue to characterize the integration pattern in the human genome. DNA sequence analysis revealed mostly reconstituted oriT sequences, indicating that TrwC is active and recircularizes transferred DNA in human cells. One TrwC-mediated site-specific integration event was detected, proving that TrwC is capable of mediating site-specific integration in the human genome, albeit with very low efficiency compared to the rate of random integration. Our results suggest that TrwC may stabilize the plasmid DNA molecules in the nucleus of the human cell, probably by recircularization of the transferred DNA strand. This stabilization would increase the opportunities for integration of the DNA by the host machinery. IMPORTANCE Different biotechnological applications, including gene therapy strategies, require permanent modification of target cells. Long-term expression is achieved either by extrachromosomal persistence or by integration of the introduced DNA. Here, we studied the utility of conjugative relaxase TrwC, a bacterial protein with site-specific integrase activity in bacteria, as an integrase in human cells. Although it is not efficient as a site-specific integrase, we found that TrwC is active in human cells and promotes random integration of the transferred DNA in the human genome, probably acting as a DNA chaperone until it is integrated by host mechanisms. TrwC-DNA complexes can be delivered to human cells through a type IV secretion system involved in pathogenesis. Thus, TrwC could be used in vivo to transfer the DNA of interest into the appropriate cell and promote its integration. If used in combination with a site-specific nuclease, it could lead to site-specific integration of the incoming DNA by homologous recombination. PMID:28411218

Parallel conjugate gradient algorithms for manipulator dynamic simulation

NASA Technical Reports Server (NTRS)

Fijany, Amir; Scheld, Robert E.

1989-01-01

Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).

Controlling of free radical copolymerization of styrene and maleic anhydride via RAFT process for the preparation of acetaminophen drug conjugates

NASA Astrophysics Data System (ADS)

Sütekin, S. Duygu; Atıcı, Ayşe Bakar; Güven, Olgun; Hoffman, Allan S.

2018-07-01

The presence of maleic anhydride moiety in styrene-maleic anhydride (SMA) copolymer makes it a versatile substrate for conjugation of drugs. In this study biocompatible styrene-maleic anhydride (SMA) copolymer with alternating structure was synthesized by gamma irradiation at room temperature in the presence of 2-phenyl-2-propyl benzodithioate (PPB). The poly(styrene-alt-maleic anhydride) (poly(St-alt-MA)) with narrow molecular weight distribution (Đ: 1.1-1.3) was prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization. The synthesized poly(St-alt-MA) structure was characterized by ATR-FTIR spectroscopy, elemental analysis and 1H NMR spectroscopy and molecular weight and dispersity were determined by size exclusion chromatography (SEC). SMA copolymers were further conjugated with acetaminophen via ester linkage and FT-IR, 1H NMR investigation indicated that the acetaminophen was attached to poly(St-alt-MA). Drug release profile of the polymer-drug conjugate was followed by high performance liquid chromatography (HPLC). The drug-conjugate system was found to follow first order release kinetics with Hixson-Crowell model while drug release mechanism was found as non-Fickian diffusion after testing various kinetic models.

Microreactor and method for preparing a radiolabeled complex or a biomolecule conjugate

DOEpatents

Reichert, David E; Kenis, Paul J. A.; Wheeler, Tobias D; Desai, Amit V; Zeng, Dexing; Onal, Birce C

2015-03-17

A microreactor for preparing a radiolabeled complex or a biomolecule conjugate comprises a microchannel for fluid flow, where the microchannel comprises a mixing portion comprising one or more passive mixing elements, and a reservoir for incubating a mixed fluid. The reservoir is in fluid communication with the microchannel and is disposed downstream of the mixing portion. A method of preparing a radiolabeled complex includes flowing a radiometal solution comprising a metallic radionuclide through a downstream mixing portion of a microchannel, where the downstream mixing portion includes one or more passive mixing elements, and flowing a ligand solution comprising a bifunctional chelator through the downstream mixing portion. The ligand solution and the radiometal solution are passively mixed while in the downstream mixing portion to initiate a chelation reaction between the metallic radionuclide and the bifunctional chelator. The chelation reaction is completed to form a radiolabeled complex.

Application of Conjugate Gradient methods to tidal simulation

USGS Publications Warehouse

Barragy, E.; Carey, G.F.; Walters, R.A.

1993-01-01

A harmonic decomposition technique is applied to the shallow water equations to yield a complex, nonsymmetric, nonlinear, Helmholtz type problem for the sea surface and an accompanying complex, nonlinear diagonal problem for the velocities. The equation for the sea surface is linearized using successive approximation and then discretized with linear, triangular finite elements. The study focuses on applying iterative methods to solve the resulting complex linear systems. The comparative evaluation includes both standard iterative methods for the real subsystems and complex versions of the well known Bi-Conjugate Gradient and Bi-Conjugate Gradient Squared methods. Several Incomplete LU type preconditioners are discussed, and the effects of node ordering, rejection strategy, domain geometry and Coriolis parameter (affecting asymmetry) are investigated. Implementation details for the complex case are discussed. Performance studies are presented and comparisons made with a frontal solver. ?? 1993.

A rapid approach for characterization of thiol-conjugated antibody-drug conjugates and calculation of drug-antibody ratio by liquid chromatography mass spectrometry.

PubMed

Firth, David; Bell, Leonard; Squires, Martin; Estdale, Sian; McKee, Colin

2015-09-15

We present the demonstration of a rapid "middle-up" liquid chromatography mass spectrometry (LC-MS)-based workflow for use in the characterization of thiol-conjugated maleimidocaproyl-monomethyl auristatin F (mcMMAF) and valine-citrulline-monomethyl auristatin E (vcMMAE) antibody-drug conjugates. Deconvoluted spectra were generated following a combination of deglycosylation, IdeS (immunoglobulin-degrading enzyme from Streptococcus pyogenes) digestion, and reduction steps that provide a visual representation of the product for rapid lot-to-lot comparison-a means to quickly assess the integrity of the antibody structure and the applied conjugation chemistry by mass. The relative abundance of the detected ions also offer information regarding differences in drug conjugation levels between samples, and the average drug-antibody ratio can be calculated. The approach requires little material (<100 μg) and, thus, is amenable to small-scale process development testing or as an early component of a complete characterization project facilitating informed decision making regarding which aspects of a molecule might need to be examined in more detail by orthogonal methodologies. Copyright © 2015 Elsevier Inc. All rights reserved.

Physicochemical properties and biocompatibility of a polymer-paclitaxel conjugate for cancer treatment.

PubMed

Yang, Danbo; Van, Sang; Liu, Jian; Wang, Jing; Jiang, Xinguo; Wang, Yiting; Yu, Lei

2011-01-01

Poly(L-γ-glutamylglutamine) paclitaxel (PGG-PTX) conjugate is a non-diblock polymeric drug nanoparticle intended to improve the therapeutic index of paclitaxel. The purpose of the present study was to elucidate further the physicochemical properties of PGG-PTX in order to proceed with its clinical development. PGG-PTX was designed by integration of a hydrophobic paclitaxel conjugate through an added hydrophilic glutamic acid onto poly(L-glutamic acid). The addition of a flexible glutamic linker between PGA and paclitaxel resulted in spontaneous self-assembly of a PGG-PTX conjugate into nanoparticles. The PGG-PTX conjugate was stable as a lyophilized solid form. An in vitro viability experiment showed that PGG-PTX was effective after a longer incubation period, the same trend as Taxol. In vitro studies using NCI-H460 and B16F0 cancer cells demonstrated significantly high cellular uptake after 30 minutes of incubation. The in vivo biocompatibility of PGG-PTX conjugate was evaluated in the NCI-H460 tumor model, the assessment of tissue seemed to be normal after 21 days of treatment. These results are encouraging for further development of non-block polymeric paclitaxel nanoparticles for treatment of cancer.

Regular patterns of Cs-137 distribution in natural conjugated elementary landscapes as a result of a balanced surface and depth water migration

NASA Astrophysics Data System (ADS)

Korobova, Elena; Romanov, Sergey

2016-04-01

Distribution of artificial radionuclides in the environment has long been used successfully for revealing migration pathways of their stable analogues. Migration of water in natural conjugated elementary landscapes characterizing the system of top-slope-resulting depression, has a specific structure and the radionuclide tracer is inevitably reflecting it by specific sorption and exchange processes. Other important issues are the concentration levels and the difference in characteristic time of chemical element dispersion. Modern biosphere has acquired its sustainable structure within a long period of time and is formed by basic macroelements allowing the water soluble portion of elements functioning as activators of chemical exchange. Water migration is controlled by gravitation, climate and relief while fixation depends upon the parameters of surfaces and chemical composition. The resulting structure depends on specificity and duration of the process. The long-term redistribution of chemical elements in terrestrial environment has led to a distinct geochemical structure of conjugated landscapes with a specific geometry of redistribution and accumulation of chemical elements. Migration of the newly born anthropogenic radionuclides followed natural pathways in biosphere. The initial deposition of the Chernobyl's radionuclides within the elementary landscape-geochemical system was even by condition of aerial deposition. But further exchange process is controlled by the strength of fixation and migration ability of the carriers. Therefore patterns of spatial distribution of artificial radionuclides in natural landscapes are considerably different as compared to those of the long-term forming the basic structure of chemical fields in biosphere. Our monitoring of Cs-137 radial and lateral distribution in the test plots characterizing natural undisturbed conjugated elementary landscapes performed in the period from 2005 until now has revealed a stable and specifically polycentric structure of radiocesium distribution believed to reflect the character of radial and lateral water body migration and a high sensitivity of water distribution to surface parameters. This leads to an unusual wavy type of Cs-137 distribution down, along and across all the slopes examined for surface Cs-137 activity at every measured point. The finding is believed to have an important practical outcome allowing much more detailed evaluation of micronutrients distribution and optimization of their application.

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

DOE PAGES

Reeve, Wayne; Sullivan, John; Ronson, Clive; ...

2015-08-14

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-Quality draft genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain CJ3Sym

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

Reeve, Wayne; Sullivan, John; Ronson, Clive

Mesorhizobium loti strain CJ3Sym was isolated in 1998 following transfer of the integrative and conjugative element ICE Ml Sym R7A , also known as the R7A symbiosis island, in a laboratory mating from the donor M. loti strain R7A to a nonsymbiotic recipient Mesorhizobium strain CJ3. Strain CJ3 was originally isolated from a field site in the Rocklands range in New Zealand in 1994. CJ3Sym is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain CJ3Sym currently comprises 70 scaffolds totaling 7,563,725 bp. In conclusion, the high-quality draft genome is arranged in 70 scaffolds ofmore » 71 contigs, contains 7,331 protein-coding genes and 70 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Holography and optical information processing; Proceedings of the Soviet-Chinese Joint Seminar, Bishkek, Kyrgyzstan, Sept. 21-26, 1991

NASA Astrophysics Data System (ADS)

Mikaelian, Andrei L.

Attention is given to data storage, devices, architectures, and implementations of optical memory and neural networks; holographic optical elements and computer-generated holograms; holographic display and materials; systems, pattern recognition, interferometry, and applications in optical information processing; and special measurements and devices. Topics discussed include optical immersion as a new way to increase information recording density, systems for data reading from optical disks on the basis of diffractive lenses, a new real-time optical associative memory system, an optical pattern recognition system based on a WTA model of neural networks, phase diffraction grating for the integral transforms of coherent light fields, holographic recording with operated sensitivity and stability in chalcogenide glass layers, a compact optical logic processor, a hybrid optical system for computing invariant moments of images, optical fiber holographic inteferometry, and image transmission through random media in single pass via optical phase conjugation.

Substrate specificity of the ubiquitin and Ubl proteases

PubMed Central

Ronau, Judith A; Beckmann, John F; Hochstrasser, Mark

2016-01-01

Conjugation and deconjugation of ubiquitin and ubiquitin-like proteins (Ubls) to cellular proteins are highly regulated processes integral to cellular homeostasis. Most often, the C-termini of these small polypeptides are attached to lysine side chains of target proteins by an amide (isopeptide) linkage. Deubiquitinating enzymes (DUBs) and Ubl-specific proteases (ULPs) comprise a diverse group of proteases that recognize and remove ubiquitin and Ubls from their substrates. How DUBs and ULPs distinguish among different modifiers, or different polymeric forms of these modifiers, remains poorly understood. The specificity of ubiquitin/Ubl-deconjugating enzymes for particular substrates depends on multiple factors, ranging from the topography of specific substrate features, as in different polyubiquitin chain types, to structural elements unique to each enzyme. Here we summarize recent structural and biochemical studies that provide insights into mechanisms of substrate specificity among various DUBs and ULPs. We also discuss the unexpected specificities of non-eukaryotic proteases in these families. PMID:27012468

Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline.

PubMed

Da Cunha, Violette; Davies, Mark R; Douarre, Pierre-Emmanuel; Rosinski-Chupin, Isabelle; Margarit, Immaculada; Spinali, Sebastien; Perkins, Tim; Lechat, Pierre; Dmytruk, Nicolas; Sauvage, Elisabeth; Ma, Laurence; Romi, Benedetta; Tichit, Magali; Lopez-Sanchez, Maria-José; Descorps-Declere, Stéphane; Souche, Erika; Buchrieser, Carmen; Trieu-Cuot, Patrick; Moszer, Ivan; Clermont, Dominique; Maione, Domenico; Bouchier, Christiane; McMillan, David J; Parkhill, Julian; Telford, John L; Dougan, Gordan; Walker, Mark J; Holden, Matthew T G; Poyart, Claire; Glaser, Philippe

2014-08-04

Streptococcus agalactiae (Group B Streptococcus, GBS) is a commensal of the digestive and genitourinary tracts of humans that emerged as the leading cause of bacterial neonatal infections in Europe and North America during the 1960s. Due to the lack of epidemiological and genomic data, the reasons for this emergence are unknown. Here we show by comparative genome analysis and phylogenetic reconstruction of 229 isolates that the rise of human GBS infections corresponds to the selection and worldwide dissemination of only a few clones. The parallel expansion of the clones is preceded by the insertion of integrative and conjugative elements conferring tetracycline resistance (TcR). Thus, we propose that the use of tetracycline from 1948 onwards led in humans to the complete replacement of a diverse GBS population by only few TcR clones particularly well adapted to their host, causing the observed emergence of GBS diseases in neonates.

A physico-chemical assessment of the thermal stability of pneumococcal conjugate vaccine components

PubMed Central

Gao, Fang; Lockyer, Kay; Burkin, Karena; Crane, Dennis T; Bolgiano, Barbara

2014-01-01

Physico-chemical analysis of pneumococcal polysaccharide (PS)-protein conjugate vaccine components used for two commercially licensed vaccines was performed to compare the serotype- and carrier protein-specific stabilities of these vaccines. Nineteen different monovalent pneumococcal conjugates from commercial vaccines utilizing CRM197, diphtheria toxoid (DT), Protein D (PD) or tetanus toxoid (TT) as carrier proteins were incubated at temperatures up to 56°C for up to eight weeks or were subjected to freeze-thawing (F/T). Structural stability was evaluated by monitoring their size, integrity and carrier protein conformation. The molecular size of the vaccine components was well maintained for Protein D, TT and DT conjugates at -20°C, 4°C and F/T, and for CRM197 conjugates at 4°C and F/T. It was observed that four of the eight serotypes of Protein D conjugates tended to form high molecular weight complexes at 37°C or above. The other conjugated carrier proteins also appeared to form oligomers or ‘aggregates’ at elevated temperatures, but rarely when frozen and thawed. There was evidence of degradation in some of the conjugates as evidenced by the formation of lower molecular weight materials which correlated with measured free saccharide. In conclusion, pneumococcal-Protein D/TT/DT and most CRM197 bulk conjugate vaccines were stable when stored at 2–8°C, the recommended temperature. In common between the conjugates produced by the two manufacturers, serotypes 1, 5, and 19F were relatively less stable and 6B was the most stable, with types 7F and 23F also showing good stability. PMID:25483488

Complex Conjugated certificateless-based signcryption with differential integrated factor for secured message communication in mobile network

PubMed Central

Rajagopalan, S. P.

2017-01-01

Certificateless-based signcryption overcomes inherent shortcomings in traditional Public Key Infrastructure (PKI) and Key Escrow problem. It imparts efficient methods to design PKIs with public verifiability and cipher text authenticity with minimum dependency. As a classic primitive in public key cryptography, signcryption performs validity of cipher text without decryption by combining authentication, confidentiality, public verifiability and cipher text authenticity much more efficiently than the traditional approach. In this paper, we first define a security model for certificateless-based signcryption called, Complex Conjugate Differential Integrated Factor (CC-DIF) scheme by introducing complex conjugates through introduction of the security parameter and improving secured message distribution rate. However, both partial private key and secret value changes with respect to time. To overcome this weakness, a new certificateless-based signcryption scheme is proposed by setting the private key through Differential (Diff) Equation using an Integration Factor (DiffEIF), minimizing computational cost and communication overhead. The scheme is therefore said to be proven secure (i.e. improving the secured message distributing rate) against certificateless access control and signcryption-based scheme. In addition, compared with the three other existing schemes, the CC-DIF scheme has the least computational cost and communication overhead for secured message communication in mobile network. PMID:29040290

Complex Conjugated certificateless-based signcryption with differential integrated factor for secured message communication in mobile network.

PubMed

Alagarsamy, Sumithra; Rajagopalan, S P

2017-01-01

Certificateless-based signcryption overcomes inherent shortcomings in traditional Public Key Infrastructure (PKI) and Key Escrow problem. It imparts efficient methods to design PKIs with public verifiability and cipher text authenticity with minimum dependency. As a classic primitive in public key cryptography, signcryption performs validity of cipher text without decryption by combining authentication, confidentiality, public verifiability and cipher text authenticity much more efficiently than the traditional approach. In this paper, we first define a security model for certificateless-based signcryption called, Complex Conjugate Differential Integrated Factor (CC-DIF) scheme by introducing complex conjugates through introduction of the security parameter and improving secured message distribution rate. However, both partial private key and secret value changes with respect to time. To overcome this weakness, a new certificateless-based signcryption scheme is proposed by setting the private key through Differential (Diff) Equation using an Integration Factor (DiffEIF), minimizing computational cost and communication overhead. The scheme is therefore said to be proven secure (i.e. improving the secured message distributing rate) against certificateless access control and signcryption-based scheme. In addition, compared with the three other existing schemes, the CC-DIF scheme has the least computational cost and communication overhead for secured message communication in mobile network.

Status Report on NEAMS System Analysis Module Development

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

Hu, R.; Fanning, T. H.; Sumner, T.

2015-12-01

Under the Reactor Product Line (RPL) of DOE-NE’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, an advanced SFR System Analysis Module (SAM) is being developed at Argonne National Laboratory. The goal of the SAM development is to provide fast-running, improved-fidelity, whole-plant transient analyses capabilities. SAM utilizes an object-oriented application framework MOOSE), and its underlying meshing and finite-element library libMesh, as well as linear and non-linear solvers PETSc, to leverage modern advanced software environments and numerical methods. It also incorporates advances in physical and empirical models and seeks closure models based on information from high-fidelity simulations and experiments. This reportmore » provides an update on the SAM development, and summarizes the activities performed in FY15 and the first quarter of FY16. The tasks include: (1) implement the support of 2nd-order finite elements in SAM components for improved accuracy and computational efficiency; (2) improve the conjugate heat transfer modeling and develop pseudo 3-D full-core reactor heat transfer capabilities; (3) perform verification and validation tests as well as demonstration simulations; (4) develop the coupling requirements for SAS4A/SASSYS-1 and SAM integration.« less

Krylov subspace iterative methods for boundary element method based near-field acoustic holography.

PubMed

Valdivia, Nicolas; Williams, Earl G

2005-02-01

The reconstruction of the acoustic field for general surfaces is obtained from the solution of a matrix system that results from a boundary integral equation discretized using boundary element methods. The solution to the resultant matrix system is obtained using iterative regularization methods that counteract the effect of noise on the measurements. These methods will not require the calculation of the singular value decomposition, which can be expensive when the matrix system is considerably large. Krylov subspace methods are iterative methods that have the phenomena known as "semi-convergence," i.e., the optimal regularization solution is obtained after a few iterations. If the iteration is not stopped, the method converges to a solution that generally is totally corrupted by errors on the measurements. For these methods the number of iterations play the role of the regularization parameter. We will focus our attention to the study of the regularizing properties from the Krylov subspace methods like conjugate gradients, least squares QR and the recently proposed Hybrid method. A discussion and comparison of the available stopping rules will be included. A vibrating plate is considered as an example to validate our results.

Spatial-temporal light modulation by a liquid crystal-polymer photoconductor structure with conjugate bonds

NASA Astrophysics Data System (ADS)

Sliusar', A. V.; Myl'Nikov, V. S.

1991-11-01

A method is proposed for the spatial-temporal modulation of light by a polymer photoconductor-liquid crystal structure using conjugate-bond organic polymers as photosensitive elements. The preparation of such structures and their modulation characteristics are described. It is shown that the spectral absorption and photosensitivity characteristics of the structures are largely determined by the heat treament of the polymer film. Sensitivity limits of a modulator using a polyacrylonitrile film are 5 x 10 exp -6 J/sq cm and 5 x 10 exp -4 W/sq cm for the write and read light, respectively.

Facile rhenium-peptide conjugate synthesis using a one-pot derived Re(CO)3 reagent.

PubMed

Chanawanno, Kullapa; Kondeti, Vinay; Caporoso, Joel; Paruchuri, Sailaja; Leeper, Thomas C; Herrick, Richard S; Ziegler, Christopher J

2016-03-21

We have synthesized two Re(CO)3-modified lysine complexes (1 and 2), where the metal is attached to the amino acid at the Nε position, via a one-pot Schiff base formation reaction. These compounds can be used in the solid phase synthesis of peptides, and to date we have produced four conjugate systems incorporating neurotensin, bombesin, leutenizing hormone releasing hormone, and a nuclear localization sequence. We observed uptake into human umbilical vascular endothelial cells as well as differential uptake depending on peptide sequence identity, as characterized by fluorescence and rhenium elemental analysis.

Molecular characterization of the 2011 Hong Kong scarlet fever outbreak.

PubMed

Tse, Herman; Bao, Jessie Y J; Davies, Mark R; Maamary, Peter; Tsoi, Hoi-Wah; Tong, Amy H Y; Ho, Tom C C; Lin, Chi-Ho; Gillen, Christine M; Barnett, Timothy C; Chen, Jonathan H K; Lee, Mianne; Yam, Wing-Cheong; Wong, Chi-Kin; Ong, Cheryl-Lynn Y; Chan, Yee-Wai; Wu, Cheng-Wei; Ng, Tony; Lim, Wilina W L; Tsang, Thomas H F; Tse, Cindy W S; Dougan, Gordon; Walker, Mark J; Lok, Si; Yuen, Kwok-Yung

2012-08-01

A scarlet fever outbreak occurred in Hong Kong in 2011. The majority of cases resulted in the isolation of Streptococcus pyogenes emm12 with multiple antibiotic resistances. Phylogenetic analysis of 22 emm12 scarlet fever outbreak isolates, 7 temporally and geographically matched emm12 non-scarlet fever isolates, and 18 emm12 strains isolated during 2005-2010 indicated the outbreak was multiclonal. Genome sequencing of 2 nonclonal scarlet fever isolates (HKU16 and HKU30), coupled with diagnostic polymerase chain reaction assays, identified 2 mobile genetic elements distributed across the major lineages: a 64.9-kb integrative and conjugative element encoding tetracycline and macrolide resistance and a 46.4-kb prophage encoding superantigens SSA and SpeC and the DNase Spd1. Phenotypic comparison of HKU16 and HKU30 with the S. pyogenes M1T1 strain 5448 revealed that HKU16 displays increased adherence to HEp-2 human epithelial cells, whereas HKU16, HKU30, and 5448 exhibit equivalent resistance to neutrophils and virulence in a humanized plasminogen murine model. However, in contrast to M1T1, the virulence of HKU16 and HKU30 was not associated with covRS mutation. The multiclonal nature of the emm12 scarlet fever isolates suggests that factors such as mobile genetic elements, environmental factors, and host immune status may have contributed to the 2011 scarlet fever outbreak.

Molecular Characterization of the 2011 Hong Kong Scarlet Fever Outbreak

PubMed Central

Tse, Herman; Bao, Jessie Y. J.; Davies, Mark R.; Maamary, Peter; Tsoi, Hoi-Wah; Tong, Amy H. Y.; Ho, Tom C. C.; Lin, Chi-Ho; Gillen, Christine M.; Barnett, Timothy C.; Chen, Jonathan H. K.; Lee, Mianne; Yam, Wing-Cheong; Wong, Chi-Kin; Ong, Cheryl-lynn Y.; Chan, Yee-Wai; Wu, Cheng-Wei; Ng, Tony; Lim, Wilina W. L.; Tsang, Thomas H. F.; Tse, Cindy W. S.; Dougan, Gordon; Walker, Mark J.; Lok, Si; Yuen, Kwok-Yung

2012-01-01

A scarlet fever outbreak occurred in Hong Kong in 2011. The majority of cases resulted in the isolation of Streptococcus pyogenes emm12 with multiple antibiotic resistances. Phylogenetic analysis of 22 emm12 scarlet fever outbreak isolates, 7 temporally and geographically matched emm12 non–scarlet fever isolates, and 18 emm12 strains isolated during 2005–2010 indicated the outbreak was multiclonal. Genome sequencing of 2 nonclonal scarlet fever isolates (HKU16 and HKU30), coupled with diagnostic polymerase chain reaction assays, identified 2 mobile genetic elements distributed across the major lineages: a 64.9-kb integrative and conjugative element encoding tetracycline and macrolide resistance and a 46.4-kb prophage encoding superantigens SSA and SpeC and the DNase Spd1. Phenotypic comparison of HKU16 and HKU30 with the S. pyogenes M1T1 strain 5448 revealed that HKU16 displays increased adherence to HEp-2 human epithelial cells, whereas HKU16, HKU30, and 5448 exhibit equivalent resistance to neutrophils and virulence in a humanized plasminogen murine model. However, in contrast to M1T1, the virulence of HKU16 and HKU30 was not associated with covRS mutation. The multiclonal nature of the emm12 scarlet fever isolates suggests that factors such as mobile genetic elements, environmental factors, and host immune status may have contributed to the 2011 scarlet fever outbreak. PMID:22615319

Modular Integration of Upconverting Nanocrystal-Dendrimer Composites for Folate Receptor-Specific NIR Imaging and Light-Triggered Drug Release.

PubMed

Wong, Pamela T; Chen, Dexin; Tang, Shengzhuang; Yanik, Sean; Payne, Michael; Mukherjee, Jhindan; Coulter, Alexa; Tang, Kenny; Tao, Ke; Sun, Kang; Baker, James R; Choi, Seok Ki

2015-12-02

Upconversion nanocrystals (UCNs) display near-infrared (NIR)-responsive photoluminescent properties for NIR imaging and drug delivery. The development of effective strategies for UCN integration with other complementary nanostructures for targeting and drug conjugation is highly desirable. This study reports on a core/shell-based theranostic system designed by UCN integration with a folate (FA)-conjugated dendrimer for tumor targeting and with photocaged doxorubicin as a cytotoxic agent. Two types of UCNs (NaYF4:Yb/Er (or Yb/Tm); diameter = ≈50 to 54 nm) are described, each displaying distinct emission properties upon NIR (980 nm) excitation. The UCNs are surface modified through covalent attachment of photocaged doxorubicin (ONB-Dox) and a multivalent FA-conjugated polyamidoamine (PAMAM) dendrimer G5(FA)6 to prepare UCN@(ONB-Dox)(G5FA). Surface plasmon resonance experiments performed with G5(FA)6 dendrimer alone show nanomolar binding avidity (KD = 5.9 × 10(-9) M) to the folate binding protein. This dendrimer binding corresponds with selective binding and uptake of UCN@(ONB-Dox)(G5FA) by FAR-positive KB carcinoma cells in vitro. Furthermore, UCN@(ONB-Dox)(G5FA) treatment of FAR(+) KB cells inhibits cell growth in a light dependent manner. These results validate the utility of modularly integrated UCN-dendrimer nanocomposites for cell type specific NIR imaging and light-controlled drug release, thus serving as a new theranostic system. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Population Biology of Bacterial Plasmids: A PRIORI Conditions for the Existence of Conjugationally Transmitted Factors

PubMed Central

Stewart, Frank M.; Levin, Bruce R.

1977-01-01

A mathematical model for the population dynamics of conjugationally transmitted plasmids in bacterial populations is presented and its properties analyzed. Consideration is given to nonbacteriocinogenic factors that are incapable of incorporation into the chromosome of their host cells, and to bacterial populations maintained in either continuous (chemostat) or discrete (serial transfer) culture. The conditions for the establishment and maintenance of these infectious extrachromosomal elements and equilibrium frequencies of cells carrying them are presented for different values of the biological parameters: population growth functions, conjugational transfer and segregation rate constants. With these parameters in a biologically realistic range, the theory predicts a broad set of physical conditions, resource concentrations and dilution rates, where conjugationally transmitted plasmids can become established and where cells carrying them will maintain high frequencies in bacterial populations. This can occur even when plasmid-bearing cells are much less fit (i.e., have substantially lower growth rates) than cells free of these factors. The implications of these results and the reality and limitations of the model are discussed and the values of its parameters in natural populations speculated upon. PMID:17248761

Improving the in vivo therapeutic index of siRNA polymer conjugates through increasing pH responsiveness.

PubMed

Guidry, Erin N; Farand, Julie; Soheili, Arash; Parish, Craig A; Kevin, Nancy J; Pipik, Brenda; Calati, Kathleen B; Ikemoto, Nori; Waldman, Jacob H; Latham, Andrew H; Howell, Bonnie J; Leone, Anthony; Garbaccio, Robert M; Barrett, Stephanie E; Parmar, Rubina Giare; Truong, Quang T; Mao, Bing; Davies, Ian W; Colletti, Steven L; Sepp-Lorenzino, Laura

2014-02-19

Polymer based carriers that aid in endosomal escape have proven to be efficacious siRNA delivery agents in vitro and in vivo; however, most suffer from cytotoxicity due in part to a lack of selectivity for endosomal versus cell membrane lysis. For polymer based carriers to move beyond the laboratory and into the clinic, it is critical to find carriers that are not only efficacious, but also have margins that are clinically relevant. In this paper we report three distinct categories of polymer conjugates that improve the selectivity of endosomal membrane lysis by relying on the change in pH associated with endosomal trafficking, including incorporation of low pKa heterocycles, acid cleavable amino side chains, or carboxylic acid pH sensitive charge switches. Additionally, we determine the therapeutic index of our polymer conjugates in vivo and demonstrate that the incorporation of pH responsive elements dramatically expands the therapeutic index to 10-15, beyond that of the therapeutic index (less than 3), for polymer conjugates previously reported.

Incorporating fluorinated moieties in fully conjugated donor-acceptor block copolymers

NASA Astrophysics Data System (ADS)

Lee, Youngmin; Wang, Qing; Gomez, Enrique D.

Fully conjugated donor-acceptor block copolymers are promising candidates for photovoltaics due to their ability to microphase separate at length scales commensurate with exciton diffusion lengths. These materials can also serve as model systems to study the relationship between molecular structure, microstructure, and optoelectronic properties of conjugated polymers. The development of new donor-acceptor block copolymers relies on the manipulation of the chemical structure to fine tune properties and improve overall performance when employed in photovoltaic devices. To this end, we have demonstrated the incorporation of fluorinated moieties in conjugated block copolymers. The introduction of fluorine, a strong electron withdrawing element, is known to influence phase separation and the bandgap, and as a result, optoelectronic properties. Fluorine was introduced to the acceptor block of poly(3-hexylthiophene-2,5-diyl)-block-poly((9,9-bis(2-octyl)fluorene-2,7-diyl)-alt-(4,7-di(thiophene-2-yl)-2,1,3-benzothiadiazole)-5 ',5?-diyl) (P3HT- b-PFTBT). PFTBTs were prepared with di-fluorinated and mono-fluorinated TBT. We find that fluorination impacts the bandgap, morphology and performance in devices.

A multi-conjugate adaptive optics testbed using two MEMS deformable mirrors

NASA Astrophysics Data System (ADS)

Andrews, Jonathan R.; Martinez, Ty; Teare, Scott W.; Restaino, Sergio R.; Wilcox, Christopher C.; Santiago, Freddie; Payne, Don M.

2011-03-01

Adaptive optics (AO) systems are well demonstrated in the literature with both laboratory and real-world systems being developed. Some of these systems have employed MEMS deformable mirrors as their active corrective element. More recent work in AO for astronomical applications has focused on providing correction in more than one conjugate plane. Additionally, horizontal path AO systems are exploring correction in multiple conjugate planes. This provides challenges for a laboratory system as the aberrations need to be generated and corrected in more than one plane in the optical system. Our work with compact AO systems employing MEMS technology in addition to liquid crystal spatial light modulator (SLM) driven aberration generators has been scaled up to a two conjugate plane testbed. Using two SLM based aberration generators and two separate wavefront sensors, the system can apply correction with two MEMS deformable mirrors. The challenges in such a system are to properly match non-identical components and weight the correction algorithm for correcting in two planes. This paper demonstrates preliminary results and analysis with this system with wavefront data and residual error measurements.

Design, Synthesis, and Pharmacokinetics of a Bone-Targeting Dual-Action Prodrug for the Treatment of Osteoporosis.

PubMed

Xie, Haibo; Chen, Gang; Young, Robert N

2017-08-24

A dual-action bone-targeting prodrug has been designed, synthesized, and evaluated for in vitro and in vivo metabolic stability, in vivo tissue distribution, and rates of release of the active constituents after binding to bones through the use of differentially double-labeled derivatives. The conjugate (general structure 7) embodies the merger of a very potent and proven anabolic selective agonist of the prostaglandin EP4 receptor, compound 5, and alendronic acid, a potent inhibitor of bone resorption, optimally linked through a differentially hydrolyzable linker unit, N-4-carboxymethylphenyl-methyloxycarbonyl-leucinyl-argininyl-para-aminophenylmethylalcohol (Leu-Arg-PABA). Optimized conjugate 16 was designed so that esterase activity will liberate 5 and cathepsin K cleavage of the Leu-Arg-PABA element will liberate alendronic acid. Studies with doubly radiolabeled 16 provide a proof-of-concept for the use of a cathepsin K cleavable peptide-linked conjugate for targeting of bisphosphonate prodrugs to bone and slow release liberation of the active constituents in vivo. Such conjugates are potential therapies for the treatment of bone disorders such as osteoporosis.

On Spaces of Commuting Elements in Lie Groups

DTIC Science & Technology

2014-02-25

G given by θ(g, t) = gtg −1 = tg, with more details given in Section 2. Definition 1.6. Define Θ : G×NT Assoc(T )→ Comm(G) by the formula Θ(g, (t1...conjugation θn : G× Tn → Hom(Zn, G)1G g × (t1, . . . , tn) 7→ (tg1, . . . , tgn), ON SPACES OF COMMUTING ELEMENTS IN LIE GROUPS 11 where tg = gtg −1. An n

Promotion of spinosad biosynthesis by chromosomal integration of the Vitreoscilla hemoglobin gene in Saccharopolyspora spinosa.

PubMed

Luo, Yushuang; Kou, Xiaoxiao; Ding, Xuezhi; Hu, Shengbiao; Tang, Ying; Li, Wenping; Huang, Fan; Yang, Qi; Chen, Hanna; Xia, Liqiu

2012-02-01

To promote spinosad biosynthesis by improving the limited oxygen supply during high-density fermentation of Saccharopolyspora spinosa, the open reading frame of the Vitreoscilla hemoglobin gene was placed under the control of the promoter for the erythromycin resistance gene by splicing using overlapping extension PCR. This was cloned into the integrating vector pSET152, yielding the Vitreoscilla hemoglobin gene expression plasmid pSET152EVHB. This was then introduced into S. spinosa SP06081 by conjugal transfer, and integrated into the chromosome by site-specific recombination at the integration site ΦC31 on pSET152EVHB. The resultant conjugant, S. spinosa S078-1101, was genetically stable. The integration was further confirmed by PCR and Southern blotting analysis. A carbon monoxide differential spectrum assay showed that active Vitreoscilla hemoglobin was successfully expressed in S. spinosa S078-1101. Fermentation results revealed that expression of the Vitreoscilla hemoglobin gene significantly promoted spinosad biosynthesis under normal oxygen and moderately oxygen-limiting conditions (P<0.01). These findings demonstrate that integrating expression of the Vitreoscilla hemoglobin gene improves oxygen uptake and is an effective means for the genetic improvement of S. spinosa fermentation.

Naked-eye 3D imaging employing a modified MIMO micro-ring conjugate mirrors

NASA Astrophysics Data System (ADS)

Youplao, P.; Pornsuwancharoen, N.; Amiri, I. S.; Thieu, V. N.; Yupapin, P.

2018-03-01

In this work, the use of a micro-conjugate mirror that can produce the 3D image incident probe and display is proposed. By using the proposed system together with the concept of naked-eye 3D imaging, a pixel and a large volume pixel of a 3D image can be created and displayed as naked-eye perception, which is valuable for the large volume naked-eye 3D imaging applications. In operation, a naked-eye 3D image that has a large pixel volume will be constructed by using the MIMO micro-ring conjugate mirror system. Thereafter, these 3D images, formed by the first micro-ring conjugate mirror system, can be transmitted through an optical link to a short distance away and reconstructed via the recovery conjugate mirror at the other end of the transmission. The image transmission is performed by the Fourier integral in MATLAB and compares to the Opti-wave program results. The Fourier convolution is also included for the large volume image transmission. The simulation is used for the manipulation, where the array of a micro-conjugate mirror system is designed and simulated for the MIMO system. The naked-eye 3D imaging is confirmed by the concept of the conjugate mirror in both the input and output images, in terms of the four-wave mixing (FWM), which is discussed and interpreted.

Recent Advances in Conjugated Polymer Materials for Disease Diagnosis.

PubMed

Lv, Fengting; Qiu, Tian; Liu, Libing; Ying, Jianming; Wang, Shu

2016-02-10

The extraordinary optical amplification and light-harvesting properties of conjugated polymers impart sensing systems with higher sensitivity, which meets the primary demands of early cancer diagnosis. Recent advances in the detection of DNA methylation and mutation with polyfluorene derivatives based fluorescence resonance energy transfer (FRET) as a means to modulate fluorescent responses attest to the great promise of conjugated polymers as powerful tools for the clinical diagnosis of diseases. To facilitate the ever-changing needs of diagnosis, the development of detection approaches and FRET signal analysis are highlighted in this review. Due to their exceptional brightness, excellent photostability, and low or absent toxicity, conjugated polymers are verified as superior materials for in-vivo imaging, and provide feasibility for future clinical molecular-imaging applications. The integration of conjugated polymers with clinical research has shown profound effects on diagnosis for the early detection of disease-related biomarkers, as well as in-vivo imaging, which leads to a multidisciplinary scientific field with perspectives in both basic research and application issues. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interaction of Vaccination and Reduction of Antibiotic Use Drives Unexpected Increase of Pneumococcal Meningitis

PubMed Central

de Cellès, Matthieu Domenech; Pons-Salort, Margarita; Varon, Emmanuelle; Vibet, Marie-Anne; Ligier, Caroline; Letort, Véronique; Opatowski, Lulla; Guillemot, Didier

2015-01-01

Antibiotic-use policies may affect pneumococcal conjugate-vaccine effectiveness. The reported increase of pneumococcal meningitis from 2001 to 2009 in France, where a national campaign to reduce antibiotic use was implemented in parallel to the introduction of the 7-valent conjugate vaccine, provides unique data to assess these effects. We constructed a mechanistic pneumococcal transmission model and used likelihood to assess the ability of competing hypotheses to explain that increase. We find that a model integrating a fitness cost of penicillin resistance successfully explains the overall and age-stratified pattern of serotype replacement. By simulating counterfactual scenarios of public health interventions in France, we propose that this fitness cost caused a gradual and pernicious interaction between the two interventions by increasing the spread of nonvaccine, penicillin-susceptible strains. More generally, our results indicate that reductions of antibiotic use may counteract the benefits of conjugate vaccines introduced into countries with low vaccine-serotype coverages and high-resistance frequencies. Our findings highlight the key role of antibiotic use in vaccine-induced serotype replacement and suggest the need for more integrated approaches to control pneumococcal infections. PMID:26063589

Interaction of Vaccination and Reduction of Antibiotic Use Drives Unexpected Increase of Pneumococcal Meningitis.

PubMed

de Cellès, Matthieu Domenech; Pons-Salort, Margarita; Varon, Emmanuelle; Vibet, Marie-Anne; Ligier, Caroline; Letort, Véronique; Opatowski, Lulla; Guillemot, Didier

2015-06-11

Antibiotic-use policies may affect pneumococcal conjugate-vaccine effectiveness. The reported increase of pneumococcal meningitis from 2001 to 2009 in France, where a national campaign to reduce antibiotic use was implemented in parallel to the introduction of the 7-valent conjugate vaccine, provides unique data to assess these effects. We constructed a mechanistic pneumococcal transmission model and used likelihood to assess the ability of competing hypotheses to explain that increase. We find that a model integrating a fitness cost of penicillin resistance successfully explains the overall and age-stratified pattern of serotype replacement. By simulating counterfactual scenarios of public health interventions in France, we propose that this fitness cost caused a gradual and pernicious interaction between the two interventions by increasing the spread of nonvaccine, penicillin-susceptible strains. More generally, our results indicate that reductions of antibiotic use may counteract the benefits of conjugate vaccines introduced into countries with low vaccine-serotype coverages and high-resistance frequencies. Our findings highlight the key role of antibiotic use in vaccine-induced serotype replacement and suggest the need for more integrated approaches to control pneumococcal infections.

Collagen-Gold Nanoparticle Conjugates for Versatile Biosensing

PubMed Central

Unser, Sarah; Holcomb, Samuel; Cary, ReJeana; Sagle, Laura

2017-01-01

Integration of noble metal nanoparticles with proteins offers promising potential to create a wide variety of biosensors that possess both improved selectivity and versatility. The multitude of functionalities that proteins offer coupled with the unique optical properties of noble metal nanoparticles can allow for the realization of simple, colorimetric sensors for a significantly larger range of targets. Herein, we integrate the structural protein collagen with 10 nm gold nanoparticles to develop a protein-nanoparticle conjugate which possess the functionality of the protein with the desired colorimetric properties of the nanoparticles. Applying the many interactions that collagen undergoes in the extracellular matrix, we are able to selectively detect both glucose and heparin with the same collagen-nanoparticle conjugate. Glucose is directly detected through the cross-linking of the collagen fibrils, which brings the attached nanoparticles into closer proximity, leading to a red-shift in the LSPR frequency. Conversely, heparin is detected through a competition assay in which heparin-gold nanoparticles are added to solution and compete with heparin in the solution for the binding sites on the collagen fibrils. The collagen-nanoparticle conjugates are shown to detect both glucose and heparin in the physiological range. Lastly, glucose is selectively detected in 50% mouse serum with the collagen-nanoparticle devices possessing a linear range of 3–25 mM, which is also within the physiologically relevant range. PMID:28212282

Fiber bundle phase conjugate mirror

DOEpatents

Ward, Benjamin G.

2012-05-01

An improved method and apparatus for passively conjugating the phases of a distorted wavefronts resulting from optical phase mismatch between elements of a fiber laser array are disclosed. A method for passively conjugating a distorted wavefront comprises the steps of: multiplexing a plurality of probe fibers and a bundle pump fiber in a fiber bundle array; passing the multiplexed output from the fiber bundle array through a collimating lens and into one portion of a non-linear medium; passing the output from a pump collection fiber through a focusing lens and into another portion of the non-linear medium so that the output from the pump collection fiber mixes with the multiplexed output from the fiber bundle; adjusting one or more degrees of freedom of one or more of the fiber bundle array, the collimating lens, the focusing lens, the non-linear medium, or the pump collection fiber to produce a standing wave in the non-linear medium.

Solution Adsorption Formation of a π-Conjugated Polymer/Graphene Composite for High-Performance Field-Effect Transistors.

PubMed

Liu, Yun; Hao, Wei; Yao, Huiying; Li, Shuzhou; Wu, Yuchen; Zhu, Jia; Jiang, Lei

2018-01-01

Semiconducting polymers with π-conjugated electronic structures have potential application in the large-scale printable fabrication of high-performance electronic and optoelectronic devices. However, owing to their poor environmental stability and high-cost synthesis, polymer semiconductors possess limited device implementation. Here, an approach for constructing a π-conjugated polymer/graphene composite material to circumvent these limitations is provided, and then this material is patterned into 1D arrays. Driven by the π-π interaction, several-layer polymers can be adsorbed onto the graphene planes. The low consumption of the high-cost semiconductor polymers and the mass production of graphene contribute to the low-cost fabrication of the π-conjugated polymer/graphene composite materials. Based on the π-conjugated system, a reduced π-π stacking distance between graphene and the polymer can be achieved, yielding enhanced charge-transport properties. Owing to the incorporation of graphene, the composite material shows improved thermal stability. More generally, it is believed that the construction of the π-conjugated composite shows clear possibility of integrating organic molecules and 2D materials into microstructure arrays for property-by-design fabrication of functional devices with large area, low cost, and high efficiency. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer

PubMed Central

Madsen, Jonas Stenløkke; Riber, Leise; Kot, Witold; Basfeld, Alrun; Burmølle, Mette; Hansen, Lars Hestbjerg; Sørensen, Søren Johannes

2016-01-01

Horizontal gene transfer (HGT), the transmission of genetic material to a recipient that is not the progeny of the donor, is fundamental in bacterial evolution. HGT is often mediated by mobile genetic elements such as conjugative plasmids, which may be in conflict with the chromosomal elements of the genome because they are independent replicons that may petition their own evolutionary strategy. Here we study differences between type 3 fimbriae encoded on wild type plasmids and in chromosomes. Using known and newly characterized plasmids we show that the expression of type 3 fimbriae encoded on plasmids is systematically different, as MrkH, a c-di-GMP dependent transcriptional activator is not needed for strong expression of the fimbriae. MrkH is required for expression of type 3 fimbriae of the Klebsiella pneumoniae chromosome, wherefrom the fimbriae operon (mrkABCDF) of plasmids is believed to have originated. We find that mrkABCDFs of plasmids are highly expressed via a unique promoter that differs from the original Klebsiella promoter resulting in fundamental behavioral consequences. Plasmid associated mrkABCDFs did not influence the swimming behavior of the host, that hereby acquired an exceptional phenotype being able to both actively swim (planktonic behavior) and express biofilm associated fimbriae (sessile behavior). We show that this exceptional phenotype enhances the conjugal transfer of the plasmid. PMID:27627107

Inversion of Robin coefficient by a spectral stochastic finite element approach

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

Jin Bangti; Zou Jun

2008-03-01

This paper investigates a variational approach to the nonlinear stochastic inverse problem of probabilistically calibrating the Robin coefficient from boundary measurements for the steady-state heat conduction. The problem is formulated into an optimization problem, and mathematical properties relevant to its numerical computations are investigated. The spectral stochastic finite element method using polynomial chaos is utilized for the discretization of the optimization problem, and its convergence is analyzed. The nonlinear conjugate gradient method is derived for the optimization system. Numerical results for several two-dimensional problems are presented to illustrate the accuracy and efficiency of the stochastic finite element method.

Genetic information transfer promotes cooperation in bacteria

PubMed Central

Dimitriu, Tatiana; Lotton, Chantal; Bénard-Capelle, Julien; Misevic, Dusan; Brown, Sam P.; Lindner, Ariel B.; Taddei, François

2014-01-01

Many bacterial species are social, producing costly secreted “public good” molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria. PMID:25024219

Preparation of radioactive iodinated cholylhistamine for use in the radioimmunoassay of cholic acid

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

Weinberg, P.B.; Kinkade, J.M. Jr.; Collins, D.C.

1977-11-01

A major handicap in the development of simple and accurate radioimmunoassay procedures for bile acids has been the lack of a radioactive standard of high specific activity. To provide such a compound, we first synthesized cholylhistamine using the carbodiimide reaction. The hypothesized structure was confirmed by elemental analysis, thin-layer chromatography, infrared and mass spectral analysis. The cholylhistamine was then iodinated with /sup 125/I, using the choloramine-T method. The /sup 125/I-cholylhistamine was bound by antisera raised against a cholic acid-bovine serum albumin conjugate. This procedure should prove useful in preparing radioactive conjugates for all of the bile acids.

Enhancement of high-resolution photoacoustic imaging with indocyanine green-conjugated carbon nanotubes

NASA Astrophysics Data System (ADS)

Phuc Nguyen, Van; Oh, Yunok; Ha, Kanglyeol; Oh, Junghwan; Kang, Hyun Wook

2015-07-01

The current study indicates the feasibility of photoacoustic imaging (PAI) enhanced with contrast agents. A single-element ultrasound transducer (20 MHz) was used to detect PA signals for image reconstruction. To improve PA sensitivity, single-walled carbon nanotubes (SWNTs) conjugated with indocyanine green (ICG) were injected into samples at various concentrations. PA signal amplitudes linearly increased with SWNT-ICG concentration owing to strong light absorption. Compared with SWNTs, SWNT-ICG augmented the signal intensity by approximately 2-fold (concentration: 300 nM). The enhanced optical absorption can allow the application of SWNT-ICG to enable PAI for specifically identifying tumors with high sensitivity.

Nature of non-nuclear (3, -3) π-attractor and π-bonding: Theoretical analysis on π-electron density

NASA Astrophysics Data System (ADS)

Lv, Jiao; Yang, Lihua; Sun, Zheng; Meng, Lingpeng; Li, Xiaoyan

2018-01-01

Understanding the nature of π-electron density is important to characterize the conjugate π molecular systems. In this work, the π-electron densities of some typical conjugated π molecular systems were separated from their total electron densities; the positions and natures of non-nuclear (3, -3) π-attractors and the π-bond critical points (π-BCPs) are investigated. The calculated results show that for the same element, the position of the π-attractor is constant, regardless of the chemical surroundings. The position of the π-BCP is closer to the atom with the larger electronegativity.

Use of a three-layer distributed RC network to produce two pairs of complex conjugate zeros

NASA Technical Reports Server (NTRS)

Huelsman, L. P.

1972-01-01

The properties of a three layer distributed RC network consisting of two layers of resistive material separated by a dielectric are described. When the three layer network is used as a three terminal element by connecting conducting terminal strips across the ends of one of the resistive layers and the center of the other resistive layer, the network may be used to produce pairs of complex conjugate transmission zeros. The location of these zeros are determined by the parameters of the network. Design charts for determining the zero positions are included as part of the report.

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.

PubMed

Mehdizadeh Gohari, Iman; Kropinski, Andrew M; Weese, Scott J; Parreira, Valeria R; Whitehead, Ashley E; Boerlin, Patrick; Prescott, John F

2016-01-01

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus.

Self-assembly of conjugated oligomers and polymers at the interface: structure and properties.

PubMed

Xu, Lirong; Yang, Liu; Lei, Shengbin

2012-08-07

In this review, we give a brief account on the recent scanning tunneling microscopy investigation of interfacial structures and properties of π-conjugated semiconducting oligomers and polymers, either at the solid-air (including solid-vacuum) or at the solid-liquid interface. The structural aspects of the self-assembly of both oligomers and polymers are highlighted. Conjugated oligomers can form well ordered supramolecular assemblies either at the air-solid or liquid-solid interface, thanks to the relatively high mobility and structural uniformity in comparison with polymers. The backbone structure, substitution of side chains and functional groups can affect the assembling behavior significantly, which offers the opportunity to tune the supramolecular structure of these conjugated oligomers at the interface. For conjugated polymers, the large molecular weight limits the mobility on the surface and the distribution in size also prevents the formation of long range ordered supramolecular assembly. The submolecular resolution obtained on the assembling monolayers enables a detailed investigation of the chain folding at the interface, both the structural details and the effect on electronic properties. Besides the ability in studying the assembling structures at the interfaces, STM also provides a reasonable way to evaluate the distribution of the molecular weight of conjugated polymers by statistic of the contour length of the adsorbed polymer chains. Both conjugated oligomers and polymers can form composite assemblies with other materials. The ordered assembly of oligomers can act as a template to controllably disperse other molecules such as coronene or fullerene. These investigations open a new avenue to fine tune the assembling structure at the interface and in turn the properties of the composite materials. To summarize scanning tunneling microscopy has demonstrated its surprising ability in the investigation of the assembling structures and properties of conjugated oligomers and polymers. The information obtained could benefit the understanding of the elements affecting the film morphology and helps the optimization of device performance.

Oriented conjugation of single-domain antibodies and quantum dots.

PubMed

Brazhnik, Kristina; Nabiev, Igor; Sukhanova, Alyona

2014-01-01

Nanoparticle-based biodetection routinely employs monoclonal antibodies (mAbs) for targeting. However, the large size of mAbs limits the number of ligands per nanoparticle and severely restricts the bioavailability and distribution of these probes in a sample. Furthermore, conventional conjugation techniques provide nanoprobes with irregular orientation of mAbs on the nanoparticle surface and often provoke mAb unfolding. Here, we describe a protocol for engineering a new generation of ultrasmall diagnostic nanoprobes through oriented conjugation of semiconductor quantum dots (QDs) with 13 kDa single-domain antibodies (sdAbs) derived from llama immunoglobulin G (IgG). The sdAbs are conjugated with QDs in a highly oriented manner via an additional cysteine residue specifically integrated into the sdAb C-terminus. The resultant nanoprobes are <12 nm in diameter, ten times smaller in volume compared to the known alternatives. They have been proved highly efficient in flow cytometry and immunuhistochemical diagnostics. This approach can be easily extended to other semiconductor and plasmonic nanoparticles.

[Oxidative stress in women with insomnia in different stages of menopause].

PubMed

Kolesnikova, L I; Semenova, N V; Solodova, E I; Madaeva, I M

To investigate of a lipid peroxidation (LPO) process and the antioxidant defense system (ADS) in peri- and postmenopausal women with insomnia. 47 perimenopausal women and 71 postmenopausal ones were examined. Each group was divided into 2 subgroups: 1) individuals with insomnia and 2) controls. LPO-ADS spectrophotometric studies were used in the investigation. There was an increase in the serum levels of ketodienes and conjugated trienes and a decrease in those of α-tocopherol and retinol in postmenopause versus in perimenopause. In insomnia, there was a rise in the level of ketodienes and conjugated trienes in perimenopause; LPO substrates with conjugated double bonds, diene conjugates, and thiobarbituric acid-active products in postmenopause. The indicators of ADS do not differ from those in the controls. The integral indicator of oxidative stress assessment suggests that there is a LPO-ADS imbalance in the menopausal women with insomnia, which is most pronounced in postmenopause. The findings suggest that the patients with insomnia develop oxidative stress that is more marked in postmenopause.

When SUMO met splicing.

PubMed

Pozzi, Berta; Mammi, Pablo; Bragado, Laureano; Giono, Luciana E; Srebrow, Anabella

2018-05-09

Spliceosomal proteins have been revealed as SUMO conjugation targets. Moreover, we have reported that many of these are in a SUMO-conjugated form when bound to a pre-mRNA substrate during a splicing reaction. We demonstrated that SUMOylation of Prp3 (PRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6•U5 tri-snRNP formation and/or recruitment to active spliceosomes. Expanding upon our previous results, we have shown that the splicing factor SRSF1 stimulates SUMO conjugation to several spliceosomal proteins. Given the relevance of the splicing process, as well as the complex and dynamic nature of its governing machinery, the spliceosome, the molecular mechanisms that modulate its function represent an attractive topic of research. We posit that SUMO conjugation could represent a way of modulating spliceosome assembly and thus, splicing efficiency. How cycles of SUMOylation/de-SUMOylation of spliceosomal proteins become integrated throughout the highly choreographed spliceosomal cycle awaits further investigation.

E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis

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

Pruneda, Jonathan N.; Smith, F. Donelson; Daurie, Angela

Pathogenic bacteria introduce effector proteins directly into the cytosol of eukaryotic cells to promote invasion and colonization. OspG, a Shigella spp. effector kinase, plays a role in this process by helping to suppress the host inflammatory response. OspG has been reported to bind host E2 ubiquitin-conjugating enzymes activated with ubiquitin (E2~Ub), a key enzyme complex in ubiquitin transfer pathways. A cocrystal structure of the OspG/UbcH5c~Ub complex reveals that complex formation has important ramifications for the activity of both OspG and the UbcH5c~Ub conjugate. OspG is a minimal kinase domain containing only essential elements required for catalysis. UbcH5c~Ub binding stabilizes anmore » active conformation of the kinase, greatly enhancing OspG kinase activity. In contrast, interaction with OspG stabilizes an extended, less reactive form of UbcH5c~Ub. Recognizing conserved E2 features, OspG can interact with at least ten distinct human E2s~Ub. Mouse oral infection studies indicate that E2~Ub conjugates act as novel regulators of OspG effector kinase function in eukaryotic host cells.« less

Multivalent interaction based carbohydrate biosensors for signal amplification

PubMed Central

Wang, Yanyan; Chalagalla, Srinivas; Li, Tiehai; Sun, Xue-long; Zhao, Wei; Wang, Peng; Zeng, Xiangqun

2010-01-01

Multivalent interaction between boronic acids immobilized on Quartz Crystal Microbalance (QCM) sensor surface and the carbohydrates modified Au - nanoparticle (AuNP) has been demonstrated for the development of a sensitive carbohydrate biosensor. Briefly, a boronic acid - containing polymer (boropolymer) as multivalent carbohydrate receptor was oriented immobilized on the cysteamine coated electrode through isourea bond formation. Carbohydrates were conjugated to AuNPs to generate a multivalent carbohydrates moiety to amplify the response signal. Thus, the binding of the carbohydrate conjugated AuNPs to the boropolymer surface are multivalent which could simultaneously increase the binding affinity and specificity. We systematically studied the binding between five carbohydrate conjugated AuNPs and the boropolymer. Our studies show that the associate constant (Ka) was in the order of fucose < glucose < mannose < galactose < maltose. A linear response in the range from 23 µM to 3.83 mM was observed for mannose conjugated AuNPs and the boropolymer recognition elements, with the lower detection limit of 1.5 µM for the carbohydrate analytes. Furthermore, the multivalent binding between carbohydrates and boronic acids are reversible and allow the regeneration of boropolymer surface by using 1M acetic acid so as to sequentially capture and release the carbohydrate analytes. PMID:20863680

Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability.

PubMed

Birch, Ditlev; Christensen, Malene Vinther; Staerk, Dan; Franzyk, Henrik; Nielsen, Hanne Mørck

2017-12-01

Cell-penetrating peptides constitute efficient delivery vectors, and studies of their uptake and mechanism of translocation typically involve fluorophore-labeled conjugates. In the present study, the influence of a number of specific fluorophores on the physico-chemical properties and uptake-related characteristics of penetratin were studied. An array of seven fluorophores belonging to distinct structural classes was examined, and the impact of fluorophore labeling on intracellular distribution and cytotoxicity was correlated to the physico-chemical properties of the conjugates. Exposure of several mammalian cell types to fluorophore-penetratin conjugates revealed a strong structure-dependent reduction in viability (1.5- to 20-fold lower IC 50 values as compared to those of non-labeled penetratin). Also, the degree of less severe effects on membrane integrity, as well as intracellular distribution patterns differed among the conjugates. Overall, neutral hydrophobic fluorophores or negatively charged fluorophores conferred less cytotoxicity as compared to the effect exerted by positively charged, hydrophobic fluorophores. The latter conjugates, however, exhibited less membrane association and more clearly defined intracellular distribution patterns. Thus, selection of the appropriate flurophore is critical. Copyright © 2017 Elsevier B.V. All rights reserved.

Hybrid mesh finite volume CFD code for studying heat transfer in a forward-facing step

NASA Astrophysics Data System (ADS)

Jayakumar, J. S.; Kumar, Inder; Eswaran, V.

2010-12-01

Computational fluid dynamics (CFD) methods employ two types of grid: structured and unstructured. Developing the solver and data structures for a finite-volume solver is easier than for unstructured grids. But real-life problems are too complicated to be fitted flexibly by structured grids. Therefore, unstructured grids are widely used for solving real-life problems. However, using only one type of unstructured element consumes a lot of computational time because the number of elements cannot be controlled. Hence, a hybrid grid that contains mixed elements, such as the use of hexahedral elements along with tetrahedral and pyramidal elements, gives the user control over the number of elements in the domain, and thus only the domain that requires a finer grid is meshed finer and not the entire domain. This work aims to develop such a finite-volume hybrid grid solver capable of handling turbulence flows and conjugate heat transfer. It has been extended to solving flow involving separation and subsequent reattachment occurring due to sudden expansion or contraction. A significant effect of mixing high- and low-enthalpy fluid occurs in the reattached regions of these devices. This makes the study of the backward-facing and forward-facing step with heat transfer an important field of research. The problem of the forward-facing step with conjugate heat transfer was taken up and solved for turbulence flow using a two-equation model of k-ω. The variation in the flow profile and heat transfer behavior has been studied with the variation in Re and solid to fluid thermal conductivity ratios. The results for the variation in local Nusselt number, interface temperature and skin friction factor are presented.

Fully-Implicit Navier-Stokes (FIN-S)

NASA Technical Reports Server (NTRS)

Kirk, Benjamin S.

2010-01-01

FIN-S is a SUPG finite element code for flow problems under active development at NASA Lyndon B. Johnson Space Center and within PECOS: a) The code is built on top of the libMesh parallel, adaptive finite element library. b) The initial implementation of the code targeted supersonic/hypersonic laminar calorically perfect gas flows & conjugate heat transfer. c) Initial extension to thermochemical nonequilibrium about 9 months ago. d) The technologies in FIN-S have been enhanced through a strongly collaborative research effort with Sandia National Labs.

Formation of the Thiol Conjugates and Active Metabolite of Clopidogrel by Human Liver Microsomes

PubMed Central

Lau, Wei C.; Hollenberg, Paul F.

2012-01-01

We reported previously the formation of a glutathionyl conjugate of the active metabolite (AM) of clopidogrel and the covalent modification of a cysteinyl residue of human cytochrome P450 2B6 in a reconstituted system (Mol Pharmacol 80:839–847, 2011). In this work, we extended our studies of the metabolism of clopidogrel to human liver microsomes in the presence of four reductants, namely, GSH, l-Cys, N-acetyl-l-cysteine (NAC), and ascorbic acid. Our results demonstrated that formation of the AM was greatly affected by the reductant used and the relative amounts of the AM formed were increased in the following order: NAC (17%) < l-Cys (53%) < ascorbic acid (61%) < GSH (100%). AM-thiol conjugates were observed in the presence of NAC, l-Cys, and GSH. In the case of GSH, the formation of both the AM and the glutathionyl conjugate was dependent on the GSH concentrations, with similar Km values of ∼0.5 mM, which indicates that formation of the thiol conjugates constitutes an integral part of the bioactivation processes for clopidogrel. It was observed that the AM was slowly converted to the thiol conjugate, with a half-life of ∼10 h. Addition of dithiothreitol to the reaction mixture reversed the conversion, which resulted in a decrease in AM-thiol conjugate levels and a concomitant increase in AM levels, whereas addition of NAC led to the formation of AM-NAC and a concomitant decrease in AM-GSH levels. These results not only confirm that the AM is formed through oxidative opening of the thiolactone ring but also suggest the existence of an equilibrium between the AM, the thiol conjugates, and the reductants. These factors may affect the effective concentrations of the AM in vivo. PMID:22584220

Season-induced changes in bovine sperm motility following a freeze-thaw procedure.

PubMed

Orgal, Shlomo; Zeron, Yoel; Elior, Nili; Biran, David; Friedman, Eran; Druker, Shaked; Roth, Zvi

2012-01-01

Decreased conception rate of dairy cows in the summer is mainly associated with the deleterious effects of environmental thermal stress on the female reproductive tract. Here, we suggest that decreased reproductive performance might be partially due to inferior-quality semen. Semen from five representative bulls was collected in summer (August to September) and winter (December to January) and evaluated with a computerized sperm-quality analyzer for bulls (SQA-Vb). No seasonal effect was found in fresh ejaculate, but sperm examined post-thawing showed lower velocity, motility and progressive motility (P<0.04) in summer vs. winter samples. Element concentrations in the seminal plasma, determined by inductively coupled plasma-atomic emission spectrometry, differed between seasons, with higher (P<0.01) concentration values of K, Mg, Na and S elements in winter vs. summer samples. Therefore, season-induced alterations in seminal plasma element concentration should be taken into account when using an extender for cryopreservation. Acrosome integrity was assessed by a triple-fluorescence test using Hoechst 33342, fluorescein isothiocyanate-conjugated Pisum sativum agglutinin (FITC-PSA) and propidium iodide. Acrosome reaction was examined by a one-step staining method using FITC-PSA. The proportion of sperm cells with a damaged acrosome post-thawing tended to be higher (P<0.07) in semen collected during the summer vs. winter. Such alterations suggest that seasonal reductions in sperm function might also be involved in the decreased conception rate of dairy cows in summer.

Plasmid-Mediated Antimicrobial Resistance in Staphylococci and Other Firmicutes.

PubMed

Schwarz, Stefan; Shen, Jianzhong; Wendlandt, Sarah; Fessler, Andrea T; Wang, Yang; Kadlec, Kristina; Wu, Cong-Ming

2014-12-01

In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.

A globally distributed mobile genetic element inhibits natural transformation of Vibrio cholerae

PubMed Central

Dalia, Ankur B.; Seed, Kimberley D.; Calderwood, Stephen B.; Camilli, Andrew

2015-01-01

Natural transformation is one mechanism of horizontal gene transfer (HGT) in Vibrio cholerae, the causative agent of cholera. Recently, it was found that V. cholerae isolates from the Haiti outbreak were poorly transformed by this mechanism. Here, we show that an integrating conjugative element (ICE)-encoded DNase, which we name IdeA, is necessary and sufficient for inhibiting natural transformation of Haiti outbreak strains. We demonstrate that IdeA inhibits this mechanism of HGT in cis via DNA endonuclease activity that is localized to the periplasm. Furthermore, we show that natural transformation between cholera strains in a relevant environmental context is inhibited by IdeA. The ICE encoding IdeA is globally distributed. Therefore, we analyzed the prevalence and role for this ICE in limiting natural transformation of isolates from Bangladesh collected between 2001 and 2011. We found that IdeA+ ICEs were nearly ubiquitous in isolates from 2001 to 2005; however, their prevalence decreased to ∼40% from 2006 to 2011. Thus, IdeA+ ICEs may have limited the role of natural transformation in V. cholerae. However, the rise in prevalence of strains lacking IdeA may now increase the role of this conserved mechanism of HGT in the evolution of this pathogen. PMID:26240317

All conjugate-maximal-helicity-violating amplitudes from topological open string theory in twistor space.

PubMed

Roiban, Radu; Volovich, Anastasia

2004-09-24

It has recently been proposed that the D-instanton expansion of the open topological B model on P(3|4) is equivalent to the perturbative expansion of the maximally supersymmetric Yang-Mills theory in four dimensions. In this letter we show how to construct the gauge theory results for all n-point conjugate-maximal-helicity-violating amplitudes by computing the integral over the moduli space of curves of degree n-3 in P(3|4), providing strong support to the string theory construction.

Conjugate Heat Transfer Analyses on the Manifold for Ramjet Fuel Injectors

NASA Technical Reports Server (NTRS)

Wang, Xiao-Yen J.

2006-01-01

Three-dimensional conjugate heat transfer analyses on the manifold located upstream of the ramjet fuel injector are performed using CFdesign, a finite-element computational fluid dynamics (CFD) software. The flow field of the hot fuel (JP-7) flowing through the manifold is simulated and the wall temperature of the manifold is computed. The three-dimensional numerical results of the fuel temperature are compared with those obtained using a one-dimensional analysis based on empirical equations, and they showed a good agreement. The numerical results revealed that it takes around 30 to 40 sec to reach the equilibrium where the fuel temperature has dropped about 3 F from the inlet to the exit of the manifold.

Double diffusive conjugate heat transfer: Part II

NASA Astrophysics Data System (ADS)

Azeem, Soudagar, Manzoor Elahi M.

2018-05-01

Conjugate heat transfer in porous medium is an important study involved in many practical applications. The current study is aimed to investigate the double diffusive flow in a square porous cavity subjected to left vertical surface heating and right vertical surface cooling respectively along with left and right surfaces maintained at high and low concentration. The three governing equations are converted into algebraic form of equations by applying finite element method and solved in iterative manner. The study is focused to investigate the effect of presence of solid inside the cavity with respect to varying buoyancy ratio. It is found that the local heat and mass transfer rate decreases along the height of cavity.

New Convex and Spherical Structures of Bare Boron Clusters

NASA Astrophysics Data System (ADS)

Boustani, Ihsan

1997-10-01

New stable structures of bare boron clusters can easily be obtained and constructed with the help of an "Aufbau Principle" suggested by a systematicab initioHF-SCF and direct CI study. It is concluded that boron cluster formation can be established by elemental units of pentagonal and hexagonal pyramids. New convex and small spherical clusters different from the classical known forms of boron crystal structures are obtained by a combination of both basic units. Convex structures simulate boron surfaces which can be considered as segments of open or closed spheres. Both convex clusters B16and B46have energies close to those of their conjugate quasi-planar clusters, which are relatively stable and can be considered to act as a calibration mark. The closed spherical clusters B12, B22, B32, and B42are less stable than the corresponding conjugated quasi-planar structures. As a consequence, highly stable spherical boron clusters can systematically be predicted when their conjugate quasi-planar clusters are determined and energies are compared.

Phased laser array for generating a powerful laser beam

DOEpatents

Holzrichter, John F.; Ruggiero, Anthony J.

2004-02-17

A first injection laser signal and a first part of a reference laser beam are injected into a first laser element. At least one additional injection laser signal and at least one additional part of a reference laser beam are injected into at least one additional laser element. The first part of a reference laser beam and the at least one additional part of a reference laser beam are amplified and phase conjugated producing a first amplified output laser beam emanating from the first laser element and an additional amplified output laser beam emanating from the at least one additional laser element. The first amplified output laser beam and the additional amplified output laser beam are combined into a powerful laser beam.

All-integrated and highly sensitive paper based device with sample treatment platform for Cd2+ immunodetection in drinking/tap waters.

PubMed

López Marzo, Adaris M; Pons, Josefina; Blake, Diane A; Merkoçi, Arben

2013-04-02

Nowadays, the development of systems, devices, or methods that integrate several process steps into one multifunctional step for clinical, environmental, or industrial purposes constitutes a challenge for many ongoing research projects. Here, we present a new integrated paper based cadmium (Cd(2+)) immunosensing system in lateral flow format, which integrates the sample treatment process with the analyte detection process. The principle of Cd(2+) detection is based on competitive reaction between the cadmium-ethylenediaminetetraacetic acid-bovine serum albumin-gold nanoparticles (Cd-EDTA-BSA-AuNP) conjugate deposited on the conjugation pad strip and the Cd-EDTA complex formed in the analysis sample for the same binding sites of the 2A81G5 monoclonal antibody (mAb), specific to Cd-EDTA but not Cd(2+) free, which is immobilized onto the test line. This platform operates without any sample pretreatment step for Cd(2+) detection thanks to an extra conjugation pad that ensures Cd(2+) complexation with EDTA and interference masking through ovalbumin (OVA). The detection and quantification limits found for the device were 0.1 and 0.4 ppb, respectively, these being the lowest limits reported up to now for metal sensors based on paper. The accuracy of the device was evaluated by addition of known quantities of Cd(2+) to different drinking water samples and subsequent Cd(2+) content analysis. Sample recoveries ranged from 95 to 105% and the coefficient of variation for the intermediate precision assay was less than 10%. In addition, the results obtained here were compared with those obtained with the well-established inductively coupled plasma emission spectroscopy (ICPES) and the analysis of certificate standard samples.

Therapeutic Targeting of the Mitochondria Initiates Excessive Superoxide Production and Mitochondrial Depolarization Causing Decreased mtDNA Integrity

PubMed Central

Pokrzywinski, Kaytee L.; Biel, Thomas G.; Kryndushkin, Dmitry; Rao, V. Ashutosh

2016-01-01

Mitochondrial dysregulation is closely associated with excessive reactive oxygen species (ROS) production. Altered redox homeostasis has been implicated in the onset of several diseases including cancer. Mitochondrial DNA (mtDNA) and proteins are particularly sensitive to ROS as they are in close proximity to the respiratory chain (RC). Mitoquinone (MitoQ), a mitochondria-targeted redox agent, selectively damages breast cancer cells possibly through damage induced via enhanced ROS production. However, the effects of MitoQ and other triphenylphosphonium (TPP+) conjugated agents on cancer mitochondrial homeostasis remain unknown. The primary objective of this study was to determine the impact of mitochondria-targeted agent [(MTAs) conjugated to TPP+: mitoTEMPOL, mitoquinone and mitochromanol-acetate] on mitochondrial physiology and mtDNA integrity in breast (MDA-MB-231) and lung (H23) cancer cells. The integrity of the mtDNA was assessed by quantifying the degree of mtDNA fragmentation and copy number, as well as by measuring mitochondrial proteins essential to mtDNA stability and maintenance (TFAM, SSBP1, TWINKLE, POLG and POLRMT). Mitochondrial status was evaluated by measuring superoxide production, mitochondrial membrane depolarization, oxygen consumption, extracellular acidification and mRNA or protein levels of the RC complexes along with TCA cycle activity. In this study, we demonstrated that all investigated MTAs impair mitochondrial health and decrease mtDNA integrity in MDA-MB-231 and H23 cells. However, differences in the degree of mitochondrial damage and mtDNA degradation suggest unique properties among each MTA that may be cell line, dose and time dependent. Collectively, our study indicates the potential for TPP+ conjugated molecules to impair breast and lung cancer cells by targeting mitochondrial homeostasis. PMID:28030582

Therapeutic Targeting of the Mitochondria Initiates Excessive Superoxide Production and Mitochondrial Depolarization Causing Decreased mtDNA Integrity.

PubMed

Pokrzywinski, Kaytee L; Biel, Thomas G; Kryndushkin, Dmitry; Rao, V Ashutosh

2016-01-01

Mitochondrial dysregulation is closely associated with excessive reactive oxygen species (ROS) production. Altered redox homeostasis has been implicated in the onset of several diseases including cancer. Mitochondrial DNA (mtDNA) and proteins are particularly sensitive to ROS as they are in close proximity to the respiratory chain (RC). Mitoquinone (MitoQ), a mitochondria-targeted redox agent, selectively damages breast cancer cells possibly through damage induced via enhanced ROS production. However, the effects of MitoQ and other triphenylphosphonium (TPP+) conjugated agents on cancer mitochondrial homeostasis remain unknown. The primary objective of this study was to determine the impact of mitochondria-targeted agent [(MTAs) conjugated to TPP+: mitoTEMPOL, mitoquinone and mitochromanol-acetate] on mitochondrial physiology and mtDNA integrity in breast (MDA-MB-231) and lung (H23) cancer cells. The integrity of the mtDNA was assessed by quantifying the degree of mtDNA fragmentation and copy number, as well as by measuring mitochondrial proteins essential to mtDNA stability and maintenance (TFAM, SSBP1, TWINKLE, POLG and POLRMT). Mitochondrial status was evaluated by measuring superoxide production, mitochondrial membrane depolarization, oxygen consumption, extracellular acidification and mRNA or protein levels of the RC complexes along with TCA cycle activity. In this study, we demonstrated that all investigated MTAs impair mitochondrial health and decrease mtDNA integrity in MDA-MB-231 and H23 cells. However, differences in the degree of mitochondrial damage and mtDNA degradation suggest unique properties among each MTA that may be cell line, dose and time dependent. Collectively, our study indicates the potential for TPP+ conjugated molecules to impair breast and lung cancer cells by targeting mitochondrial homeostasis.

Current developments in optical engineering and diffraction phenomena; Proceedings of the Meeting, San Diego, CA, Aug. 21, 22, 1986

NASA Astrophysics Data System (ADS)

Fischer, Robert E.; Smith, Warren J.; Harvey, James

1986-01-01

Papers dealing with current materials for gradient-index optics, an intelligent data-base system for optical designers; tilted mirror systems; a null-lens design approach for centrally obscured components; the use of the vector aberration theory to optimize an unobscured optical system; multizone bifocal contact lens design; and the concentric meniscus element are presented. Topics discussed include optical manufacturing in the Far East; the optical performance of molded-glass lenses for optical memory applications; through-wafer optical interconnects for multiwafer wafer-scale integrated architecture; optical thin-flim monitoring using optical fibers; aerooptical testing; optical inspection; and a system analysis program for a 32K microcomputer. Consideration is given to various theories, algorithms, and applications of diffraction, a vector formulation of a ray-equivalent method for Gaussian beam propagation; Fourier optical analysis of aberrations in focused laser beams; holography and moire interferometry; and phase-conjugate optical correctors for diffraction-limited applications.

Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae†

PubMed Central

Vasconcelos, Ana Tereza R.; Ferreira, Henrique B.; Bizarro, Cristiano V.; Bonatto, Sandro L.; Carvalho, Marcos O.; Pinto, Paulo M.; Almeida, Darcy F.; Almeida, Luiz G. P.; Almeida, Rosana; Alves-Filho, Leonardo; Assunção, Enedina N.; Azevedo, Vasco A. C.; Bogo, Maurício R.; Brigido, Marcelo M.; Brocchi, Marcelo; Burity, Helio A.; Camargo, Anamaria A.; Camargo, Sandro S.; Carepo, Marta S.; Carraro, Dirce M.; de Mattos Cascardo, Júlio C.; Castro, Luiza A.; Cavalcanti, Gisele; Chemale, Gustavo; Collevatti, Rosane G.; Cunha, Cristina W.; Dallagiovanna, Bruno; Dambrós, Bibiana P.; Dellagostin, Odir A.; Falcão, Clarissa; Fantinatti-Garboggini, Fabiana; Felipe, Maria S. S.; Fiorentin, Laurimar; Franco, Gloria R.; Freitas, Nara S. A.; Frías, Diego; Grangeiro, Thalles B.; Grisard, Edmundo C.; Guimarães, Claudia T.; Hungria, Mariangela; Jardim, Sílvia N.; Krieger, Marco A.; Laurino, Jomar P.; Lima, Lucymara F. A.; Lopes, Maryellen I.; Loreto, Élgion L. S.; Madeira, Humberto M. F.; Manfio, Gilson P.; Maranhão, Andrea Q.; Martinkovics, Christyanne T.; Medeiros, Sílvia R. B.; Moreira, Miguel A. M.; Neiva, Márcia; Ramalho-Neto, Cicero E.; Nicolás, Marisa F.; Oliveira, Sergio C.; Paixão, Roger F. C.; Pedrosa, Fábio O.; Pena, Sérgio D. J.; Pereira, Maristela; Pereira-Ferrari, Lilian; Piffer, Itamar; Pinto, Luciano S.; Potrich, Deise P.; Salim, Anna C. M.; Santos, Fabrício R.; Schmitt, Renata; Schneider, Maria P. C.; Schrank, Augusto; Schrank, Irene S.; Schuck, Adriana F.; Seuanez, Hector N.; Silva, Denise W.; Silva, Rosane; Silva, Sérgio C.; Soares, Célia M. A.; Souza, Kelly R. L.; Souza, Rangel C.; Staats, Charley C.; Steffens, Maria B. R.; Teixeira, Santuza M. R.; Urmenyi, Turan P.; Vainstein, Marilene H.; Zuccherato, Luciana W.; Simpson, Andrew J. G.; Zaha, Arnaldo

2005-01-01

This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae. PMID:16077101

Stereo multiplexed holographic particle image velocimeter

DOEpatents

Adrian, Ronald J.; Barnhart, Donald H.; Papen, George A.

1996-01-01

A holographic particle image velocimeter employs stereoscopic recording of particle images, taken from two different perspectives and at two distinct points in time for each perspective, on a single holographic film plate. The different perspectives are provided by two optical assemblies, each including a collecting lens, a prism and a focusing lens. Collimated laser energy is pulsed through a fluid stream, with elements carried in the stream scattering light, some of which is collected by each collecting lens. The respective focusing lenses are configured to form images of the scattered light near the holographic plate. The particle images stored on the plate are reconstructed using the same optical assemblies employed in recording, by transferring the film plate and optical assemblies as a single integral unit to a reconstruction site. At the reconstruction site, reconstruction beams, phase conjugates of the reference beams used in recording the image, are directed to the plate, then selectively through either one of the optical assemblies, to form an image reflecting the chosen perspective at the two points in time.

Stereo multiplexed holographic particle image velocimeter

DOEpatents

Adrian, R.J.; Barnhart, D.H.; Papen, G.A.

1996-08-20

A holographic particle image velocimeter employs stereoscopic recording of particle images, taken from two different perspectives and at two distinct points in time for each perspective, on a single holographic film plate. The different perspectives are provided by two optical assemblies, each including a collecting lens, a prism and a focusing lens. Collimated laser energy is pulsed through a fluid stream, with elements carried in the stream scattering light, some of which is collected by each collecting lens. The respective focusing lenses are configured to form images of the scattered light near the holographic plate. The particle images stored on the plate are reconstructed using the same optical assemblies employed in recording, by transferring the film plate and optical assemblies as a single integral unit to a reconstruction site. At the reconstruction site, reconstruction beams, phase conjugates of the reference beams used in recording the image, are directed to the plate, then selectively through either one of the optical assemblies, to form an image reflecting the chosen perspective at the two points in time. 13 figs.

pA506, a Conjugative Plasmid of the Plant Epiphyte Pseudomonas fluorescens A506

PubMed Central

Stockwell, Virginia O.; Davis, Edward W.; Carey, Alyssa; Shaffer, Brenda T.; Mavrodi, Dmitri V.; Hassan, Karl A.; Hockett, Kevin; Thomashow, Linda S.; Paulsen, Ian T.

2013-01-01

Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease of pear and apple. Twenty-nine of the 67 open reading frames (ORFs) of pA506 have putative functions in conjugation, including a type IV secretion system related to that of MOBP6 family plasmids and a gene cluster for type IV pili. We demonstrate that pA506 is self-transmissible via conjugation between A506 and strains of Pseudomonas spp. or the Enterobacteriaceae. The origin of vegetative replication (oriV) of pA506 is typical of those in pPT23A family plasmids, which are present in many pathovars of Pseudomonas syringae, but pA506 lacks repA, a defining locus for pPT23A plasmids, and has a novel partitioning region. We selected a plasmid-cured derivative of A506 and compared it to the wild type to identify plasmid-encoded phenotypes. pA506 conferred UV resistance, presumably due to the plasmid-borne rulAB genes, but did not influence epiphytic fitness of A506 on pear or apple blossoms in the field. pA506 does not appear to confer resistance to antibiotics or other toxic elements. Based on the conjugative nature of pA506 and the large number of its genes that are shared with plasmids from diverse groups of environmental bacteria, the plasmid is likely to serve as a vehicle for genetic exchange between A506 and its coinhabitants on plant surfaces. PMID:23811504

In-situ fabrication of diketopyrrolopyrrole-carbazole-based conjugated polymer/TiO2 heterojunction for enhanced visible light photocatalysis

NASA Astrophysics Data System (ADS)

Yang, Long; Yu, Yuyan; Zhang, Jianling; Chen, Fu; Meng, Xiao; Qiu, Yong; Dan, Yi; Jiang, Long

2018-03-01

Aiming at developing highly efficient photocatalysts by broadening the light-harvesting region and suppressing photo-generated electron-hole recombination simultaneously, this work reports rational design and fabrication of donor-acceptor (D-A) conjugated polymer/TiO2 heterojunction catalyst with strong interfacial interactions by a facile in-situ thermal treatment. To expand the light-harvesting window, soluable conjugated copolymers with D-A architecture are prepared by Pd-mediated polycondensation of diketopyrrolopyrrole (DPP) and t-butoxycarbonyl (t-Boc) modified carbazole (Car), and used as visible-light-harvesting antenna to couple with TiO2 nanocrystals. The DPP-Car/TiO2 composites show wide range absorption in 300-1000 nm. To improve the interfacial binding at the interface, a facile in-situ thermal treatment is carried out to cleave the pendant t-Boc groups in carbazole units and liberate the polar amino groups (-NH-) which strongly bind to the surface of TiO2 through dipole-dipole interactions, forming a heterojunction interface. This in-situ thermal treatment changes the surface elemental distribution of TiO2, reinforces the interface bonding at the boundary of conjugated polymers/TiO2 and finally improves the photocatalytic efficiency of DPP-Car/TiO2 under visible-light irradiation. The interface changes are characterized and verified through Fourier-transform infrared spectroscopy (FT-IR), photo images, UV/Vis (solution state and powder diffuse reflection spectroscopy), X-ray powder diffraction (XRD), X-ray photoelectron spectroscopy (XPS), fluorescence, scanning electron microscopy(SEM) and transmission electron microscopy (TEM) techniques. This study provides a new strategy to avoid the low solubility of D-A conjugated polymers and construct highly-efficient conjugated polymer/TiO2 heterojunction by enforcing the interface contact and facilitating charge or energy transfer for the applications in photocatalysis.

Plasmid Capture by the Bacillus thuringiensis Conjugative Plasmid pXO16▿

PubMed Central

Timmery, Sophie; Modrie, Pauline; Minet, Olivier; Mahillon, Jacques

2009-01-01

Conjugation, mobilization, and retromobilization are three related mechanisms of horizontal gene transfer in bacteria. They have been extensively studied in gram-negative species, where retromobilization, the capture of DNA from a recipient by a donor cell, was shown to result from two successive steps: the transfer of the conjugative plasmid from the donor to the recipient followed by the retrotransfer of the mobilizable plasmid to the donor. This successive model was established for gram-negative bacteria but was lacking experimental data from the gram-positive counterparts. In the present work, the mobilization and retromobilization abilities of the conjugative plasmid pXO16 from Bacillus thuringiensis subsp. israelensis were studied using the mobilizable plasmids pUB110 and pE194 and the “nonmobilizable” element pC194 lacking the mob and oriT features (all from Staphylococcus aureus). Experimental data suggested a successive model, since different retromobilization frequencies were observed between the small plasmids. More importantly, retromobilization was shown to be delayed by 50 and 150 min for pUB110 and pE194, respectively, compared to pXO16 conjugation. Natural liquid foods (cow milk, soy milk, and rice milk) were used to evaluate the putative ecological impact of these transfers. In cow and soy milk, conjugation, mobilization, and retromobilization were shown to occur at frequencies of 8.0 × 10−1, 1.0 × 10−2, and 1.2 × 10−4 transconjugants per recipient, respectively. These data are comparable to those obtained with LB medium and about 10-fold lower than in the case of rice milk. Taken together, these results emphasize the potential role of plasmid capture played by B. thuringiensis in natural environments. PMID:19181805

A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle

PubMed Central

Joardar, Vinita; Williams, Kelly P.; Driscoll, Timothy; Hostetler, Jessica B.; Nordberg, Eric; Shukla, Maulik; Walenz, Brian; Hill, Catherine A.; Nene, Vishvanath M.; Azad, Abdu F.; Sobral, Bruno W.; Caler, Elisabet

2012-01-01

We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ∼35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity. PMID:22056929

Using the GeoFEST Faulted Region Simulation System

NASA Technical Reports Server (NTRS)

Parker, Jay W.; Lyzenga, Gregory A.; Donnellan, Andrea; Judd, Michele A.; Norton, Charles D.; Baker, Teresa; Tisdale, Edwin R.; Li, Peggy

2004-01-01

GeoFEST (the Geophysical Finite Element Simulation Tool) simulates stress evolution, fault slip and plastic/elastic processes in realistic materials, and so is suitable for earthquake cycle studies in regions such as Southern California. Many new capabilities and means of access for GeoFEST are now supported. New abilities include MPI-based cluster parallel computing using automatic PYRAMID/Parmetis-based mesh partitioning, automatic mesh generation for layered media with rectangular faults, and results visualization that is integrated with remote sensing data. The parallel GeoFEST application has been successfully run on over a half-dozen computers, including Intel Xeon clusters, Itanium II and Altix machines, and the Apple G5 cluster. It is not separately optimized for different machines, but relies on good domain partitioning for load-balance and low communication, and careful writing of the parallel diagonally preconditioned conjugate gradient solver to keep communication overhead low. Demonstrated thousand-step solutions for over a million finite elements on 64 processors require under three hours, and scaling tests show high efficiency when using more than (order of) 4000 elements per processor. The source code and documentation for GeoFEST is available at no cost from Open Channel Foundation. In addition GeoFEST may be used through a browser-based portal environment available to approved users. That environment includes semi-automated geometry creation and mesh generation tools, GeoFEST, and RIVA-based visualization tools that include the ability to generate a flyover animation showing deformations and topography. Work is in progress to support simulation of a region with several faults using 16 million elements, using a strain energy metric to adapt the mesh to faithfully represent the solution in a region of widely varying strain.

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

PubMed

Shmakov, Sergey A; Sitnik, Vassilii; Makarova, Kira S; Wolf, Yuri I; Severinov, Konstantin V; Koonin, Eugene V

2017-09-19

Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR- cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.

The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation.

PubMed

Miguel-Arribas, Andrés; Hao, Jian-An; Luque-Ortega, Juan R; Ramachandran, Gayetri; Val-Calvo, Jorge; Gago-Córdoba, César; González-Álvarez, Daniel; Abia, David; Alfonso, Carlos; Wu, Ling J; Meijer, Wilfried J J

2017-01-01

Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer ( oriT ), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis . We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1 LS20 and aux2 LS20 , and which we show are essential for conjugation. Both Aux1 LS20 and Aux2 LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1 LS20 and Aux2 LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriT LS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1 LS20 and/or Aux2 LS20 are located upstream of almost 400 relaxase genes of the Rel LS20 family (MOB L ) of relaxases. Thus, Aux1 LS20 and Aux2 LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.

Amphotericin B-conjugated biogenic silver nanoparticles as an innovative strategy for fungal infections.

PubMed

Ahmad, Aftab; Wei, Yun; Syed, Fatima; Tahir, Kamran; Taj, Raheela; Khan, Arif Ullah; Hameed, Muhammad Usman; Yuan, Qipeng

2016-10-01

New strategies are required to improve the efficacy of drugs and to treat the emerging microbial resistance. An effective strategy is to combine drugs with metal nanoparticles for the control of microbial infections and resistance. Keeping in view this fact, we developed a facile and eco-friendly protocol for the synthesis of amphotericin B-conjugated silver nanoparticles and their assessment as an antifungal agent. Phytochemicals from the aqueous extract of Maytenus royleanus and amphotericin B were used as capping agents to prepare two types of silver nanoparticles i.e. (i) biogenic silver nanoparticles (b-AgNPs) and (ii) amphotericin B-conjugated biogenic silver nanoparticles (Amp-bAgNPs). UV-Vis spectroscopy was used to detect the characteristic surface Plasmon resonance peaks (SPR) for the prepared nanoparticles (424-433 nm). High-resolution transmission electron microscopy (HRTEM) study revealed the formation of well dispersed and spherical silver nanoparticles and Amp-bAgNPs with an average particles size of 10 and 15 nm. EDX and FTIR studies confirmed the elemental composition and surface adhered biomolecules in the prepared nanoparticles respectively. Biogenic silver nanoparticles revealed low to moderate antifungal activity (4-8 mm ± 0.2), however, the amphotericin B conjugated silver nanoparticles exhibited significant activity against Candida albicans (16 mm ± 1.4) and Candida tropicalis (18 mm ± 1.5). In conclusion, the enhanced antifungal activity of the Amp-AgNPs conjugate system is due to the synergy between the antifungal activity of amphotericin B and the antimicrobial property of silver. The findings of this study suggest that the conjugated nanoparticles could be used as efficient antifungal agents and drug delivery vehicles. Furthermore, this is the first report describing the synthesis of silver nanoparticles using the aqueous extract of Maytenus royleanus and the conjugation of amphotericin B, an antifungal drug, to the phytosynthesized silver nanoparticles. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deformation of conjugate compliant fault zones induced by the 2013 Mw7.7 Baluchistan (Pakistan) earthquake

NASA Astrophysics Data System (ADS)

Dutta, Rishabh; Wang, Teng; Feng, Guangcai; Harrington, Jonathan; Vasyura-Bathke, Hannes; Jónsson, Sigurjón

2017-04-01

Strain localizations in compliant fault zones (with elastic moduli lower than the surrounding rocks) induced by nearby earthquakes have been detected using geodetic observations in a few cases in the past. Here we observe small-scale changes in interferometric Synthetic Aperture Radar (InSAR) measurements along multiple conjugate faults near the rupture of the 2013 Mw7.7 Baluchistan (Pakistan) earthquake. After removing the main coseismic deformation signal in the interferograms and correcting them for topography-related phase, we observe 2-3 cm signal along several conjugate faults that are 15-30 km from the mainshock fault rupture. These conjugate compliant faults have strikes of N30°E and N45°W. The sense of motion indicates left-lateral deformation across the N30°E faults and right-lateral deformation across the N45°W faults, which suggests the conjugate faults were subjected to extensional coseismic stresses along the WSW-ENE direction. The spacing between the different sets of faults is around 5 to 8 km. We explain the observed strain localizations as an elastic response of the compliant conjugate faults induced by the Baluchistan earthquake. Using 3D Finite Element models (FEM), we impose coseismic static displacements due to the earthquake along the boundaries of the FEM domain to reproduce the coseismic stress changes acting across the compliant faults. The InSAR measurements are used to constrain the geometry and rigidity variations of the compliant faults with respect to the surrounding rocks. The best fitting models show the compliant fault zones to have a width of 0.5 km to 2 km and a reduction of the shear modulus by a factor of 3 to 4. Our study yields similar values as were found for compliant fault zones near the 1992 Landers and the 1999 Hector Mine earthquakes in California, although here the strain localization is occurring on more complex conjugate sets of faults.

Sparse matrix methods based on orthogonality and conjugacy

NASA Technical Reports Server (NTRS)

Lawson, C. L.

1973-01-01

A matrix having a high percentage of zero elements is called spares. In the solution of systems of linear equations or linear least squares problems involving large sparse matrices, significant saving of computer cost can be achieved by taking advantage of the sparsity. The conjugate gradient algorithm and a set of related algorithms are described.

Targeted Mutagenesis of the Mycobacterium smegmatis mca Gene, Encoding a Mycothiol-Dependent Detoxification Protein

PubMed Central

Rawat, Mamta; Uppal, Mandeep; Newton, Gerald; Steffek, Micah; Fahey, Robert C.; Av-Gay, Yossef

2004-01-01

Mycothiol (MSH), a functional analogue of glutathione (GSH) that is found exclusively in actinomycetes, reacts with electrophiles and toxins to form MSH-toxin conjugates. Mycothiol S-conjugate amidase (Mca) then catalyzes the hydrolysis of an amide bond in the S conjugates, producing a mercapturic acid of the toxin, which is excreted from the bacterium, and glucosaminyl inositol, which is recycled back to MSH. In this study, we have generated and characterized an allelic exchange mutant of the mca gene of Mycobacterium smegmatis. The mca mutant accumulates the S conjugates of the thiol-specific alkylating agent monobromobimane and the antibiotic rifamycin S. Introduction of M. tuberculosis mca epichromosomally or introduction of M. smegmatis mca integratively resulted in complementation of Mca activity and reduced levels of S conjugates. The mutation in mca renders the mutant strain more susceptible to electrophilic toxins, such as N-ethylmalemide, iodoacetamide, and chlorodinitrobenzene, and to several oxidants, such as menadione and plumbagin. Additionally we have shown that the mca mutant is also more susceptible to the antituberculous antibiotic streptomycin. Mutants disrupted in genes belonging to MSH biosynthesis are also more susceptible to streptomycin, providing further evidence that Mca detoxifies streptomycin in the mycobacterial cell in an MSH-dependent manner. PMID:15342574

Quantification and imaging of HER2 protein using nanocrystals conjugated with single-domain antibodies

NASA Astrophysics Data System (ADS)

Glukhov, S.; Berestovoy, M.; Chames, P.; Baty, D.; Nabiev, I.; Sukhanova, A.

2017-01-01

This study dealt with quantification and imaging of human epidermal growth factor receptor 2 (HER2), an important prognostic marker for cancer diagnosis and treatment, using specific quantum-dot-based conjugates. Fluorescent inorganic nanocrystals or quantum dots (QDs) are extremely highly resistant to photobleaching and have a high emission quantum yield and a continuous range of emission spectra, from the ultraviolet to the infrared regions. Ultrasmall nanoprobes consisting of highly affine anti-HER2 single-domain antibodies (sdAbs or "nanobodies") conjugated with QDs in a strictly oriented manner have been designed. QDs with a fluorescence peak maxima at wavelengths of 562 nm, 569 nm, 570 nm or in the near-infrared region were used. Here, we present our results of ISA quantification of HER2 protein, in situ imaging of HER2 protein on the surface of HER2-positive SK-BR-3 cells in immunohistochemical experiments, and counting of stained with anti-HER2 conjugates HER2-positive SK-BR-3 cells in their mixture with unstained cells of the same culture in flow cytometry experiments. The data demonstrate that the anti-HER2 QD-sdAb conjugates obtained are highly specific and sensitive and could be used in numerous applications for advanced integrated diagnosis.

Measuring In-Plane Displacements with Variable Sensitivity Using Diffractive Optic Interferometry

NASA Technical Reports Server (NTRS)

Shepherd, Robert L.; Gilbert, John A.; Cole, Helen J.; Ashley, Paul R.

1998-01-01

This paper introduces a method called diffractive optic interferometry (DOI) which allows in-plane displacement components to be measured with variable sensitivity. DOI relies on binary optical elements fabricated as phase-type Dammann gratings which produce multiple diffraction orders of nearly equal intensity. Sensitivity is varied by combining the different wavefronts produced by a conjugate pair of these binary optical elements; a transmission element is used to produce several illumination beams while a reflective element, replicated on the surface of a specimen, provides the reference for the undeformed state. The steps taken to design and fabricate these binary optical elements are described. The specimen grating is characterized, and tested on a disk subjected to diametrical compression. Overall, the results are excellent, with experimental data agreeing to within a few percent of the theoretical predictions.

Exact posterior computation in non-conjugate Gaussian location-scale parameters models

NASA Astrophysics Data System (ADS)

Andrade, J. A. A.; Rathie, P. N.

2017-12-01

In Bayesian analysis the class of conjugate models allows to obtain exact posterior distributions, however this class quite restrictive in the sense that it involves only a few distributions. In fact, most of the practical applications involves non-conjugate models, thus approximate methods, such as the MCMC algorithms, are required. Although these methods can deal with quite complex structures, some practical problems can make their applications quite time demanding, for example, when we use heavy-tailed distributions, convergence may be difficult, also the Metropolis-Hastings algorithm can become very slow, in addition to the extra work inevitably required on choosing efficient candidate generator distributions. In this work, we draw attention to the special functions as a tools for Bayesian computation, we propose an alternative method for obtaining the posterior distribution in Gaussian non-conjugate models in an exact form. We use complex integration methods based on the H-function in order to obtain the posterior distribution and some of its posterior quantities in an explicit computable form. Two examples are provided in order to illustrate the theory.

Amine-Reactive Fluorene Probes: Synthesis, Optical Characterization, Bioconjugation, and Two-Photon Fluorescence Imaging

PubMed Central

2008-01-01

With the increasing demand for confocal and two-photon fluorescence imaging, the availability of reactive probes that possess high two-photon absorptivity, high fluorescence quantum yield, and high photostability is of paramount importance. To address the demand for better-performing probes, we prepared two-photon absorbing amine-reactive fluorenyl-based probes 2-(9,9-bis(2-(2-methoxyethoxy)ethyl)-2-isothiocyanato-9H-fluoren-7-yl)benzothiazole (1) and 2-(4-(2-(9,9-bis(2-(2-ethoxyethoxy)ethyl)-2-isothiocyanato-9H-fluoren-7-yl)vinyl)phenyl)benzothiazole (2), incorporating the isothiocyanate as a reactive linker. Probe design was augmented by integrating high optical nonlinearities, increased hydrophilicity, and coupling with reactive functional groups for specific targeting of biomolecules, assuring a better impact on two-photon fluorescence microscopy (2PFM) imaging. The isothiocyanate (NCS) derivatives were conjugated with cyclic peptide RGDfK and Reelin protein. The study of the chemical and photophysical properties of the new labeling reagents, as well as the conjugates, is described. The conjugates displayed high chemical stability and photostability. The NCS derivatives had low fluorescence quantum yields, while their bioconjugates exhibited high fluorescence quantum yields, essentially “lighting up” after conjugation. Conventional and 2PFM imaging and fluorescence lifetime imaging (FLIM) of HeLa, NT2, and H1299 cells, incubated with two-photon absorbing amine-reactive probe (1), RGDfK-dye conjugate (7), and Reelin-dye conjugate (6), was demonstrated. PMID:19090700

Covalent modification of a ten-residue cationic antimicrobial peptide with levofloxacin

NASA Astrophysics Data System (ADS)

Rodriguez, Carlos; Papanastasiou, Emilios; Juba, Melanie; Bishop, Barney

2014-09-01

The rampant spread of antibiotic resistant bacteria has spurred interest in alternative strategies for developing next-generation antibacterial therapies. As such, there has been growing interest in cationic antimicrobial peptides (CAMPs) and their therapeutic applications. Modification of CAMPs via conjugation to auxiliary compounds, including small molecule drugs, is a new approach to developing effective, broad-spectrum antibacterial agents with novel physicochemical properties and versatile antibacterial mechanisms. Here, we’ve explored design parameters for engineering CAMPs conjugated to small molecules with favorable physicochemical and antibacterial properties by covalently affixing a fluoroquinolone antibiotic, levofloxacin, to the ten-residue CAMP Pep-4. Relative to the unmodified Pep-4, the conjugate was found to demonstrate substantially increased antibacterial potency under high salt concentrations. Historically, it has been observed that most CAMPs lose antibacterial effectiveness in such high ionic strength environments, a fact that has presented a challenge to their development as therapeutics. Physicochemical studies revealed that P4LC was more hydrophobic than Pep-4, while mechanistic findings indicated that the conjugate was more effective at disrupting bacterial membrane integrity. Although the inherent antibacterial effect of the incorporated levofloxacin molecules did not appear to be substantially realized in this conjugate, these findings nevertheless suggest that covalent attachment of small molecule antibiotics with favorable physicochemical properties to CAMPs could be a promising strategy for enhancing peptide performance and overall therapeutic potential. These results have broader applicability to the development of future CAMP-antibiotic conjugates for potential therapeutic applications.

Quorum Sensing and Quorum Quenching in Agrobacterium: A "Go/No Go System"?

PubMed

Dessaux, Yves; Faure, Denis

2018-04-16

The pathogen Agrobacterium induces gall formation on a wide range of dicotyledonous plants. In this bacteria, most pathogenicity determinants are borne on the tumour inducing (Ti) plasmid. The conjugative transfer of this plasmid between agrobacteria is regulated by quorum sensing (QS). However, processes involved in the disturbance of QS also occur in this bacteria under the molecular form of a protein, TraM, inhibiting the sensing of the QS signals, and two lactonases BlcC (AttM) and AiiB that degrade the acylhomoserine lactone (AHL) QS signal. In the model Agrobacterium fabrum strain C58, several data, once integrated, strongly suggest that the QS regulation may not be reacting only to cell concentration. Rather, these QS elements in association with the quorum quenching (QQ) activities may constitute an integrated and complex “go/no go system” that finely controls the biologically costly transfer of the Ti plasmid in response to multiple environmental cues. This decision mechanism permits the bacteria to sense whether it is in a gall or not, in a living or decaying tumor, in stressed plant tissues, etc. In this scheme, the role of the lactonases selected and maintained in the course of Ti plasmid and agrobacterial evolution appears to be pivotal.

Identification of genetic and environmental factors stimulating excision from Streptomyces scabiei chromosome of the toxicogenic region responsible for pathogenicity.

PubMed

Chapleau, Mélanie; Guertin, Julien F; Farrokhi, Ali; Lerat, Sylvain; Burrus, Vincent; Beaulieu, Carole

2016-05-01

The genes conferring pathogenicity in Streptomyces turgidiscabies, a pathogen causing common scab of potato, are grouped together on a pathogenicity island (PAI), which has been found to be mobile and appears to transfer and disseminate like an integrative and conjugative element (ICE). However, in Streptomyces scabiei, another common scab-inducing species, the pathogenicity genes are clustered in two regions: the toxicogenic region (TR) and the colonization region. The S. scabiei 87.22 genome was analysed to investigate the potential mobility of the TR. Attachment sites (att), short homologous sequences that delineate ICEs, were identified at both extremities of the TR. An internal att site was also found, suggesting that the TR has a composite structure (TR1 and TR2). Thaxtomin biosynthetic genes, essential for pathogenicity, were found in TR1, whereas candidate genes with known functions in recombination, replication and conjugal transfer were found in TR2. Excision of the TR1 or TR2 subregions alone, or of the entire TR region, was observed, although the excision frequency of TR was low. However, the excision frequency was considerably increased in the presence of either mitomycin C or Streptomyces coelicolor cells. A composite TR structure was not observed in all S. scabiei and Streptomyces acidiscabies strains tested. Of the ten strains analysed, seven lacked TR2 and no TR excision event could be detected in these strains, thus suggesting the implication of TR2 in the mobilization of S. scabiei TR. © 2015 BSPP AND JOHN WILEY & SONS LTD.

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii

PubMed Central

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A.; Smits, Theo H. M.; Venter, Stephanus N.; Coutinho, Teresa A.

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart’s wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range. PMID:28959245

Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.

PubMed

De Maayer, Pieter; Aliyu, Habibu; Vikram, Surendra; Blom, Jochen; Duffy, Brion; Cowan, Don A; Smits, Theo H M; Venter, Stephanus N; Coutinho, Teresa A

2017-01-01

Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes , has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis . While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.

Investigations of conjugate MSTIDS over the Brazilian sector during daytime

NASA Astrophysics Data System (ADS)

Jonah, O. F.; Kherani, E. A.; De Paula, E. R.

2017-09-01

This study focuses on the daytime medium-scale traveling ionospheric disturbances (MSTIDs) observed at conjugate hemispheres. It is the first time that the geomagnetical conjugate daytime MSTIDs are observed over the South America sector. To observe the MSTID characteristics, we used detrended total electron content (TEC) derived from Global Navigation Satellite Systems receivers located at Brazilian sector covering the Northern and Southern Hemispheres along the same magnetic meridian. The geographic grid of 1°N to 14°S in latitude and 60°S to 50°S in longitude was selected for this study. The cross-correlation method between two latitudes and longitudes in time was used to observe the propagation of the MSTID waves. The following features are noted: (a) MSTIDs are well developed at both hemispheres; (b) the peak MSTIDs amplitudes vary from one hemisphere to another; hence, we suppose that MSTIDs generated in Southern Hemisphere or Northern Hemisphere mirrored in the conjugate hemisphere; (c) the gravity wave-induced electric fields from one hemisphere map along the field lines and generate the mirrored MSTIDs in the conjugate region. To investigate the hemispheric mapping mechanism, a rough approximation for the integrated field line conductivity ratio of E and F regions is calculated using digisonde E and F region parameters. We noted that during the period of mapping the decrease in E region conductivity results in an increase in total conductivity. This shows that the E region was partially short circuited; hence, electric field generated at F region could map to the conjugate hemisphere during daytime: daytime MSTIDs at conjugate regions; mechanisms responsible for daytime electrified MSTIDs; gravity wave-induced electric field role in daytime MSTIDs.

Asymmetric rifting, breakup and magmatism across conjugate margin pairs: insights from Newfoundland to Ireland

NASA Astrophysics Data System (ADS)

Peace, Alexander L.; Welford, J. Kim; Foulger, Gillian R.; McCaffrey, Ken J. W.

2017-04-01

Continental extension, subsequent rifting and eventual breakup result in the development of passive margins with transitional crust between extended continental crust and newly created oceanic crust. Globally, passive margins are typically classified as either magma-rich or magma-poor. Despite this simple classification, magma-poor margins like the West Orphan Basin, offshore Newfoundland, do exhibit some evidence of localized magmatism, as magmatism to some extent invariably accompanies all continental breakup. For example, on the Newfoundland margin, a small volcanic province has been interpreted near the termination of the Charlie Gibbs Fracture Zone, whereas on the conjugate Irish margin within the Rockall Basin, magmatism appears to be more widespread and has been documented both in the north and in the south. The broader region over which volcanism has been identified on the Irish margin is suggestive of magmatic asymmetry across this conjugate margin pair and this may have direct implications for the mechanisms governing the nature of rifting and breakup. Possible causes of the magmatic asymmetry include asymmetric rifting (simple shear), post-breakup thermal anomalies in the mantle, or pre-existing compositional zones in the crust that predispose one of the margins to more melting than its conjugate. A greater understanding of the mechanisms leading to conjugate margin asymmetry will enhance our fundamental understanding of rifting processes and will also reduce hydrocarbon exploration risk by better characterizing the structural and thermal evolution of hydrocarbon bearing basins on magma-poor margins where evidence of localized magmatism exists. Here, the latest results of a conjugate margin study of the Newfoundland-Ireland pair utilizing seismic interpretation integrated with other geological and geophysical datasets are presented. Our analysis has begun to reveal the nature and timing of rift-related magmatism and the degree to which magmatic asymmetry exists between these conjugate margins. The main implications from this work are that different processes may have operated during and after rifting on these conjugate margins. This concept should be carried forward when conducting conjugate margin studies elsewhere, particularly when exploring for hydrocarbons as prospectivity on one margin may not be predictive for its conjugate as different thermal and structural regimes may have been in operation during conjugate basin evolution.

Versatile molybdenum disulfide based antibacterial composites for in vitro enhanced sterilization and in vivo focal infection therapy

NASA Astrophysics Data System (ADS)

Zhang, Wentao; Shi, Shuo; Wang, Yanru; Yu, Shaoxuan; Zhu, Wenxin; Zhang, Xu; Zhang, Daohong; Yang, Baowei; Wang, Xin; Wang, Jianlong

2016-06-01

Biologically, MoS2-based nanostructures have been intensely applied for the photothermal therapy of cancer, but rarely for antibacterial uses. In this contribution, a multifunctional chitosan (CS) functionalized magnetic MoS2 (abbreviated to CFM) was constructed to nonspecifically combat bacterial infection by integrating bacterial conjugation and enrichment, and NIR-triggered photothermal sterilization. Owing to the abundant introduced amino groups, the CFM complex offers a significantly enhanced conjugation efficiency without obvious specificity towards both Gram-positive and -negative bacteria compared to amino-free magnetic MoS2. The magnetic properties of CFM obtained from iron oxide facilitate the enrichment of a CFM-bacteria conjugate, improving the photothermal efficiency of CFM as a photothermal antibacterial agent. Specifically, after being trapped together with bacteria cells, CFM shows an enhanced in vitro photothermal sterilization ability. In vivo S. aureus-induced abscess treatment studies show faster healing when CFM is used as subcutaneous nano-localized heating sources with the assistance of an external magnet to concentrate the CFM-bacteria conjugate. This work establishes an innovative solution and a novel antimicrobial agent for combating bacterial infections without the use of antibiotics, which may open a new area of application and research for MoS2-based nanostructures.Biologically, MoS2-based nanostructures have been intensely applied for the photothermal therapy of cancer, but rarely for antibacterial uses. In this contribution, a multifunctional chitosan (CS) functionalized magnetic MoS2 (abbreviated to CFM) was constructed to nonspecifically combat bacterial infection by integrating bacterial conjugation and enrichment, and NIR-triggered photothermal sterilization. Owing to the abundant introduced amino groups, the CFM complex offers a significantly enhanced conjugation efficiency without obvious specificity towards both Gram-positive and -negative bacteria compared to amino-free magnetic MoS2. The magnetic properties of CFM obtained from iron oxide facilitate the enrichment of a CFM-bacteria conjugate, improving the photothermal efficiency of CFM as a photothermal antibacterial agent. Specifically, after being trapped together with bacteria cells, CFM shows an enhanced in vitro photothermal sterilization ability. In vivo S. aureus-induced abscess treatment studies show faster healing when CFM is used as subcutaneous nano-localized heating sources with the assistance of an external magnet to concentrate the CFM-bacteria conjugate. This work establishes an innovative solution and a novel antimicrobial agent for combating bacterial infections without the use of antibiotics, which may open a new area of application and research for MoS2-based nanostructures. Electronic supplementary information (ESI) available: Experimental details, characterization and supporting figures. See DOI: 10.1039/c6nr01243d

Least-squares solution of incompressible Navier-Stokes equations with the p-version of finite elements

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan; Sonnad, Vijay

1991-01-01

A p-version of the least squares finite element method, based on the velocity-pressure-vorticity formulation, is developed for solving steady state incompressible viscous flow problems. The resulting system of symmetric and positive definite linear equations can be solved satisfactorily with the conjugate gradient method. In conjunction with the use of rapid operator application which avoids the formation of either element of global matrices, it is possible to achieve a highly compact and efficient solution scheme for the incompressible Navier-Stokes equations. Numerical results are presented for two-dimensional flow over a backward facing step. The effectiveness of simple outflow boundary conditions is also demonstrated.

Modeling update for the Thirty Meter Telescope laser guide star dual-conjugate adaptive optics system

NASA Astrophysics Data System (ADS)

Gilles, Luc; Wang, Lianqi; Ellerbroek, Brent

2010-07-01

This paper describes the modeling efforts undertaken in the past couple of years to derive wavefront error (WFE) performance estimates for the Narrow Field Infrared Adaptive Optics System (NFIRAOS), which is the facility laser guide star (LGS) dual-conjugate adaptive optics (AO) system for the Thirty Meter Telescope (TMT). The estimates describe the expected performance of NFIRAOS as a function of seeing on Mauna Kea, zenith angle, and galactic latitude (GL). They have been developed through a combination of integrated AO simulations, side analyses, allocations, lab and lidar experiments.

Double diffusive conjugate heat transfer: Part I

NASA Astrophysics Data System (ADS)

Azeem, Soudagar, Manzoor Elahi M.

2018-05-01

The present work is undertaken to investigate the effect of solid wall being placed at left of square cavity filled with porous medium. The presence of a solid wall in the porous medium turns the situation into a conjugate heat transfer problem. The boundary conditions are such that the left vertical surface is maintained at highest temperature and concentration whereas right vertical surface at lowest temperature and concentration in the medium. The top and bottom surfaces are adiabatic. The additional conduction equation along with the regular momentum and energy equations of porous medium are solved in an iterative manner with the help of finite element method. It is seen that the heat and mass transfer rate is lesser due to smaller thermal and concentration gradients.

Preconditioned conjugate residual methods for the solution of spectral equations

NASA Technical Reports Server (NTRS)

Wong, Y. S.; Zang, T. A.; Hussaini, M. Y.

1986-01-01

Conjugate residual methods for the solution of spectral equations are described. An inexact finite-difference operator is introduced as a preconditioner in the iterative procedures. Application of these techniques is limited to problems for which the symmetric part of the coefficient matrix is positive definite. Although the spectral equation is a very ill-conditioned and full matrix problem, the computational effort of the present iterative methods for solving such a system is comparable to that for the sparse matrix equations obtained from the application of either finite-difference or finite-element methods to the same problems. Numerical experiments are shown for a self-adjoint elliptic partial differential equation with Dirichlet boundary conditions, and comparison with other solution procedures for spectral equations is presented.

Sequence analysis of the lactococcal plasmid pNP40: a mobile replicon for coping with environmental hazards.

PubMed

O'Driscoll, Jonathan; Glynn, Frances; Fitzgerald, Gerald F; van Sinderen, Douwe

2006-09-01

The conjugative lactococcal plasmid pNP40, identified in Lactococcus lactis subsp. diacetylactis DRC3, possesses a potent complement of bacteriophage resistance systems, which has stimulated its application as a fitness-improving, food-grade genetic element for industrial starter cultures. The complete sequence of this plasmid allowed the mapping of previously known functions including replication, conjugation, bacteriocin resistance, heavy metal tolerance, and bacteriophage resistance. In addition, functions for cold shock adaptation and DNA damage repair were identified, further confirming pNP40's contribution to environmental stress protection. A plasmid cointegration event appears to have been part of the evolution of pNP40, resulting in a "stockpiling" of bacteriophage resistance systems.

Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains.

PubMed

Athey, Taryn B T; Teatero, Sarah; Takamatsu, Daisuke; Wasserscheid, Jessica; Dewar, Ken; Gottschalk, Marcelo; Fittipaldi, Nahuel

2016-01-01

Strains of serotype 2 Streptococcus suis are responsible for swine and human infections. Different serotype 2 genetic backgrounds have been defined using multilocus sequence typing (MLST). However, little is known about the genetic diversity within each MLST sequence type (ST). Here, we used whole-genome sequencing to test the hypothesis that S. suis serotype 2 strains of the ST25 lineage are genetically heterogeneous. We evaluated 51 serotype 2 ST25 S. suis strains isolated from diseased pigs and humans in Canada, the United States of America, and Thailand. Whole-genome sequencing revealed numerous large-scale rearrangements in the ST25 genome, compared to the genomes of ST1 and ST28 S. suis strains, which result, among other changes, in disruption of a pilus island locus. We report that recombination and lateral gene transfer contribute to ST25 genetic diversity. Phylogenetic analysis identified two main and distinct Thai and North American clades grouping most strains investigated. These clades also possessed distinct patterns of antimicrobial resistance genes, which correlated with acquisition of different integrative and conjugative elements (ICEs). Some of these ICEs were found to be integrated at a recombination hot spot, previously identified as the site of integration of the 89K pathogenicity island in serotype 2 ST7 S. suis strains. Our results highlight the limitations of MLST for phylogenetic analysis of S. suis, and the importance of lateral gene transfer and recombination as drivers of diversity in this swine pathogen and zoonotic agent.

Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains

PubMed Central

Athey, Taryn B. T.; Teatero, Sarah; Takamatsu, Daisuke; Wasserscheid, Jessica; Dewar, Ken; Gottschalk, Marcelo; Fittipaldi, Nahuel

2016-01-01

Strains of serotype 2 Streptococcus suis are responsible for swine and human infections. Different serotype 2 genetic backgrounds have been defined using multilocus sequence typing (MLST). However, little is known about the genetic diversity within each MLST sequence type (ST). Here, we used whole-genome sequencing to test the hypothesis that S. suis serotype 2 strains of the ST25 lineage are genetically heterogeneous. We evaluated 51 serotype 2 ST25 S. suis strains isolated from diseased pigs and humans in Canada, the United States of America, and Thailand. Whole-genome sequencing revealed numerous large-scale rearrangements in the ST25 genome, compared to the genomes of ST1 and ST28 S. suis strains, which result, among other changes, in disruption of a pilus island locus. We report that recombination and lateral gene transfer contribute to ST25 genetic diversity. Phylogenetic analysis identified two main and distinct Thai and North American clades grouping most strains investigated. These clades also possessed distinct patterns of antimicrobial resistance genes, which correlated with acquisition of different integrative and conjugative elements (ICEs). Some of these ICEs were found to be integrated at a recombination hot spot, previously identified as the site of integration of the 89K pathogenicity island in serotype 2 ST7 S. suis strains. Our results highlight the limitations of MLST for phylogenetic analysis of S. suis, and the importance of lateral gene transfer and recombination as drivers of diversity in this swine pathogen and zoonotic agent. PMID:26954687

Immunogenicity and thermal stability of a combined vaccine against Haemophilus influenzae type b and Neisseria meningitidis serogroup C diseases.

PubMed

Saydam, Manolya; Burkin, Karena; Care, Rory; Rigsby, Peter; Bolgiano, Barbara; Mawas, Fatme

2010-08-31

The immunogenicity, structure and stability of a combined conjugate vaccine against Haemophilus influenzae type b and meningococcal serogroup C (Hib/MenC) were investigated. A rat model for immunogenicity showed that antibody responses to Hib and MenC in the combined vaccine were similar to or higher than those of individual conjugates given alone, or concomitantly at separate sites. At elevated temperatures, the combination vaccine was slightly more stable than a monovalent Hib-TT vaccine, with respect to molecular size, which could be attributed to differences in the formulations. Following 5 weeks incubation at 56 degrees C, there was some dissociation of high molecular weight conjugate without significant loss of saccharide integrity; however, this did not significantly affect the vaccine immunogenicity, demonstrating the stability of this lyophilized vaccine. (c) 2010 Elsevier Ltd. All rights reserved.

Method for fabrication and verification of conjugated nanoparticle-antibody tuning elements for multiplexed electrochemical biosensors.

PubMed

La Belle, Jeffrey T; Fairchild, Aaron; Demirok, Ugur K; Verma, Aman

2013-05-15

There is a critical need for more accurate, highly sensitive and specific assay for disease diagnosis and management. A novel, multiplexed, single sensor using rapid and label free electrochemical impedance spectroscopy tuning method has been developed. The key challenges while monitoring multiple targets is frequency overlap. Here we describe the methods to circumvent the overlap, tune by use of nanoparticle (NP) and discuss the various fabrication and characterization methods to develop this technique. First sensors were fabricated using printed circuit board (PCB) technology and nickel and gold layers were electrodeposited onto the PCB sensors. An off-chip conjugation of gold NP's to molecular recognition elements (with verification technique) is described as well. A standard covalent immobilization of the molecular recognition elements is also discussed with quality control techniques. Finally use and verification of sensitivity and specificity is also presented. By use of gold NP's of various sizes, we have demonstrated the possibility and shown little loss of sensitivity and specificity in the molecular recognition of inflammatory markers as "model" targets for our tuning system. By selection of other sized NP's or NP's of various materials, the tuning effect can be further exploited. The novel platform technology developed could be utilized in critical care, clinical management and at home health and disease management. Copyright © 2013 Elsevier Inc. All rights reserved.

Unveiling the pan-genome of the SXT/R391 family of ICEs: molecular characterisation of new variable regions of SXT/R391-like ICEs detected in Pseudoalteromonas sp. and Vibrio scophthalmi.

PubMed

Rodríguez-Blanco, Arturo; Lemos, Manuel L; Osorio, Carlos R

2016-08-01

Integrating conjugative elements (ICEs) of the SXT/R391 family have been identified in fish-isolated bacterial strains collected from marine aquaculture environments of the northwestern Iberian Peninsula. Here we analysed the variable regions of two ICEs, one preliminarily characterised in a previous study (ICEVscSpa3) and one newly identified (ICEPspSpa1). Bacterial strains harboring these ICEs were phylogenetically assigned to Vibrio scophthalmi and Pseudoalteromonas sp., thus constituting the first evidence of SXT/R391-like ICEs in the genus Pseudoalteromonas to date. Variable DNA regions, which confer element-specific properties to ICEs of this family, were characterised. Interestingly, the two ICEs contained 29 genes not found in variable DNA insertions of previously described ICEs. Most notably, variable gene content for ICEVscSpa3 showed similarity to genes potentially involved in housekeeping functions of replication, nucleotide metabolism and transcription. For these genes, closest homologues were found clustered in the genome of Pseudomonas psychrotolerans L19, suggesting a transfer as a block to ICEVscSpa3. Genes encoding antibiotic resistance, restriction modification systems and toxin/antitoxin systems were absent from hotspots of ICEVscSpa3. In contrast, the variable gene content of ICEPspSpa1 included genes involved in restriction/modification functions in two different hotspots and genes related to ICE maintenance. The present study unveils a relatively large number of novel genes in SXT/R391-ICEs, and demonstrates the major role of ICE elements as contributors to horizontal gene transfer.

A Reexamination of Active and Passive Tumor Targeting by Using Rod-Shaped Gold Nanocrystals and Covalently Conjugated Peptide Ligands

PubMed Central

Huang, Xiaohua; Peng, Xianghong; Wang, Yiqing; Wang, Yuxiang; Shin, Dong M.; El-Sayed, Mostafa A.; Nie, Shuming

2010-01-01

The targeted delivery of nanoparticles to solid tumors is one of the most important and challenging problems in cancer nanomedicine, but the detailed delivery mechanisms and design principles are still not well understood. Here we report quantitative tumor uptake studies for a class of elongated gold nanocrystals (called nanorods) that are covalently conjugated to tumor-targeting peptides. A major advantage in using gold as a “tracer” is that the accumulated gold in tumors and other organs can be quantitatively determined by elemental mass spectrometry (gold is not a natural element found in animals). Thus, colloidal gold nanorods are stabilized with a layer of polyethylene glycols (PEGs), and are conjugated to three different ligands: (i) a single-chain variable fragment (ScFv) peptide that recognizes the epidermal growth factor receptor (EGFR); (ii) an amino terminal fragment (ATF) peptide that recognizes the urokinase plasminogen activator receptor (uPAR); and (iii) a cyclic RGD peptide that recognizes the avb3 integrin receptor. Quantitative pharmacokinetic and biodistribution data show that these targeting ligands only marginally improve the total gold accumulation in xenograft tumor models in comparison with nontargeted controls, but their use could greatly alter the intracellular and extracellular nanoparticle distributions. When the gold nanorods are administered via intravenous injection, we also find that active molecular targeting of the tumor microenvironments (e.g., fibroblasts, macrophages, and vasculatures) does not significantly influence the tumor nanoparticle uptake. These results suggest that for photothermal cancer therapy, the preferred route of gold nanorod administration is intra-tumoral injection instead of intravenous injection. PMID:20863096

User's Guide for ENSAERO_FE Parallel Finite Element Solver

NASA Technical Reports Server (NTRS)

Eldred, Lloyd B.; Guruswamy, Guru P.

1999-01-01

A high fidelity parallel static structural analysis capability is created and interfaced to the multidisciplinary analysis package ENSAERO-MPI of Ames Research Center. This new module replaces ENSAERO's lower fidelity simple finite element and modal modules. Full aircraft structures may be more accurately modeled using the new finite element capability. Parallel computation is performed by breaking the full structure into multiple substructures. This approach is conceptually similar to ENSAERO's multizonal fluid analysis capability. The new substructure code is used to solve the structural finite element equations for each substructure in parallel. NASTRANKOSMIC is utilized as a front end for this code. Its full library of elements can be used to create an accurate and realistic aircraft model. It is used to create the stiffness matrices for each substructure. The new parallel code then uses an iterative preconditioned conjugate gradient method to solve the global structural equations for the substructure boundary nodes.

Fusion and erosion of cell walls during confugation in the fussion yeast (Schizosaccharomyces pombe).

PubMed

Calleja, G B; Yoo, B Y; Johnson, B F

1977-06-01

Conjugation in Schizosaccharomyces pombe was studied by transmission electron microscopy. Mural and nuclear events were scored from induction, the initial event, to meiosis I, the start of sporulation. These morphogenic markers were separately identifiable as flocculation, copulation, conjugation-tube formation, cross-wall formation, cross-wall erosion, conjugation-tube expansion, cytoplasmic fusion, de-differentiation of site of union, nuclear migration and karyogamy. The following were identified as new structural elements: sex hairs, which presumably mediate hydrogen bonding between cells during flocculation; crimp at the site of union; dark patch, which presumably serves as a leak-proof seal at the time of cross-wall erosion; suture, an electron-dense seam formed by the union of a copulant pair; and small electron-dense particles close to the site of wall erosion. No special structures on the cell wall could be identified as indicative of specific sites for potential copulatory activity. The discontinuity of the 2 cell walls at the site of union became so de-differentiated after fusion and erosion that it was no longer possible to pinpoint the site of union.

Thiolated citrus low-methoxyl pectin: Synthesis, characterization and rheological and oxidation-responsive gelling properties.

PubMed

Chen, Jinfeng; Ye, Fayin; Zhou, Yun; Zhao, Guohua

2018-02-01

In the present study, citrus low-methoxyl pectin was modified by conjugating cysteine via amide bonds, and the resultant polymer (CYS-PEC) was characterized. CYS-PEC conjugates with thiol contents varying from 77.8μmol/g to 296μmol/g were synthesized, and the successful conjugation was evidenced by elemental, and FT-IR analyses. The sulfur in CYS-PEC is predominately in the thiol form, with a minor fraction forming disulfide bonds (∼15%), which occur when thiol/disulfide interchange interrupts the intended thiolation. Both native and modified pectin dispersions exhibited strong pseudoplastic properties, and the frequency sweeps revealed them to be dispersions containing microgel particles. Dynamic viscoelastic analysis was used to determine the oxidation-response gelling capacities of polymer dispersions containing H 2 O 2 , especially those that are highly thiolated and have cross-linked gel properties. For oxidation-induced CYS-PEC gels, their gelation time, hardness, viscosity and elastic moduli and swelling-disintegration ratio are dependent on the thiol group content, H 2 O 2 concentration and polymer concentration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Crosstalk between vertical and horizontal gene transfer: plasmid replication control by a conjugative relaxase

PubMed Central

Lorenzo-Díaz, Fabián; Fernández-López, Cris; Lurz, Rudi

2017-01-01

Abstract Horizontal gene transfer is a key process in the evolution of bacteria and also represents a source of genetic variation in eukaryotes. Among elements participating in gene transfer, thousands of small (<10 kb) mobile bacterial plasmids that replicate by the rolling circle mechanism represent a driving force in the spread of antibiotic resistances. In general, these plasmids are built as genetic modules that encode a replicase, an antibiotic-resistance determinant, and a relaxase that participates in their conjugative mobilization. Further, they control their relatively high copy number (∼30 copies per genome equivalent) by antisense RNAs alone or combined with a repressor protein. We report here that the MobM conjugative relaxase encoded by the promiscuous plasmid pMV158 participates in regulation of the plasmid copy number by transcriptional repression of the antisense RNA, thus increasing the number of plasmid molecules ready to be horizontally transferred (mobilization) and/or vertically inherited (replication). This type of crosstalk between genetic modules involved in vertical and horizontal gene flow has not been reported before. PMID:28525572

Conjugative DNA Transfer Is Enhanced by Plasmid R1 Partitioning Proteins

PubMed Central

Gruber, Christian J.; Lang, Silvia; Rajendra, Vinod K. H.; Nuk, Monika; Raffl, Sandra; Schildbach, Joel F.; Zechner, Ellen L.

2016-01-01

Bacterial conjugation is a form of type IV secretion used to transport protein and DNA directly to recipient bacteria. The process is cell contact-dependent, yet the mechanisms enabling extracellular events to trigger plasmid transfer to begin inside the cell remain obscure. In this study of plasmid R1 we investigated the role of plasmid proteins in the initiation of gene transfer. We find that TraI, the central regulator of conjugative DNA processing, interacts physically, and functionally with the plasmid partitioning proteins ParM and ParR. These interactions stimulate TraI catalyzed relaxation of plasmid DNA in vivo and in vitro and increase ParM ATPase activity. ParM also binds the coupling protein TraD and VirB4-like channel ATPase TraC. Together, these protein-protein interactions probably act to co-localize the transfer components intracellularly and promote assembly of the conjugation machinery. Importantly these data also indicate that the continued association of ParM and ParR at the conjugative pore is necessary for plasmid transfer to start efficiently. Moreover, the conjugative pilus and underlying secretion machinery assembled in the absence of Par proteins mediate poor biofilm formation and are completely dysfunctional for pilus specific R17 bacteriophage uptake. Thus, functional integration of Par components at the interface of relaxosome, coupling protein, and channel ATPases appears important for an optimal conformation and effective activation of the transfer machinery. We conclude that low copy plasmid R1 has evolved an active segregation system that optimizes both its vertical and lateral modes of dissemination. PMID:27486582

An Efficient Intergeneric Conjugation of DNA from Escherichia coli to Mycelia of the Lincomycin-Producer Streptomyces lincolnensis

PubMed Central

Du, Lei; Liu, Rui-Hua; Ying, Li; Zhao, Guang-Rong

2012-01-01

Streptomyces lincolnensis is a producer of lincomycin, which is a lincosamide antibiotic for the treatment of infective diseases caused by Gram-positive bacteria. S. lincolnensis is refractory to introducing plasmid DNA into cells because of resistance of foreign DNAs and poor sporulation. In this study, a simple and efficient method of transferring plasmids into S. lincolnensis through the intergeneric Escherichia coli-mycelia conjugation was established and optimized for the first time. The recipient mycelia of S. lincolnensis were prepared in liquid SM medium containing 10.3% sucrose for three days. The dispersed mycelia were conjugated with competent E. coli donor cells. The exconjugants were regenerated efficiently on solid mannitol soya flour (MS) medium containing 20 mM MgCl2. The average conjugation frequency was observed at 1.1 × 10−4 per input donor cell and validated functionally by transferring two types of vectors containing lincomycin resistance genes lmrA, lmrB and lmrC into S. lincolnensis mycelia. The data of fermentation in shaking flasks showed the lincomycin yield of the exconjugants increased by 52.9% for the multiple copy vector and 38.3% for the integrative one, compared with the parental strain. The efficient and convenient method of intergeneric E. coli-mycelia conjugation in this study provides a promising procedure to introduce plasmid DNA into other refractory streptomycetes. PMID:22606009

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis

PubMed Central

Mehdizadeh Gohari, Iman; Kropinski, Andrew M.; Weese, Scott J.; Parreira, Valeria R.; Whitehead, Ashley E.; Boerlin, Patrick; Prescott, John F.

2016-01-01

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus. PMID:26859667

Integrated transient thermal-structural finite element analysis

NASA Technical Reports Server (NTRS)

Thornton, E. A.; Dechaumphai, P.; Wieting, A. R.; Tamma, K. K.

1981-01-01

An integrated thermal structural finite element approach for efficient coupling of transient thermal and structural analysis is presented. Integrated thermal structural rod and one dimensional axisymmetric elements considering conduction and convection are developed and used in transient thermal structural applications. The improved accuracy of the integrated approach is illustrated by comparisons with exact transient heat conduction elasticity solutions and conventional finite element thermal finite element structural analyses.

Relationships for electron-vibrational coupling in conjugated π organic systems

NASA Astrophysics Data System (ADS)

O'Neill, L.; Lynch, P.; McNamara, M.; Byrne, H. J.

2005-06-01

A series of π conjugated systems were studied by absorption, photoluminescence and vibrational spectroscopy. As is common for these systems, a linear relationship between the positioning of the absorption and photoluminescence maxima plotted against inverse conjugation length is observed. The relationships are in good agreement with the simple particle in a box method, one of the earliest descriptions of the properties of one-dimensional organic molecules. In addition to the electronic transition energies, it was observed that the Stokes shift also exhibited a well-defined relationship with increasing conjugation length, implying a correlation between the electron-vibrational coupling and chain length. This correlation is further examined using Raman spectroscopy, whereby the integrated Raman scattering is seen to behave superlinearly with chain length. There is a clear indication that the vibrational activity and thus nonradiative decay processes are controllable through molecular structure. The correlations between the Stokes energies and the vibrational structure are also observed in a selection of PPV based polymers and a clear trend of increasing luminescence efficiency with decreasing vibrational activity and Stokes shift is observable. The implications of such structure property relationships in terms of materials design are discussed.

Methotrexate conjugated magnetic nanoparticle for targeted drug delivery and thermal therapy

NASA Astrophysics Data System (ADS)

Gupta, Jagriti; Bhargava, Parag; Bahadur, D.

2014-05-01

A simple soft chemical approach is used for the preparation of citrate functionalized iron oxide (Fe3O4) aqueous colloidal magnetic nanoparticles (CA-MNPs) of average size ˜10 nm. The CA-MNPs exhibit superparamagnetic behavior at room temperature with strong field dependent magnetic responsivity. The CA-MNPs can be conjugated with Methotrexate (MTX) drug through amide bonds between the carboxylic group on the surface of MNPs and amine group of MTX. The surface functionalization of Fe3O4 nanoparticles with citric acid and conjugation of MTX drug is evident from FTIR spectroscopy, zeta-potential measurement, and elemental and thermal analyses. From the drug release study, it has been observed that this bonding of MTX conjugated MNPs (MTX-MNPs) is cleaved by the intracellular enzymes in lysosome, and MTX is delivered largely inside target cancerous cells at lower pH, thereby reducing toxicity to normal cells. Also, it has been observed that the intercellular uptake of MTX-MNPs is higher compared to CA-MNPs. In addition, the aqueous colloidal stability, optimal magnetization, and good specific absorption rate (under external AC magnetic field) of CA-MNPs act as effective heating source for thermal therapy. Cytotoxicity study of MTX-MNPs shows the reduction of cellular viability for human cervical cancer cells (HeLa). Further, a synergistic effect of MTX-MNPs shows a more effective tumor cell death due to the combined effect of thermo-chemotherapy.

Gd-Complexes of New Arylpiperazinyl Conjugates of DTPA-Bis(amides): Synthesis, Characterization and Magnetic Relaxation Properties.

PubMed

Ba-Salem, Abdullah O; Ullah, Nisar; Shaikh, M Nasiruzzaman; Faiz, Mohamed; Ul-Haq, Zaheer

2015-04-29

Two new DTPA-bis(amide) based ligands conjugated with the arylpiperazinyl moiety were synthesized and subsequently transformed into their corresponding Gd(III) complexes 1 and 2 of the type [Gd(L)H2O]·nH2O. The relaxivity (R1) of these complexes was measured, which turned out to be comparable with that of Omniscan®, a commercially available MRI contrast agent. The cytotoxicity studies of these complexes indicated that they are non-toxic, which reveals their potential and physiological suitability as MRI contrast agents. All the synthesized ligands and complexes were characterized with the aid of analytical and spectroscopic methods, including elemental analysis, 1H-NMR, FT-IR, XPS and fast atom bombardment (FAB) mass spectrometry.

Heat transfer in rocket engine combustion chambers and regeneratively cooled nozzles

NASA Technical Reports Server (NTRS)

1993-01-01

A conjugate heat transfer computational fluid dynamics (CFD) model to describe regenerative cooling in the main combustion chamber and nozzle and in the injector faceplate region for a launch vehicle class liquid rocket engine was developed. An injector model for sprays which treats the fluid as a variable density, single-phase media was formulated, incorporated into a version of the FDNS code, and used to simulate the injector flow typical of that in the Space Shuttle Main Engine (SSME). Various chamber related heat transfer analyses were made to verify the predictive capability of the conjugate heat transfer analysis provided by the FDNS code. The density based version of the FDNS code with the real fluid property models developed was successful in predicting the streamtube combustion of individual injector elements.

Organic-Inorganic Composites of Semiconductor Nanocrystals for Efficient Excitonics.

PubMed

Guzelturk, Burak; Demir, Hilmi Volkan

2015-06-18

Nanocomposites of colloidal semiconductor nanocrystals integrated into conjugated polymers are the key to soft-material hybrid optoelectronics, combining advantages of both plastics and particles. Synergic combination of the favorable properties in the hybrids of colloidal nanocrystals and conjugated polymers offers enhanced performance and new functionalities in light-generation and light-harvesting applications, where controlling and mastering the excitonic interactions at the nanoscale are essential. In this Perspective, we highlight and critically consider the excitonic interactions in the organic-inorganic nanocomposites to achieve highly efficient exciton transfer through rational design of the nanocomposites. The use of strong excitonic interactions in optoelectronic devices can trigger efficiency breakthroughs in hybrid optoelectronics.

Influence of Magnetically Conjugate Fragments of Auroral Emission Images on the Accuracy of Determining E av of Precipitating Electrons

NASA Astrophysics Data System (ADS)

Banshchikova, M. A.; Chuvashov, I. N.; Kuzmin, A. K.; Kruchenitskii, G. M.

2018-05-01

Results of magnetic conjugation of image fragments of auroral emissions at different altitudes along the magnetic field lines and preliminary results of evaluation of their influence on the accuracy of remote mapping of energy characteristics of precipitating electrons are presented. The results are obtained using the code of tracing being an integral part of the software Vector M intended for calculation of accompanying, geophysical, and astronomical information for the center of mass of a space vehicle (SV) and remote observation of aurora by means of Aurovisor-VIS/MP imager onboard the SV Meteor-MP to be launched.

Phase transition in conjugated oligomers suspended in chloroform

NASA Astrophysics Data System (ADS)

Dwivedi, Shikha; Kumar, Anupam; Yadav, S. N. S.; Mishra, Pankaj

2015-08-01

Density functional theory (DFT) has been used to investigate the isotropic-nematic (I-N) phase transition in a system of high aspect ratio conjugated oligomers suspended in chloroform. The interaction between the oligomers is modeled using Gay-Berne potential in which effect of solvent is implicit. Percus-Yevick integral equation theory has been used to evaluate the pair correlation functions of the fluid phase at several temperatures and densities. These pair correlation function has been used in the DFT to evaluate the I-N freezing parameters. Highly oriented nematic is found to stabilize at low density. The results obtained are in qualitative agreement with the simulation and are verifiable.

Conjugation in Escherichia coli

PubMed Central

Boyer, Herbert

1966-01-01

Boyer, Herbert (Yale University, New Haven, Conn.). Conjugation in Escherichia coli. J. Bacteriol. 91:1767–1772. 1966.—The sex factor of Escherichia coli K-12 was introduced into an E. coli B/r strain by circumventing the host-controlled modification and restriction incompatibilities known to exist between these closely related strains. The sexual properties of the constructed F+ B strain and its Hfr derivatives were examined. These studies showed that the E. coli strain B/r F+ and Hfr derivatives are similar to the E. coli strain K-12 F+ and Hfr derivatives. However, the site of sex factor integration was found to be dependent on the host genome. PMID:5327905

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

PubMed Central

Iyer, Lakshminarayan M.; Burroughs, A. Maxwell; Anand, Swadha; de Souza, Robson F.

2017-01-01

ABSTRACT Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems. PMID:28559295

2.5D complex resistivity modeling and inversion using unstructured grids

NASA Astrophysics Data System (ADS)

Xu, Kaijun; Sun, Jie

2016-04-01

The characteristic of complex resistivity on rock and ore has been recognized by people for a long time. Generally we have used the Cole-Cole Model(CCM) to describe complex resistivity. It has been proved that the electrical anomaly of geologic body can be quantitative estimated by CCM parameters such as direct resistivity(ρ0), chargeability(m), time constant(τ) and frequency dependence(c). Thus it is very important to obtain the complex parameters of geologic body. It is difficult to approximate complex structures and terrain using traditional rectangular grid. In order to enhance the numerical accuracy and rationality of modeling and inversion, we use an adaptive finite-element algorithm for forward modeling of the frequency-domain 2.5D complex resistivity and implement the conjugate gradient algorithm in the inversion of 2.5D complex resistivity. An adaptive finite element method is applied for solving the 2.5D complex resistivity forward modeling of horizontal electric dipole source. First of all, the CCM is introduced into the Maxwell's equations to calculate the complex resistivity electromagnetic fields. Next, the pseudo delta function is used to distribute electric dipole source. Then the electromagnetic fields can be expressed in terms of the primary fields caused by layered structure and the secondary fields caused by inhomogeneities anomalous conductivity. At last, we calculated the electromagnetic fields response of complex geoelectric structures such as anticline, syncline, fault. The modeling results show that adaptive finite-element methods can automatically improve mesh generation and simulate complex geoelectric models using unstructured grids. The 2.5D complex resistivity invertion is implemented based the conjugate gradient algorithm.The conjugate gradient algorithm doesn't need to compute the sensitivity matrix but directly computes the sensitivity matrix or its transpose multiplying vector. In addition, the inversion target zones are segmented with fine grids and the background zones are segmented with big grid, the method can reduce the grid amounts of inversion, it is very helpful to improve the computational efficiency. The inversion results verify the validity and stability of conjugate gradient inversion algorithm. The results of theoretical calculation indicate that the modeling and inversion of 2.5D complex resistivity using unstructured grids are feasible. Using unstructured grids can improve the accuracy of modeling, but the large number of grids inversion is extremely time-consuming, so the parallel computation for the inversion is necessary. Acknowledgments: We thank to the support of the National Natural Science Foundation of China(41304094).

Light and harmonicity: the golden section

NASA Astrophysics Data System (ADS)

Raftopoulos, Dionysios G.

2015-09-01

Adhering to Werner Heisenberg's and to the school of Copenhagen's physical philosophy we introduce the localized observer as an absolutely necessary element of a consistent physical description of nature. Thus we have synthesized the theory of the harmonicity of the field of light, which attempts to present a new approach to the events in the human perceptible space. It is an axiomatic theory based on the selection of the projective space as the geometrical space of choice, while its first fundamental hypothesis is none other than special relativity theory's second hypothesis, properly modified. The result is that all our observations and measurements of physical entities always refer not to their present state but rather to a previous one, a conclusion evocative of the "shadows" paradigm in Plato's cave allegory. In the kinematics of a material point this previous state we call "conjugate position", which has been called the "retarded position" by Richard Feynman. We prove that the relation of the present position with its conjugate is ruled by a harmonic tetrad. Thus the relation of the elements of the geometrical (noetic) and the perceptible space is harmonic. In this work we show a consequence of this harmonic relation: the golden section.

Defining the Diverse Cell Populations Contributing to Lignification in Arabidopsis Stems.

PubMed

Smith, Rebecca A; Schuetz, Mathias; Karlen, Steven D; Bird, David; Tokunaga, Naohito; Sato, Yasushi; Mansfield, Shawn D; Ralph, John; Samuels, A Lacey

2017-06-01

Many land plants evolved tall and sturdy growth habits due to specialized cells with thick lignified cell walls: tracheary elements that function in water transport and fibers that function in structural support. The objective of this study was to define how and when diverse cell populations contribute lignin precursors, monolignols, to secondary cell walls during lignification of the Arabidopsis ( Arabidopsis thaliana ) inflorescence stem. Previous work demonstrated that, when lignin biosynthesis is suppressed in fiber and tracheary element cells with thickened walls, fibers become lignin-depleted while vascular bundles still lignify, suggesting that nonlignifying neighboring xylem cells are contributing to lignification. In this work, we dissect the contributions of different cell types, specifically xylary parenchyma and fiber cells, to lignification of the stem using cell-type-specific promoters to either knock down an essential monolignol biosynthetic gene or to introduce novel monolignol conjugates. Analysis of either reductions in lignin in knockdown lines, or the addition of novel monolignol conjugates, directly identifies the xylary parenchyma and fiber cell populations that contribute to the stem lignification and the developmental timing at which each contribution is most important. © 2017 American Society of Plant Biologists. All Rights Reserved.

Cretaceous to Recent Asymetrical Subsidence of South American and West African Conjugate Margins

NASA Astrophysics Data System (ADS)

Kenning, J.; Mann, P.

2017-12-01

Two divergent interpretations have been proposed for South American rifted-passive margins: the "mirror hypothesis" proposes that the rifted margins form symmetrically from pure shear of the lithosphere while upper-plate-lower plate models propose that the rifted margins form asymmetrically by simple shear. Models based on seismic reflection and refraction imaging and comparison of conjugate, rifted margins generally invoke a hybrid stretching process involving elements of both end member processes along with the effects of mantle plumes active during the rift and passive margin phases. We use subsidence histories of 14, 1-7 km-deep exploration wells located on South American and West African conjugate pairs now separated by the South Atlantic Ocean, applying long-term subsidence to reveal the symmetry or asymmetry of the underlying, conjugate, rift processes. Conjugate pairs characterize the rifted margin over a distance of 3500 km and include: Colorado-South Orange, Punta Del Este-North Orange, South Pelotas-Lüderitz and the North Pelotas-Walvis Basins. Of the four conjugate pairs, more rapid subsidence on the South American plate is consistently observed with greater initial rift and syn-rift subsidence rates of >60m/Ma (compared to <15 m/Ma) between approximately 145-115 Ma. High rates of tectonically-induced subsidence >100 m/Ma are observed offshore South Africa between approximately 120-80 Ma, compatible with onset of the post-rift thermal sag phase. During this period the majority of burial is completed and rates remain low at <10 m/Ma during most of the late Cretaceous and Cenozoic. The conjugate margin of Argentina/Uruguay displays more gradual subsidence throughout the Cretaceous, consistently averaging a moderate 15-30m/Ma. By the end of this stage there is a subsequent increase to 25-60 m/Ma within the last 20 Ma, interpreted to reflect lithospheric loading due to increased sedimentation rates during the Cenozoic. This increase in subsidence rate is not seen in the African conjugate section where the majority of sediments bypassed the highly aggraded Cretaceous shelf. Initially greater on the Brazilian margin compared to Namibia, here both margins exhibit moderate-steep subsidence curves until 65-55 Ma where there is reduced subsidence during much of the Late Cretaceous until 20 Ma.

Analytic integrable systems: Analytic normalization and embedding flows

NASA Astrophysics Data System (ADS)

Zhang, Xiang

In this paper we mainly study the existence of analytic normalization and the normal form of finite dimensional complete analytic integrable dynamical systems. More details, we will prove that any complete analytic integrable diffeomorphism F(x)=Bx+f(x) in (Cn,0) with B having eigenvalues not modulus 1 and f(x)=O(|) is locally analytically conjugate to its normal form. Meanwhile, we also prove that any complete analytic integrable differential system x˙=Ax+f(x) in (Cn,0) with A having nonzero eigenvalues and f(x)=O(|) is locally analytically conjugate to its normal form. Furthermore we will prove that any complete analytic integrable diffeomorphism defined on an analytic manifold can be embedded in a complete analytic integrable flow. We note that parts of our results are the improvement of Moser's one in J. Moser, The analytic invariants of an area-preserving mapping near a hyperbolic fixed point, Comm. Pure Appl. Math. 9 (1956) 673-692 and of Poincaré's one in H. Poincaré, Sur l'intégration des équations différentielles du premier order et du premier degré, II, Rend. Circ. Mat. Palermo 11 (1897) 193-239. These results also improve the ones in Xiang Zhang, Analytic normalization of analytic integrable systems and the embedding flows, J. Differential Equations 244 (2008) 1080-1092 in the sense that the linear part of the systems can be nonhyperbolic, and the one in N.T. Zung, Convergence versus integrability in Poincaré-Dulac normal form, Math. Res. Lett. 9 (2002) 217-228 in the way that our paper presents the concrete expression of the normal form in a restricted case.

A viscoelastic higher-order beam finite element

NASA Technical Reports Server (NTRS)

Johnson, Arthur R.; Tressler, Alexander

1996-01-01

A viscoelastic internal variable constitutive theory is applied to a higher-order elastic beam theory and finite element formulation. The behavior of the viscous material in the beam is approximately modeled as a Maxwell solid. The finite element formulation requires additional sets of nodal variables for each relaxation time constant needed by the Maxwell solid. Recent developments in modeling viscoelastic material behavior with strain variables that are conjugate to the elastic strain measures are combined with advances in modeling through-the-thickness stresses and strains in thick beams. The result is a viscous thick-beam finite element that possesses superior characteristics for transient analysis since its nodal viscous forces are not linearly dependent an the nodal velocities, which is the case when damping matrices are used. Instead, the nodal viscous forces are directly dependent on the material's relaxation spectrum and the history of the nodal variables through a differential form of the constitutive law for a Maxwell solid. The thick beam quasistatic analysis is explored herein as a first step towards developing more complex viscoelastic models for thick plates and shells, and for dynamic analyses. The internal variable constitutive theory is derived directly from the Boltzmann superposition theorem. The mechanical strains and the conjugate internal strains are shown to be related through a system of first-order, ordinary differential equations. The total time-dependent stress is the superposition of its elastic and viscous components. Equations of motion for the solid are derived from the virtual work principle using the total time-dependent stress. Numerical examples for the problems of relaxation, creep, and cyclic creep are carried out for a beam made from an orthotropic Maxwell solid.

Detection of tetQ and ermF antibiotic resistance genes in Prevotella and Porphyromonas isolates from clinical specimens and resident microbiota of humans.

PubMed

Arzese, A R; Tomasetig, L; Botta, G A

2000-05-01

Gram-negative anaerobes belonging to the genera Fusobacterium, Prevotella and Porphyromonas were investigated for the presence of tetQ and ermF, which have been shown to be spread by conjugal elements. One hundred isolates from either sites of infection or various body sites in healthy subjects were studied. PCR was used to detect tetQ, and DNA-DNA hybridization studies on EcoRI chromosomal digests were undertaken to detect the presence of tetQ and ermF. Antibiotic sensitivity assays were performed on selected isolates to detect tetracycline, erythromycin and penicillin resistance. Twenty Fusobacterium isolates lacked tetQ, and were tetracycline sensitive. Twenty per cent of Prevotella spp. isolates both from clinical specimens and from healthy subjects were found to possess tetQ. Of 20 Porphyromonas isolates tested, one (Porphyromonas levii) from a case of bacterial vaginosis was shown to possess tetQ in the chromosome. The presence of tetQ was always associated with tetracycline resistance. Four isolates of Prevotella melaninogenica and one isolate of Prevotella were ermF-positive, although expression of erythromycin resistance was not consistently associated with detection of this gene. Antibiotic resistance phenotypes of Prevotella isolates were shown to be related to specific chromosomal restriction patterns by hybridization studies: tetracycline resistance and tetracycline/erythromycin resistance are conferred by Bacteroides tetracycline-resistant ERL elements, whereas the tetracycline/penicillin resistance phenotype could be due to spread of elements identified in Prevotella only. Tetracycline/erythromycin-resistant and tetracycline/erythromycin/penicillin-resistant P. melaninogenica isolates were found in this study. It appeared that the presence of tetQ and ermF in Bacteroides and Prevotella contributed to the persistence of antibiotic resistance isolates within the host and to potential spread to other organisms through conjugal elements.

Drug Resistance and Gene Transfer Mechanisms in Respiratory/Oral Bacteria.

PubMed

Jiang, S; Zeng, J; Zhou, X; Li, Y

2018-06-01

Growing evidence suggests the existence of new antibiotic resistance mechanisms. Recent studies have revealed that quorum-quenching enzymes, such as MacQ, are involved in both antibiotic resistance and cell-cell communication. Furthermore, some small bacterial regulatory RNAs, classified into RNA attenuators and small RNAs, modulate the expression of resistance genes. For example, small RNA sprX, can shape bacterial resistance to glycopeptide antibiotics via specific downregulation of protein SpoVG. Moreover, some bacterial lipocalins capture antibiotics in the extracellular space, contributing to severe multidrug resistance. But this defense mechanism may be influenced by Agr-regulated toxins and liposoluble vitamins. Outer membrane porin proteins and efflux pumps can influence intracellular concentrations of antibiotics. Alterations in target enzymes or antibiotics prevent binding to targets, which act to confer high levels of resistance in respiratory/oral bacteria. As described recently, horizontal gene transfer, including conjugation, transduction and transformation, is common in respiratory/oral microflora. Many conjugative transposons and plasmids discovered to date encode antibiotic resistance proteins and can be transferred from donor bacteria to transient recipient bacteria. New classes of mobile genetic elements are also being identified. For example, nucleic acids that circulate in the bloodstream (circulating nucleic acids) can integrate into the host cell genome by up-regulation of DNA damage and repair pathways. With multidrug resistant bacteria on the rise, new drugs have been developed to combate bacterial antibiotic resistance, such as innate defense regulators, reactive oxygen species and microbial volatile compounds. This review summaries various aspects and mechanisms of antibiotic resistance in the respiratory/oral microbiota. A better understanding of these mechanisms will facilitate minimization of the emergence of antibiotic resistance.

Self-Assembled DNA Tetrahedral Scaffolds for the Construction of Electrochemiluminescence Biosensor with Programmable DNA Cyclic Amplification.

PubMed

Feng, Qiu-Mei; Guo, Yue-Hua; Xu, Jing-Juan; Chen, Hong-Yuan

2017-05-24

A novel DNA tetrahedron-structured electrochemiluminescence (ECL) platform for bioanalysis with programmable DNA cyclic amplification was developed. In this work, glucose oxidase (GOD) was labeled to a DNA sequence (S) as functional conjugation (GOD-S), which could hybridize with other DNA sequences (L and P) to form GOD-S:L:P probe. In the presence of target DNA and a help DNA (A), the programmable DNA cyclic amplification was activated and released GOD-S via toehold-mediated strand displacement. Then, the obtained GOD-S was further immobilized on the DNA tetrahedral scaffolds with a pendant capture DNA and Ru(bpy) 3 2+ -conjugated silica nanoparticles (RuSi NPs) decorated on the electrode surface. Thus, the amount of GOD-S assembled on the electrode surface depended on the concentration of target DNA and GOD could catalyze glucose to generate H 2 O 2 in situ. The ECL signal of Ru(bpy) 3 2+ -TPrA system was quenched by the presence of H 2 O 2 . By integrating the programmable DNA cyclic amplification and in situ generating H 2 O 2 as Ru(bpy) 3 2+ ECL quencher, a sensitive DNA tetrahedron-structured ECL sensing platform was proposed for DNA detection. Under optimized conditions, this biosensor showed a wide linear range from 100 aM to 10 pM with a detection limit of 40 aM, indicating a promising application in DNA analysis. Furthermore, by labeling GOD to different recognition elements, the proposed strategy could be used for the detection of various targets. Thus, this programmable cascade amplification strategy not only retains the high selectivity and good capturing efficiency of tetrahedral-decorated electrode surface but also provides potential applications in the construction of ECL biosensor.

The Sudden Dominance of bla CTX–M Harbouring Plasmids in Shigella spp. Circulating in Southern Vietnam

PubMed Central

Nhu, Nguyen Thi Khanh; Vinh, Ha; Nga, Tran Vu Thieu; Stabler, Richard; Duy, Pham Thanh; Thi Minh Vien, Le; van Doorn, H. Rogier; Cerdeño-Tárraga, Ana; Thomson, Nicholas; Campbell, James; Van Minh Hoang, Nguyen; Thi Thu Nga, Tran; Minh, Pham Van; Thuy, Cao Thu; Wren, Brendan; Farrar, Jeremy; Baker, Stephen

2010-01-01

Background Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. Methodology We collected hospital admission data from the pediatric population attending the hospital for tropical diseases in Ho Chi Minh City with Shigella infections. Organisms were cultured from all enrolled patients and subjected to antimicrobial susceptibility testing. Those that were ESBL positive were subjected to further investigation. These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla CTX–M encoding plasmid. Principal Findings We show that two different bla CTX-M genes are circulating in this bacterial population in this location. Sequence of one of the ESBL plasmids shows that rather than the gene being integrated into a preexisting MDR plasmid, the bla CTX-M gene is located on relatively simple conjugative plasmid. The sequenced plasmid (pEG356) carried the bla CTX-M-24 gene on an ISEcp1 element and demonstrated considerable sequence homology with other IncFI plasmids. Significance The rapid dissemination, spread of antimicrobial resistance and changing population of Shigella spp. concurrent with economic growth are pertinent to many other countries undergoing similar development. Third generation cephalosporins are commonly used empiric antibiotics in Ho Chi Minh City. We recommend that these agents should not be considered for therapy of dysentery in this setting. PMID:20544028

Chemotherapy remains an essential element of personalized care for persons with lung cancers

PubMed Central

Hellmann, M. D.; Li, B. T.; Chaft, J. E.; Kris, M. G.

2016-01-01

Molecularly targeted and immunotherapies have improved the care of patients with lung cancers. These successes have rallied calls to replace or avoid chemotherapy. Yet, even in this era of precision medicine and exciting advances, cytotoxic chemotherapies remain an essential component of lung cancer treatment. In the setting of locoregional disease, chemotherapy is the only systemic therapy thus far proven to enhance curability when combined with surgery or radiation. In the metastatic setting, chemotherapy can improve the length and quality of life in many patients. Chemotherapy remains the mainstay of care for individuals whose cancers with oncogenic drivers have acquired resistance to targeted agents. Chemotherapy also has the potential to modulate the immune system to enhance the effectiveness of immune checkpoint inhibitors. In this context, chemotherapy should be framed as a critical component of the armamentarium available for optimizing cancer care rather than an unfortunate anachronism. We examine the role of chemotherapy with precision medicine in the current care of patients with lung cancers, as well as opportunities for future integration in combinations with targeted agents, angiogenesis inhibitors, immunotherapies, and antibody drug conjugates. PMID:27456296

Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.

PubMed

Kelly, Simon; Sullivan, John; Ronson, Clive; Tian, Rui; Bräu, Lambert; Munk, Christine; Goodwin, Lynne; Han, Cliff; Woyke, Tanja; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2014-01-01

Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals that the genome of M. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Bacterial sex in dental plaque.

PubMed

Olsen, Ingar; Tribble, Gena D; Fiehn, Nils-Erik; Wang, Bing-Yan

2013-01-01

Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

Upconversion nanoparticle as elemental tag for the determination of alpha-fetoprotein in human serum by inductively coupled plasma mass spectrometry.

PubMed

Liu, Zhengru; Yang, Bin; Chen, Beibei; He, Man; Hu, Bin

2016-12-19

Upconversion nanoparticles (UCNPs) have received increasing attention due to their unique optical properties. Recognizing that UCNPs are lanthanide-doped nanoparticles, we incorporated UCNPs into an immunoassay with inductively coupled plasma mass spectrometry (ICP-MS) detection for the determination of specific proteins, e.g., alpha-fetoprotein (AFP). The sensitivity of the assay was enhanced because of the ICP-MS detection of UCNPs that contained large numbers of lanthanide elemental tags. Conjugates of UCNPs and antibodies were prepared and the morphology of the conjugates was characterized by transmission electron microscopy. After a sandwich immunoreaction, the AFP was determined by the ICP-MS analysis of UCNPs. Under the optimized conditions, a limit of detection (3σ) of 0.31 ng mL -1 based on 89 Y signal and 0.22 ng mL -1 based on 174 Yb signal was obtained for AFP, with a dynamic range of 0.5-35 ng mL -1 and a relative standard deviation of 4.8% (c = 5 ng mL -1 , n = 9). The developed method was applied to the determination of AFP in human serum and the recovery for the spiked sample was in the range of 98.6-123%. The proposed method is simple, rapid, selective and sensitive, and has a good tolerance for the complex biological matrix, indicating great potential for the application of UCNP in biological research as an elemental tag.

Photothermal Nanotherapeutics and Nanodiagnostics for Selective Killing of Bacteria Targeted with Gold Nanoparticles

PubMed Central

Zharov, Vladimir P.; Mercer, Kelly E.; Galitovskaya, Elena N.; Smeltzer, Mark S.

2006-01-01

We describe a new method for selective laser killing of bacteria targeted with light-absorbing gold nanoparticles conjugated with specific antibodies. The multifunctional photothermal (PT) microscope/spectrometer provides a real-time assessment of this new therapeutic intervention. In this integrated system, strong laser-induced overheating effects accompanied by the bubble-formation phenomena around clustered gold nanoparticles are the main cause of bacterial damage. PT imaging and time-resolved monitoring of the integrated PT responses assessed these effects. Specifically, we used this technology for selective killing of the Gram-positive bacterium Staphylococcus aureus by targeting the bacterial surface using 10-, 20-, and 40-nm gold particles conjugated with anti-protein A antibodies. Labeled bacteria were irradiated with focused laser pulses (420–570 nm, 12 ns, 0.1–5 J/cm2, 100 pulses), and laser-induced bacterial damage observed at different laser fluences and nanoparticle sizes was verified by optical transmission, electron microscopy, and conventional viability testing. PMID:16239330

Oriented conjugates of monoclonal and single-domain antibodies with quantum dots for flow cytometry and immunohistochemistry diagnostic applications

NASA Astrophysics Data System (ADS)

Sukhanova, Alyona; Even-Desrumeaux, Klervi; Millot, Jean-Marc; Chames, Patrick; Baty, Daniel; Artemyev, Mikhail; Oleinikov, Vladimir; Cohen, Jacques H. M.; Nabiev, Igor

2012-03-01

Ideal diagnostic nanoprobes should not exceed 15 nm in size and should contain high-affinity homogeneously oriented capture molecules on their surface. An advanced procedure for antibody (Ab) reduction was used to cleave each Ab into two functional half-Abs, 75-kDa heavy-light chain fragments, each containing an intact antigen-binding site. Affinity purification of half-Abs followed by their linkage to quantum dots (QDs) yielded oriented QD-Ab conjugates whose functionality was considerably improved compared to those obtained using the standard protocols. Ultrasmall diagnostic nanoprobes were engineered through oriented conjugation of QDs with 13-kDa single-domain Abs (sdAbs) derived from llama IgG. sdAbs were tagged with QDs via an additional cysteine residue specifically integrated into the C-terminal region of sdAb using genetic engineering. This approach made it possible to obtain sdAb-QD nanoprobes <12 nm in diameter comprising four copies of sdAbs linked to the same QD in an oriented manner. sdAb-QD conjugates against carcinoembryonic antigen (CEA) and HER2 exhibited an extremely high specificity in flow cytometry; the quality of immunohistochemical labeling of biopsy samples was found to be superior to that of labeling according to the current "gold standard" protocols of anatomo-pathological practice. The nano-bioengineering approaches developed can be extended to oriented conjugation of Abs and sdAbs with different semiconductor, noble metal, or magnetic nanoparticles.

Augmented reality 3D display based on integral imaging

NASA Astrophysics Data System (ADS)

Deng, Huan; Zhang, Han-Le; He, Min-Yang; Wang, Qiong-Hua

2017-02-01

Integral imaging (II) is a good candidate for augmented reality (AR) display, since it provides various physiological depth cues so that viewers can freely change the accommodation and convergence between the virtual three-dimensional (3D) images and the real-world scene without feeling any visual discomfort. We propose two AR 3D display systems based on the theory of II. In the first AR system, a micro II display unit reconstructs a micro 3D image, and the mciro-3D image is magnified by a convex lens. The lateral and depth distortions of the magnified 3D image are analyzed and resolved by the pitch scaling and depth scaling. The magnified 3D image and real 3D scene are overlapped by using a half-mirror to realize AR 3D display. The second AR system uses a micro-lens array holographic optical element (HOE) as an image combiner. The HOE is a volume holographic grating which functions as a micro-lens array for the Bragg-matched light, and as a transparent glass for Bragg mismatched light. A reference beam can reproduce a virtual 3D image from one side and a reference beam with conjugated phase can reproduce the second 3D image from other side of the micro-lens array HOE, which presents double-sided 3D display feature.

A novel enzyme-linked immuno-sorbent assay (ELISA) for the quantification of total and free polysaccharide in Haemophilus influenzae b-Tetanus toxoid conjugate vaccines in monovalent and combined vaccine formulations.

PubMed

Saydam, Manolya; Rigsby, Peter; Mawas, Fatme

2014-01-01

Current Haemophilus influenzae b conjugate vaccines (Hib), which are made of purified capsular polysaccharide (poly-ribosyl-ribitol-phosphate; PRP) conjugated to a carrier protein, are almost completely evaluated by physico-chemical methods to ensure the integrity and stability of the vaccine and consistency of manufacture of batches. The absence of a potency assay makes the quantification of total PRP content (in SI units) and of % free polysaccharide in final fills or bulk components of Hib vaccines critical release tests for both manufacturers and national control authorities. Here we describe a simple and sensitive Enzyme-Linked Immuno-sorbent Assay (ELISA) which has been developed to quantify total and free PRP content in Hib-TT vaccine alone or when in combination with other vaccines. The assay is robust, specific and highly sensitive. Copyright © 2013 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

From Semi- to Full-Two-Dimensional Conjugated Side-Chain Design: A Way toward Comprehensive Solar Energy Absorption

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

Chao, Pengjie; Wang, Huan; Qu, Shiwei

Two polymers with fully two-dimensional (2D) conjugated side chains, 2D-PTB-Th and 2D-PTB-TTh, were synthesized and characterized through simultaneously integrating the 2D-TT and the 2D-BDT monomers onto the polymer backbone. Resulting from the synergistic effect from the conjugated side chains on both monomers, the two polymers showed remarkably efficient absorption of the sunlight and improved pi-pi intermolecular interactions for efficient charge carrier transport. The optimized bulk heterojunction device based on 2D-PTB-Th and PC71BM shows a higher PCE of 9.13% compared to PTB7-Th with a PCE of 8.26%, which corresponds to an approximately 10% improvement in solar energy conversion. The fully 2D-conjugatedmore » side-chain concept reported here developed a new molecular design strategy for polymer materials with enhanced sunlight absorption and efficient solar energy conversion.« less

Factorizing the factorization - a spectral-element solver for elliptic equations with linear operation count

NASA Astrophysics Data System (ADS)

Huismann, Immo; Stiller, Jörg; Fröhlich, Jochen

2017-10-01

The paper proposes a novel factorization technique for static condensation of a spectral-element discretization matrix that yields a linear operation count of just 13N multiplications for the residual evaluation, where N is the total number of unknowns. In comparison to previous work it saves a factor larger than 3 and outpaces unfactored variants for all polynomial degrees. Using the new technique as a building block for a preconditioned conjugate gradient method yields linear scaling of the runtime with N which is demonstrated for polynomial degrees from 2 to 32. This makes the spectral-element method cost effective even for low polynomial degrees. Moreover, the dependence of the iterative solution on the element aspect ratio is addressed, showing only a slight increase in the number of iterations for aspect ratios up to 128. Hence, the solver is very robust for practical applications.

A least-squares finite element method for 3D incompressible Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan; Lin, T. L.; Hou, Lin-Jun; Povinelli, Louis A.

1993-01-01

The least-squares finite element method (LSFEM) based on the velocity-pressure-vorticity formulation is applied to three-dimensional steady incompressible Navier-Stokes problems. This method can accommodate equal-order interpolations, and results in symmetric, positive definite algebraic system. An additional compatibility equation, i.e., the divergence of vorticity vector should be zero, is included to make the first-order system elliptic. The Newton's method is employed to linearize the partial differential equations, the LSFEM is used to obtain discretized equations, and the system of algebraic equations is solved using the Jacobi preconditioned conjugate gradient method which avoids formation of either element or global matrices (matrix-free) to achieve high efficiency. The flow in a half of 3D cubic cavity is calculated at Re = 100, 400, and 1,000 with 50 x 52 x 25 trilinear elements. The Taylor-Gortler-like vortices are observed at Re = 1,000.

Heterobivalent Imaging Agents for Simultaneous Targeting Prostate-Specific Membrane Antigen (PSMA) and Hepsin

DTIC Science & Technology

2014-11-01

Prostate-Specific Membrane Antigen ( PSMA ) and Hepsin PRINCIPAL INVESTIGATOR: Youngjoo Byun, Ph. D. CONTRACTING ORGANIZATION: Korea...Simultaneous Targeting Prostate-Specific Membrane Antigen ( PSMA ) and Hepsin 5b. GRANT NUMBER W81XWH-10-1-0189 5c. PROGRAM ELEMENT NUMBER 6...heterobivalent conjugates of PSMA /hepsin-binding ligands labeled with optical dyes or radionuclides. The sensitivity and accuracy of prostate cancer

The Fate of Visible Features of Invisible Elements

PubMed Central

Herzog, Michael H.; Otto, Thomas U.; Ögmen, Haluk

2012-01-01

To investigate the integration of features, we have developed a paradigm in which an element is rendered invisible by visual masking. Still, the features of the element are visible as part of other display elements presented at different locations and times (sequential metacontrast). In this sense, we can “transport” features non-retinotopically across space and time. The features of the invisible element integrate with features of other elements if and only if the elements belong to the same spatio-temporal group. The mechanisms of this kind of feature integration seem to be quite different from classical mechanisms proposed for feature binding. We propose that feature processing, binding, and integration occur concurrently during processes that group elements into wholes. PMID:22557985

Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates.

PubMed

Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P

2010-07-06

Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin < 1 < 3 < 4 < 2. Among them, the binding constant [(2.7 +/- 0.3) x 10(8) M(-1)] of 2 with poly(dA).2poly(dT) was the highest, almost 1000-fold greater than that of neomycin. The binding of compounds 1-4 with poly(dA).2poly(dT) was mostly enthalpy-driven and gave negative DeltaC(p) values. The results described here suggest that the binding affinity of intercalator-neomycin conjugates for poly(dA).2poly(dT) increases as a function of the surface area of the intercalator moiety.

1H-1,2,3-triazole-tethered uracil-ferrocene and uracil-ferrocenylchalcone conjugates: Synthesis and antitubercular evaluation.

PubMed

Singh, Amandeep; Biot, Christophe; Viljoen, Albertus; Dupont, Christian; Kremer, Laurent; Kumar, Kewal; Kumar, Vipan

2017-06-01

Copper-catalyzed azide-alkyne [3 + 2] cycloaddition has been utilized for preparing a series of 1H-1,2,3-triazoles with the purpose of probing structure-activity relationships among a uracil-ferrocene-triazole conjugate family. The antitubercular evaluation studies revealed an improvement in activity with the introduction of a ferrocene nucleus among N-alkylazido-uracil precursors, with a preference for a bromo-substituent along with moderate chain lengths of n = 2-6. The reported protocol is a successful approach for integrating uracil-ferrocene-chalcone functionalities tethered via 1H-1,2,3-triazole rings with apparent physicochemical stability. © 2016 John Wiley & Sons A/S.

Truxene-Based Hyperbranched Conjugated Polymers: Fluorescent Micelles Detect Explosives in Water.

PubMed

Huang, Wei; Smarsly, Emanuel; Han, Jinsong; Bender, Markus; Seehafer, Kai; Wacker, Irene; Schröder, Rasmus R; Bunz, Uwe H F

2017-01-25

We report two hyperbranched conjugated polymers (HCP) with truxene units as core and 1,4-didodecyl-2,5-diethynylbenzene as well as 1,4-bis(dodecyloxy)-2,5-diethynylbenzene as comonomers. Two analogous poly(para-phenyleneethynylene)s (PPE) are also prepared as comparison to demonstrate the difference between the truxene and the phenyl moieties in their optical properties and their sensing performance. The four polymers are tested for nitroaromatic analytes and display different fluorescence quenching responses. The quenching efficiencies are dependent upon the spectral overlap between the absorbance of the analyte and the emission of the fluorescent polymer. Optical fingerprints are obtained, based on the unique response patterns of the analytes toward the polymers. With this small sensor array, one can distinguish nine nitroaromatic analytes with 100% accuracy. The amphiphilic polymer F127 (a polyethylene glycol-polypropylene glycol block copolymer) carries the hydrophobic HCPs and self-assembles into micelles in water, forming highly fluorescent HCP micelles. The micelle-bound conjugated polymers detect nitroaromatic analytes effectively in water and show an increased sensitivity compared to the sensing of nitroaromatics in organic solvents. The nitroarenes are also discriminated in water using this four-element chemical tongue.

Towards the Development of a Low-Cost Device for the Detection of Explosives Vapors by Fluorescence Quenching of Conjugated Polymers in Solid Matrices.

PubMed

Martelo, Liliana M; das Neves, Tiago F Pimentel; Figueiredo, João; Marques, Lino; Fedorov, Alexander; Charas, Ana; Berberan-Santos, Mário N; Burrows, Hugh D

2017-11-03

Conjugated polymers (CPs) have proved to be promising chemosensory materials for detecting nitroaromatic explosives vapors, as they quickly convert a chemical interaction into an easily-measured high-sensitivity optical output. The nitroaromatic analytes are strongly electron-deficient, whereas the conjugated polymer sensing materials are electron-rich. As a result, the photoexcitation of the CP is followed by electron transfer to the nitroaromatic analyte, resulting in a quenching of the light-emission from the conjugated polymer. The best CP in our studies was found to be poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-bithiophene] (F8T2). It is photostable, has a good absorption between 400 and 450 nm, and a strong and structured fluorescence around 550 nm. Our studies indicate up to 96% quenching of light-emission, accompanied by a marked decrease in the fluorescence lifetime, upon exposure of the films of F8T2 in ethyl cellulose to nitrobenzene (NB) and 1,3-dinitrobenzene (DNB) vapors at room temperature. The effects of the polymeric matrix, plasticizer, and temperature have been studied, and the morphology of films determined by scanning electron microscopy (SEM) and confocal fluorescence microscopy. We have used ink jet printing to produce sensor films containing both sensor element and a fluorescence reference. In addition, a high dynamic range, intensity-based fluorometer, using a laser diode and a filtered photodiode was developed for use with this system.

Amplitude and phase controlled adaptive optics system

NASA Astrophysics Data System (ADS)

Pham, Ich; Ma, Sam

2006-06-01

An adaptive optics (AO) system is used to control the deformable mirror (DM) actuators for compensating the optical effects introduced by the turbulence in the Earth's atmosphere and distortions produced by the optical elements between the distant object and its local sensor. The typical AO system commands the DM actuators while minimizing the measured wave front (WF) phase error. This is known as the phase conjugator system, which does not work well in the strong scintillation condition because both amplitude and phase are corrupted along the propagation path. In order to compensate for the wave front amplitude, a dual DM field conjugator system may be used. The first and second DM compensate for the amplitude and the phase respectively. The amplitude controller requires the mapping from DM1 actuator command to DM2 intensity. This can be obtained from either a calibration routine or an intensity transport equation, which relates the phase to the intensity. Instead of a dual-DM, a single Spatial Light Modulator (SLM) may control the amplitude and phase independently. The technique uses the spatial carrier frequency and the resulting intensity is related to the carrier modulation, while the phase is the average carrier phase. The dynamical AO performance using the carrier modulation is limited by the actuator frequency response and not by the computational load of the controller algorithm. Simulation of the proposed field conjugator systems show significant improvement for the on-axis performance compared to the phase conjugator system.

Toxin Plasmids of Clostridium perfringens

PubMed Central

Li, Jihong; Adams, Vicki; Bannam, Trudi L.; Miyamoto, Kazuaki; Garcia, Jorge P.; Uzal, Francisco A.; Rood, Julian I.

2013-01-01

SUMMARY In both humans and animals, Clostridium perfringens is an important cause of histotoxic infections and diseases originating in the intestines, such as enteritis and enterotoxemia. The virulence of this Gram-positive, anaerobic bacterium is heavily dependent upon its prolific toxin-producing ability. Many of the ∼16 toxins produced by C. perfringens are encoded by large plasmids that range in size from ∼45 kb to ∼140 kb. These plasmid-encoded toxins are often closely associated with mobile elements. A C. perfringens strain can carry up to three different toxin plasmids, with a single plasmid carrying up to three distinct toxin genes. Molecular Koch's postulate analyses have established the importance of several plasmid-encoded toxins when C. perfringens disease strains cause enteritis or enterotoxemias. Many toxin plasmids are closely related, suggesting a common evolutionary origin. In particular, most toxin plasmids and some antibiotic resistance plasmids of C. perfringens share an ∼35-kb region containing a Tn916-related conjugation locus named tcp (transfer of clostridial plasmids). This tcp locus can mediate highly efficient conjugative transfer of these toxin or resistance plasmids. For example, conjugative transfer of a toxin plasmid from an infecting strain to C. perfringens normal intestinal flora strains may help to amplify and prolong an infection. Therefore, the presence of toxin genes on conjugative plasmids, particularly in association with insertion sequences that may mobilize these toxin genes, likely provides C. perfringens with considerable virulence plasticity and adaptability when it causes diseases originating in the gastrointestinal tract. PMID:23699255

Construction of conjugative gene transfer system between E. coli and moderately thermophilic, extremely acidophilic Acidithiobacillus caldus MTH-04.

PubMed

Liu, Xiangmei; Lin, Jianqun; Zhang, Zheng; Bian, Jiang; Zhao, Qing; Liu, Ying; Lin, Jianqiang; Yan, Wangming

2007-01-01

A genetic transfer system for introducing foreign genes to biomining microorganisms is urgently needed. Thus, a conjugative gene transfer system was investigated for a moderately thermophilic, extremely acidophilic biomining bacterium, Acidithiobacillus caldus MTH-04. The broad-host-range IncP plasmids RP4 and R68.45 were transferred directly into A. caldus MTH-04 from Escherichia coli by conjugation at relatively high frequencies. Additionally the broad-host-range IncQ plasmids pJRD215, pVLT33, and pVLT35 were also transferred into A. caldus MTH-04 with the help of plasmid RP4 or strains with plasmid RP4 integrated into their chromosome, such as E. coli SM10. The Km(r) and Sm(r) selectable markers from these plasmids were successfully expressed in A. caldus MTH-04. Futhermore, the IncP and IncQ plasmids were transferred back into E. coli cells from A. caldus MTH-04, thereby confirming the initial transfer of these plasmids from E. coli to A. caldus MTH-04. All the IncP and IncQ plasmids studied were stable in A. caldus MTH-04. Consequently, this development of a conjugational system for A. caldus MTH-04 will greatly facilitate its genetic study.

Next generation calmodulin affinity purification: Clickable calmodulin facilitates improved protein purification

PubMed Central

Kinzer-Ursem, Tamara L.

2018-01-01

As the proteomics field continues to expand, scientists are looking to integrate cross-disciplinary tools for studying protein structure, function, and interactions. Protein purification remains a key tool for many characterization studies. Calmodulin (CaM) is a calcium-binding messenger protein with over a hundred downstream binding partners, and is involved in a host of physiological processes, from learning and memory to immune and cardiac function. To facilitate biophysical studies of calmodulin, researchers have designed a site-specific labeling process for use in bioconjugation applications while maintaining high levels of protein activity. Here, we present a platform for selective conjugation of calmodulin directly from clarified cell lysates under bioorthogonal reaction conditions. Using a chemoenzymatically modified calmodulin, we employ popular click chemistry reactions for the conjugation of calmodulin to Sepharose resin, thereby streamlining a previously multi-step purification and conjugation process. We show that this “next-generation” calmodulin-Sepharose resin is not only easy to produce, but is also able to purify more calmodulin-binding proteins per volume of resin than traditional calmodulin-Sepharose resins. We expect these methods to be translatable to other proteins of interest and to other conjugation applications such as surface-based assays for the characterization of protein-protein interaction dynamics. PMID:29864125

The dual role of deposited microbead plug (DMBP): a blood filter and a conjugate reagent carrier toward point-of-care microfluidic immunoassay.

PubMed

Li, Chunyu; Liu, Chong; Xu, Zheng; Li, Jingmin

2012-08-15

To set up a point-of-care whole-blood immunoassay system, sample preparation and on-chip storage of conjugate reagents are indispensable functional units. Here, we merge these functions into a deposited microbead plug (DMBP) to simultaneously play the roles of a blood filter and a conjugate reagent carrier. The DMBP was easily fabricated by the use of natural deposition of beads without the need of weirs. Conjugate reagents (FITC labeled antibodies used here) were incorporated into the DMBP during the assembly of the DMBP. To demonstrate the ability of the DMBP, we constructed a DMBP-based microfluidic chip and used it for the detection of human IgG (hIgG). The DMBP enabled to remove blood cells from whole blood and provide the pure plasma for the downstream on-chip immunoreactions. The release of reconstituted FITC labeled antibodies from the DMBP was controlled in a passive fashion. Dry FITC labeled antibodies retained at least 81% of their activity after 60 days of storage at the room temperature. The DMBP presented here makes an important step towards the development of the self-contained, integrated, sample-to-answer microfluidic chips for point-of-care diagnostics. Copyright © 2012 Elsevier B.V. All rights reserved.

Conjugates of desferrioxamine B (DFOB) with derivatives of adamantane or with orally available chelators as potential agents for treating iron overload.

PubMed

Liu, Joe; Obando, Daniel; Schipanski, Liam G; Groebler, Ludwig K; Witting, Paul K; Kalinowski, Danuta S; Richardson, Des R; Codd, Rachel

2010-02-11

Desferrioxamine B (DFOB) conjugates with adamantane-1-carboxylic acid, 3-hydroxyadamantane-1-carboxylic acid, 3,5-dimethyladamantane-1-carboxylic acid, adamantane-1-acetic acid, 4-methylphenoxyacetic acid, 3-hydroxy-2-methyl-4-oxo-1-pyridineacetic acid (N-acetic acid derivative of deferiprone), or 4-[3,5-bis(2-hydroxyphenyl)-1,2,4-triazol-1-yl]benzoic acid (deferasirox) were prepared and the integrity of Fe(III) binding of the compounds was established from electrospray ionization mass spectrometry and RP-HPLC measurements. The extent of intracellular (59)Fe mobilized by the DFOB-3,5-dimethyladamantane-1-carboxylic acid adduct was 3-fold greater than DFOB alone, and the IC(50) value of this adduct was 6- or 15-fold greater than DFOB in two different cell types. The relationship between logP and (59)Fe mobilization for the DFOB conjugates showed that maximal mobilization of intracellular (59)Fe occurred at a logP value approximately 2.3. This parameter, rather than the affinity for Fe(III), appears to influence the extent of intracellular (59)Fe mobilization. The low toxicity-high Fe mobilization efficacy of selected adamantane-based DFOB conjugates underscores the potential of these compounds to treat iron overload disease in patients with transfusional-dependent disorders such as beta-thalassemia.

Isotropic matrix elements of the collision integral for the Boltzmann equation

NASA Astrophysics Data System (ADS)

Ender, I. A.; Bakaleinikov, L. A.; Flegontova, E. Yu.; Gerasimenko, A. B.

2017-09-01

We have proposed an algorithm for constructing matrix elements of the collision integral for the nonlinear Boltzmann equation isotropic in velocities. These matrix elements have been used to start the recurrent procedure for calculating matrix elements of the velocity-nonisotropic collision integral described in our previous publication. In addition, isotropic matrix elements are of independent interest for calculating isotropic relaxation in a number of physical kinetics problems. It has been shown that the coefficients of expansion of isotropic matrix elements in Ω integrals are connected by the recurrent relations that make it possible to construct the procedure of their sequential determination.

Nonlinear optical properties of rigid-rod polymers

NASA Technical Reports Server (NTRS)

Trimmer, Mark S.; Wang, Ying

1992-01-01

The purpose of this research project was to integrate enhanced third order nonlinear optical (NLO) properties, especially high x(exp (3)) (greater than 10(exp -8) esu), into Maxdem's novel conjugated rigid-rod polymers while retaining their desirable processing, mechanical, and thermal properties. This work primarily involved synthetic approaches to optimized materials.

An exterior Poisson solver using fast direct methods and boundary integral equations with applications to nonlinear potential flow

NASA Technical Reports Server (NTRS)

Young, D. P.; Woo, A. C.; Bussoletti, J. E.; Johnson, F. T.

1986-01-01

A general method is developed combining fast direct methods and boundary integral equation methods to solve Poisson's equation on irregular exterior regions. The method requires O(N log N) operations where N is the number of grid points. Error estimates are given that hold for regions with corners and other boundary irregularities. Computational results are given in the context of computational aerodynamics for a two-dimensional lifting airfoil. Solutions of boundary integral equations for lifting and nonlifting aerodynamic configurations using preconditioned conjugate gradient are examined for varying degrees of thinness.

Isolation of a conjugative F-like plasmid from a multidrug-resistant Escherichia coli strain CM6 using tandem shock wave-mediated transformation.

PubMed

Soto-Alonso, G; Cruz-Medina, J A; Caballero-Pérez, J; Arvizu-Hernández, I; Ávalos-Esparza, L M; Cruz-Hernández, A; Romero-Gómez, S; Rodríguez, A L; Pastrana-Martínez, X; Fernández, F; Loske, A M; Campos-Guillén, J

2015-07-01

Genetic characterization of plasmids from bacterial strains provides insight about multidrug resistance. Ten wild type Escherichia coli (E. coli) strains isolated from cow fecal samples were characterized by their antibiotic resistance profile, plasmid patterns and three different identification methods. From one of the strains, a fertility factor-like plasmid was replicated using tandem shock wave-mediated transformation. Underwater shock waves with a positive pressure peak of up to approximately 40 MPa, followed by a pressure trough of approximately -19 MPa were generated using an experimental piezoelectric shock wave source. Three different shock wave energies and a fixed delay of 750 μs were used to study the relationship between energy and transformation efficiency (TE), as well as the influence of shock wave energy on the integrity of the plasmid. Our results showed that the mean shock wave-mediated TE and the integrity of the large plasmid (~70 kb) were reduced significantly at the energy levels tested. The sequencing analysis of the plasmid revealed a high identity to the pHK17a plasmid, including the replication system, which was similar to the plasmid incompatibility group FII. It also showed that it carried an extended spectrum beta-lactamase gene, ctx-m-14. Furthermore, diverse genes for the conjugative mechanism were identified. Our results may be helpful in improving methodologies for conjugative plasmid transfer and directly selecting the most interesting plasmids from environmental samples. Copyright © 2015 Elsevier B.V. All rights reserved.

A study of methods to predict and measure the transmission of sound through the walls of light aircraft. Integration of certain singular boundary element integrals for applications in linear acoustics

NASA Technical Reports Server (NTRS)

Zimmerle, D.; Bernhard, R. J.

1985-01-01

An alternative method for performing singular boundary element integrals for applications in linear acoustics is discussed. The method separates the integral of the characteristic solution into a singular and nonsingular part. The singular portion is integrated with a combination of analytic and numerical techniques while the nonsingular portion is integrated with standard Gaussian quadrature. The method may be generalized to many types of subparametric elements. The integrals over elements containing the root node are considered, and the characteristic solution for linear acoustic problems are examined. The method may be generalized to most characteristic solutions.

Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones.

PubMed

Garcillán-Barcia, M Pilar; Ruiz del Castillo, Belén; Alvarado, Andrés; de la Cruz, Fernando; Martínez-Martínez, Luis

2015-01-01

Degenerate Primer MOB Typing is a PCR-based protocol for the classification of γ-proteobacterial transmissible plasmids in five phylogenetic relaxase MOB families. It was applied to a multiresistant E. coli collection, previously characterized by PCR-based replicon-typing, in order to compare both methods. Plasmids from 32 clinical isolates of multiresistant E. coli (19 extended spectrum beta-lactamase producers and 13 non producers) and their transconjugants were analyzed. A total of 95 relaxases were detected, at least one per isolate, underscoring the high potential of these strains for antibiotic-resistance transmission. MOBP12 and MOBF12 plasmids were the most abundant. Most MOB subfamilies detected were present in both subsets of the collection, indicating a shared mobilome among multiresistant E. coli. The plasmid profile obtained by both methods was compared, which provided useful data upon which decisions related to the implementation of detection methods in the clinic could be based. The phylogenetic depth at which replicon and MOB-typing classify plasmids is different. While replicon-typing aims at plasmid replication regions with non-degenerate primers, MOB-typing classifies plasmids into relaxase subfamilies using degenerate primers. As a result, MOB-typing provides a deeper phylogenetic depth than replicon-typing and new plasmid groups are uncovered. Significantly, MOB typing identified 17 plasmids and an integrative and conjugative element, which were not detected by replicon-typing. Four of these backbones were different from previously reported elements. Copyright © 2014 Elsevier Inc. All rights reserved.

Integration Testing of Space Flight Systems

NASA Technical Reports Server (NTRS)

Sowards, Stephanie; Honeycutt, Timothy

2008-01-01

This paper discusses the benefits of conducting multi-system integration testing of space flight elements in lieu of merely shipping and shooting to the launch site and launching. "Ship and shoot" is a philosophy that proposes to transport flight elements directly from the factory to the launch site and begin the mission without further testing. Integration testing, relevant to validation testing in this context, is a risk mitigation effort that builds upon the individual element and system levels of qualification and acceptance tests, greatly improving the confidence of operations in space. The International Space Station Program (ISSP) experience is the focus of most discussions from a historical perspective, while proposed integration testing of the Constellation Program is also discussed. The latter will include Multi-Element Integration Testing (MElT) and Flight Element Integration Testing (FElT).

Chemical patterning on preformed porous silicon photonic crystals: towards multiplex detection of protease activity at precise positions†Electronic supplementary information (ESI) available: SEM images, XPS result and more optical reflectivity data. See DOI: 10.1039/c4tb00281dClick here for additional data file.

PubMed

Zhu, Ying; Soeriyadi, Alexander H; Parker, Stephen G; Reece, Peter J; Gooding, J Justin

2014-06-21

Porous silicon (PSi) rugate filters modified with alkyne-terminated monolayers were chemically patterned using a combination of photolithography of photoresist and click chemistry. Two chemical functionalities were obtained by conjugating, via click reactions, ethylene glycol moieties containing two different terminal groups to discrete areas towards the exterior of a PSi rugate filter. The patterning of biological species to the functionalized surface was demonstrated through the conjugation of fluorescein isothiocyanate labelled bovine serum albumin (FITC-BSA). Fluorescence microscopy showed selective positioning of FITC-BSA at discretely functionalized areas. Meanwhile, the optical information from precisely defined positions on the patterned surface was monitored by optical reflectivity measurements. The optical measurements revealed successful step-wise chemical functionalization followed by immobilization of gelatin. Multiplex detection of protease activity from different array elements on the patterned surface was demonstrated by monitoring the blue shifts in the reflectivity spectra resulted from the digestion of gelatin by subtilisin. Precise information from both individual elements and average population was acquired. This technique is important for the development of PSi into a microarray platform for highly parallel biosensing applications, especially for cell-based assays.

Characterization of Bacilli Isolated from the Confined Environments of the Antarctic Concordia Station and the International Space Station

NASA Astrophysics Data System (ADS)

Timmery, Sophie; Hu, Xiaomin; Mahillon, Jacques

2011-05-01

Bacillus and related genera comprise opportunist and pathogen species that can threaten the health of a crew in confined stations required for long-term missions. In this study, 43 Bacilli from confined environments, that is, the Antarctic Concordia station and the International Space Station, were characterized in terms of virulence and plasmid exchange potentials. No specific virulence feature, such as the production of toxins or unusual antibiotic resistance, was detected. Most of the strains exhibited small or large plasmids, or both, some of which were related to the replicons of the Bacillus anthracis pXO1 and pXO2 virulence elements. One conjugative element, the capacity to mobilize and retromobilize small plasmids, was detected in a Bacillus cereus sensu lato isolate. Six out of 25 tested strains acquired foreign DNA by conjugation. Extremophilic bacteria were identified and exhibited the ability to grow at high pH and salt concentrations or at low temperatures. Finally, the clonal dispersion of an opportunist isolate was demonstrated in the Concordia station. Taken together, these results suggest that the virulence potential of the Bacillus isolates in confined environments tends to be low but genetic transfers could contribute to its capacity to spread.

Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates

PubMed Central

Botzanowski, Thomas; Erb, Stéphane; Hernandez-Alba, Oscar; Ehkirch, Anthony; Colas, Olivier; Wagner-Rousset, Elsa; Rabuka, David; Beck, Alain; Drake, Penelope M.; Cianférani, Sarah

2017-01-01

ABSTRACT Antibody-drug conjugates (ADCs) have emerged as a family of compounds with promise as efficient immunotherapies. First-generation ADCs were generated mostly via reactions on either lysine side-chain amines or cysteine thiol groups after reduction of the interchain disulfide bonds, resulting in heterogeneous populations with a variable number of drug loads per antibody. To control the position and the number of drug loads, new conjugation strategies aiming at the generation of more homogeneous site-specific conjugates have been developed. We report here the first multi-level characterization of a site-specific ADC by state-of-the-art mass spectrometry (MS) methods, including native MS and its hyphenation to ion mobility (IM-MS). We demonstrate the versatility of native MS methodologies for site-specific ADC analysis, with the unique ability to provide several critical quality attributes within one single run, along with a direct snapshot of ADC homogeneity/heterogeneity without extensive data interpretation. The capabilities of native IM-MS to directly access site-specific ADC conformational information are also highlighted. Finally, the potential of these techniques for assessing an ADC's heterogeneity/homogeneity is illustrated by comparing the analytical characterization of a site-specific DAR4 ADC to that of first-generation ADCs. Altogether, our results highlight the compatibility, versatility, and benefits of native MS approaches for the analytical characterization of all types of ADCs, including site-specific conjugates. Thus, we envision integrating native MS and IM-MS approaches, even in their latest state-of-the-art forms, into workflows that benchmark bioconjugation strategies. PMID:28406343

A computerized symbolic integration technique for development of triangular and quadrilateral composite shallow-shell finite elements

NASA Technical Reports Server (NTRS)

Anderson, C. M.; Noor, A. K.

1975-01-01

Computerized symbolic integration was used in conjunction with group-theoretic techniques to obtain analytic expressions for the stiffness, geometric stiffness, consistent mass, and consistent load matrices of composite shallow shell structural elements. The elements are shear flexible and have variable curvature. A stiffness (displacement) formulation was used with the fundamental unknowns consisting of both the displacement and rotation components of the reference surface of the shell. The triangular elements have six and ten nodes; the quadrilateral elements have four and eight nodes and can have internal degrees of freedom associated with displacement modes which vanish along the edges of the element (bubble modes). The stiffness, geometric stiffness, consistent mass, and consistent load coefficients are expressed as linear combinations of integrals (over the element domain) whose integrands are products of shape functions and their derivatives. The evaluation of the elemental matrices is divided into two separate problems - determination of the coefficients in the linear combination and evaluation of the integrals. The integrals are performed symbolically by using the symbolic-and-algebraic-manipulation language MACSYMA. The efficiency of using symbolic integration in the element development is demonstrated by comparing the number of floating-point arithmetic operations required in this approach with those required by a commonly used numerical quadrature technique.

Dip-pen patterning of poly(9,9-dioctylfluorene) chain-conformation-based nano-photonic elements.

PubMed

Perevedentsev, Aleksandr; Sonnefraud, Yannick; Belton, Colin R; Sharma, Sanjiv; Cass, Anthony E G; Maier, Stefan A; Kim, Ji-Seon; Stavrinou, Paul N; Bradley, Donal D C

2015-01-19

Metamaterials are a promising new class of materials, in which sub-wavelength physical structures, rather than variations in chemical composition, can be used to modify the nature of their interaction with electromagnetic radiation. Here we show that a metamaterials approach, using a discrete physical geometry (conformation) of the segments of a polymer chain as the vector for a substantial refractive index change, can be used to enable visible wavelength, conjugated polymer photonic elements. In particular, we demonstrate that a novel form of dip-pen nanolithography provides an effective means to pattern the so-called β-phase conformation in poly(9,9-dioctylfluorene) thin films. This can be done on length scales ≤500 nm, as required to fabricate a variety of such elements, two of which are theoretically modelled using complex photonic dispersion calculations.

Peptide Conjugates of Benzene Carboxylic Acids as Agonists and Antagonists of Amylin Aggregation.

PubMed

Profit, Adam A; Vedad, Jayson; Desamero, Ruel Z B

2017-02-15

Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37 residue peptide hormone that is stored and co-secreted with insulin. hIAPP plays a pivotal role in type 2 diabetes and is the major component of amyloid deposits found in the pancreas of patients afflicted with the disease. The self-assembly of hIAPP and the formation of amyloid is linked to the death of insulin producing β-cells. Recent findings suggest that soluble hIAPP oligomers are the cytotoxic species responsible for β-cell loss whereas amyloid fibrils themselves may indeed be innocuous. Potential avenues of therapeutic intervention include the development of compounds that prevent hIAPP self-assembly as well as those that reduce or eliminate lag time and rapidly accelerate the formation of amyloid fibrils. Both of these approaches minimize temporal exposure to soluble cytotoxic hIAPP oligomers. Toward this end our laboratory has pursued an electrostatic repulsion approach to the development of potential inhibitors and modulators of hIAPP self-assembly. Peptide conjugates were constructed in which benzene carboxylic acids of varying charge were employed as electrostatic disrupting elements and appended to the N-terminal of the hIAPP 22-29 (NFGAILSS) self-recognition sequence. The self-assembly kinetics of conjugates were characterized by turbidity measurements and the structure of aggregates probed by Raman and CD spectroscopy while the morphology was assessed using transmission electron microscopy. Several benzene carboxylic acid peptide conjugates failed to self-assemble and some were found to inhibit the aggregation of full-length amylin while others served to enhance the rate of amyloid formation and/or increase the yield of amyloid produced. Studies reveal that the geometric display of free carboxylates on the benzene ring of the conjugates plays an important role in the activity of conjugates. In addition, a number of free benzene carboxylic acids were found to modulate amylin self-assembly on their own. The results of these investigations confirm the viability of the electrostatic repulsion approach to the modulation of amyloid formation and may aid the design and development of potential therapeutic agents.

Chemiluminescence imaging ELISA using an imprinted polymer as the recognition element instead of an antibody.

PubMed

Surugiu, I; Danielsson, B; Ye, L; Mosbach, K; Haupt, K

2001-02-01

An imaging assay analogous to competitive enzyme immunoassays has been developed using a molecularly imprinted polymer instead of an antibody. The antigen 2,4-dichlorophenoxyacetic acid (2,4-D) was labeled with tobacco peroxidase, and the chemiluminescence reaction of luminol was used for detection. Microtiter plates (96 or 384 wells) were coated with polymer microspheres imprinted with 2,4-D, which were fixed in place by using poly(vinyl alcohol) as glue. In a competitive mode, the analyte-peroxidase conjugate was incubated with the free analyte in the microtiter plate, after which the bound fraction of the conjugate was quantified. After addition of the chemiluminescent substrates, light emission was measured in a high-throughput imaging format with a CCD camera. Calibration curves corresponding to analyte concentrations ranging from 0.01 to 100 microg/mL were obtained.

The Gemini-South MCAO operational model: insights on a new era of telescope operation

NASA Astrophysics Data System (ADS)

Trancho, Gelys; Bec, Matthieu; Artigau, Etienne; d'Orgeville, Celine; Gratadour, Damien; Rigaut, Francois J.; Walls, Brian

2008-07-01

The Gemini Observatory is implementing a Multi-Conjugate Adaptive Optics (MCAO) system as a facility instrument for the Gemini South telescope (GeMS). The system will include 5 Laser Guide Stars, 3 Natural Guide Stars, and 3 deformable mirrors, optically conjugated at different altitudes, to achieve near-uniform atmospheric compensation over a one arc minute square field of view. This setup implies some level of operational complexity. In this paper we describe how GeMS will be integrated into the flow of Gemini operations, from the observing procedures necessary to execute the programs in the queue (telescope control software, observing tools, sequence executor) to the safety implementation needed such as spotters/ASCAM, space command and laser traffic control software.

An Integrated Laboratory Approach toward the Preparation of Conductive Poly(phenylene vinylene) Polymers

ERIC Educational Resources Information Center

Knoerzer, Timm A.; Balaich, Gary J.; Miller, Hannah A.; Iacono, Scott T.

2014-01-01

Poly(phenylene vinylene) (PPV) represents an important class of conjugated, conducting polymers that have been readily exploited in the preparation of organic electronic materials. In this experiment, students prepare a PPV polymer via a facile multistep synthetic sequence with robust spectroscopic evaluation of synthetic intermediates and the…

Investigating bioconjugation by atomic force microscopy

PubMed Central

2013-01-01

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures. PMID:23855448

Investigating bioconjugation by atomic force microscopy.

PubMed

Tessmer, Ingrid; Kaur, Parminder; Lin, Jiangguo; Wang, Hong

2013-07-15

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.

Mobile glasses-free 3D using compact waveguide hologram

NASA Astrophysics Data System (ADS)

Pyun, K.; Choi, C.; Morozov, A.; Putilin, A.; Bovsunovskiy, I.; Kim, S.; Ahn, J.; Lee, H.-S.; Lee, S.

2013-02-01

The exploding mobile communication devices make 3D data available anywhere anytime. However, to record and reconstruct 3D, the huge number of optical components is often required, which makes overall device size bulky and image quality degraded due to the error-prone tuning. In addition, if additional glass is required, then user experience of 3D is exhausting and unpleasant. Holography is the ultimate 3D that users experience natural 3D in every direction. For mobile glasses-free 3D experience, it is critical to make holography device that can be as compact and integrated as possible. For reliable and economical mass production, integrated optics is needed as integrated circuits in semiconductor industry. Thus, we propose mobile glasses-free 3D using compact waveguide hologram in terms of overall device sizes, quantity of elements and combined functionality of each element. The main advantages of proposed solution are as follows: First, this solution utilizes various integral optical elements, where each of them is a united not adjustable optical element, replacing separate and adjustable optical elements with various forms and configurations. Second, geometrical form of integral elements provides small sizes of whole device. Third, geometrical form of integral elements allows creating flat device. And finally, absence of adjustable elements provide rigidly of whole device. The usage of integrated optical means based on waveguide holographic elements allows creating a new type of compact and high functional devices for mobile glasses-free 3D applications such as mobile medical 3D data visualization.

Electronic Switch Arrays for Managing Microbattery Arrays

NASA Technical Reports Server (NTRS)

Mojarradi, Mohammad; Alahmad, Mahmoud; Sukumar, Vinesh; Zghoul, Fadi; Buck, Kevin; Hess, Herbert; Li, Harry; Cox, David

2008-01-01

Integrated circuits have been invented for managing the charging and discharging of such advanced miniature energy-storage devices as planar arrays of microscopic energy-storage elements [typically, microscopic electrochemical cells (microbatteries) or microcapacitors]. The architecture of these circuits enables implementation of the following energy-management options: dynamic configuration of the elements of an array into a series or parallel combination of banks (subarrarys), each array comprising a series of parallel combination of elements; direct addressing of individual banks for charging/or discharging; and, disconnection of defective elements and corresponding reconfiguration of the rest of the array to utilize the remaining functional elements to obtain the desited voltage and current performance. An integrated circuit according to the invention consists partly of a planar array of field-effect transistors that function as switches for routing electric power among the energy-storage elements, the power source, and the load. To connect the energy-storage elements to the power source for charging, a specific subset of switches is closed; to connect the energy-storage elements to the load for discharging, a different specific set of switches is closed. Also included in the integrated circuit is circuitry for monitoring and controlling charging and discharging. The control and monitoring circuitry, the switching transistors, and interconnecting metal lines are laid out on the integrated-circuit chip in a pattern that registers with the array of energy-storage elements. There is a design option to either (1) fabricate the energy-storage elements in the corresponding locations on, and as an integral part of, this integrated circuit; or (2) following a flip-chip approach, fabricate the array of energy-storage elements on a separate integrated-circuit chip and then align and bond the two chips together.

Subgap Absorption in Conjugated Polymers

DOE R&D Accomplishments Database

Sinclair, M.; Seager, C. H.; McBranch, D.; Heeger, A. J; Baker, G. L.

1991-01-01

Along with X{sup (3)}, the magnitude of the optical absorption in the transparent window below the principal absorption edge is an important parameter which will ultimately determine the utility of conjugated polymers in active integrated optical devices. With an absorptance sensitivity of < 10{sup {minus}5}, Photothermal Deflection Spectroscopy (PDS) is ideal for determining the absorption coefficients of thin films of transparent'' materials. We have used PDS to measure the optical absorption spectra of the conjugated polymers poly(1,4-phenylene-vinylene) (and derivitives) and polydiacetylene-4BCMU in the spectral region from 0.55 eV to 3 eV. Our spectra show that the shape of the absorption edge varies considerably from polymer to polymer, with polydiacetylene-4BCMU having the steepest absorption edge. The minimum absorption coefficients measured varied somewhat with sample age and quality, but were typically in the range 1 cm{sup {minus}1} to 10 cm{sup {minus}1}. In the region below 1 eV, overtones of C-H stretching modes were observed, indicating that further improvements in transparency in this spectral region might be achieved via deuteration of fluorination.

Stability issues in the determination of 19 urinary (free and conjugated) monohydroxy polycyclic aromatic hydrocarbons.

PubMed

Gaudreau, Éric; Bérubé, René; Bienvenu, Jean-François; Fleury, Normand

2016-06-01

Data on the stability of monohydroxy polycyclic aromatic hydrocarbons (OH-PAHs; metabolites of PAHs) in urine are needed in order to effectively study the effects of PAHs in the body, but the relevant data are not available in the literature. Therefore, in this work, we investigated the stability of OH-PAHs in urine. For each OH-PAH studied, the free form (as opposed to the conjugated form) comprised <10 % of the total OH-PAH in urine samples obtained from a normal population, except for 9-OH-phenanthrene (where the free form represented 22.2 % of the total 9-OH-phenanthrene). 1-Naphthol and 9-OH-phenanthrene were found to be less stable in their free forms in urine than in their conjugated forms when the urine samples were stored at 4 °C or room temperature. Free 3-OH-fluoranthene was also very unstable at 4 °C or room temperature. The conjugated forms of the OH-PAHs were more stable than their corresponding free forms. However, the free and conjugated forms of all the OH-PAHs were stable in urine at -20 °C and -80 °C. A freeze and thaw assay also revealed that freezing and thawing had minimal impact on the stability of the OH-PAHs in urine. For the derivatized extracts, storing the samples under an argon atmosphere at 4 °C was found to maintain sample integrity. In order to measure the stabilities of 19 hydroxylated metabolites of PAHs in urine, we developed a method with sensitivity in the low pg/mL range using nine labeled internal standards. This method combined enzymatic deconjugation with liquid-liquid extraction, derivatization with N-methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA), and gas chromatography/tandem mass spectrometry (GC-MS/MS). Graphical abstract Stability of the conjugated forms of the OH-PAHs versus free forms (e.g. 1-naphthol).

A New Approach in the Preparation of Dendrimer-Based Bifunctional Diethylenetriaminepentaacetic Acid MR Contrast Agent Derivatives

PubMed Central

Nwe, Kido; Xu, Heng; Regino, Celeste Aida S.; Bernardo, Marcelino; Ileva, Lilia; Riffle, Lisa; Wong, Karen J.; Brechbiel, Martin W.

2009-01-01

In this paper we report a new method to prepare and characterize a contrast agent based on a fourth-generation (G4) polyamidoamine (PAMAM) dendrimer conjugated to the gadolinium complex of the bifunctional diethylenetriamine pentaacetic acid derivative (1B4M-DTPA). The method involves pre-forming the metal-ligand chelate in alcohol prior to conjugation to the dendrimer. The dendrimer-based agent was purified by a Sephadex® G-25 column and characterized by elemental analysis. The analysis and SEHPLC data gave a chelate to dendrimer ratio of 30:1 suggesting conjugation at approximately every other amine terminal on the dendrimer. Molar relaxivity of the agent measured at pH 7.4 displayed a higher value than that of the analogous G4 dendrimer based agent prepared by the post-metal incorporation method (r1 = 26.9 vs. 13.9 mM-1s-1 at 3T and 22°C). This is hypothesized to be due to the higher hydrophobicity of this conjugate, and the lack of available charged carboxylate groups from non-complexed free ligands that might coordinate to the metal and thus also reduce water exchange sites. Additionally, the distribution populations of compounds that result from the post-metal incorporation route are eliminated from the current product simplifying characterization as quality control issues pertaining to the production of such agents for clinical use as MR contrast agents. In vivo imaging in mice showed a reasonably fast clearance (t1/2 = 24 min) suggesting a viable agent for use in clinical application. PMID:19555072

A new approach in the preparation of dendrimer-based bifunctional diethylenetriaminepentaacetic acid MR contrast agent derivatives.

PubMed

Nwe, Kido; Xu, Heng; Regino, Celeste Aida S; Bernardo, Marcelino; Ileva, Lilia; Riffle, Lisa; Wong, Karen J; Brechbiel, Martin W

2009-07-01

In this paper, we report a new method to prepare and characterize a contrast agent based on a fourth-generation (G4) polyamidoamine (PAMAM) dendrimer conjugated to the gadolinium complex of the bifunctional diethylenetriamine pentaacetic acid derivative (1B4M-DTPA). The method involves preforming the metal-ligand chelate in alcohol prior to conjugation to the dendrimer. The dendrimer-based agent was purified by a Sephadex G-25 column and characterized by elemental analysis. The analysis and SE-HPLC data gave a chelate to dendrimer ratio of 30:1 suggesting conjugation at approximately every other amine terminal on the dendrimer. Molar relaxivity of the agent measured at pH 7.4 displayed a higher value than that of the analogous G4 dendrimer based agent prepared by the postmetal incorporation method (r(1) = 26.9 vs 13.9 mM(-1) s(-1) at 3 T and 22 degrees C). This is hypothesized to be due to the higher hydrophobicity of this conjugate and the lack of available charged carboxylate groups from noncomplexed free ligands that might coordinate to the metal and thus also reduce water exchange sites. Additionally, the distribution populations of compounds that result from the postmetal incorporation route are eliminated from the current product simplifying characterization as quality control issues pertaining to the production of such agents for clinical use as MR contrast agents. In vivo imaging in mice showed a reasonably fast clearance (t(1/2) = 24 min) suggesting a viable agent for use in clinical application.

Tailoring folic acid and methotrexate-attributed quantum dots for integrated cancer cell imaging and therapy

NASA Astrophysics Data System (ADS)

Fahmi, Mochamad Zakki; Chang, Jia-Yaw

2016-03-01

Potential application of folic acid and methotrexate-attributed AgInS2-ZnS quantum dots on both detection and therapeutic of cancer cell were intensively investigated on this study. In the initial step, the bright luminescent of QDs, with % QY up to 55.3, were synthesized with one-pot two-step process resulting narrow particle distribution and successfully transferred to water phase without significant effect on optical properties. The water-soluble AgInS2-ZnS quantum dots (QDs) encapsulated with oleylamine have been successfully prepared by ultrasonication assisting. Several aspect including QDs characterization, pH stability, ionic strength, and bonding properties were investigated to reach desired condition of water-soluble AgInS2-ZnS QDs. Folic acid was further conjugated to QDs for HeLa and MCF7 cancer cell imaging to performs the targeting capability. Moreover, folic acid is efficiently internalized into cell through the receptor-mediated endocytosis even when conjugated with a wide variety of molecules. Confocal imaging characterization further informs folic acid-conjugated AgInS2-ZnS QDs could most specific targeted to the human cervical (HeLa) cells. The therapeutic feature of QDs on HeLa cancer cell was conjugated by attributing methotrexate on the QDs, instead of folic acid, and the design could improve on inhibiting the cancer cell viability as well as its fluorescent intensity.

Poly(methacrylic acid)-Coated Gold Nanoparticles: Functional Platforms for Theranostic Applications.

PubMed

Yilmaz, Gokhan; Demir, Bilal; Timur, Suna; Becer, C Remzi

2016-09-12

The integration of drugs with nanomaterials have received significant interest in the efficient drug delivery systems. Conventional treatments with therapeutically active drugs may cause undesired side effects and, thus, novel strategies to perform these treatments with a combinatorial approach of therapeutic modalities are required. In this study, polymethacrylic acid coated gold nanoparticles (AuNP-PMAA), which were synthesized with reversible addition-fragmentation chain transfer (RAFT) polymerization, were combined with doxorubicin (DOX) as a model anticancer drug by creating a pH-sensitive hydrazone linkage in the presence of cysteine (Cys) and a cross-linker. Drug-AuNP conjugates were characterized via spectrofluorimetry, dynamic light scattering and zeta potential measurements as well as X-ray photoelectron spectroscopy. The particle size of AuNP-PMAA and AuNP-PMAA-Cys-DOX conjugate were calculated as found as 104 and 147 nm, respectively. Further experiments with different pH conditions (pH 5.3 and 7.4) also showed that AuNP-PMAA-Cys-DOX conjugate could release the DOX in a pH-sensitive way. Finally, cell culture applications with human cervix adenocarcinoma cell line (HeLa cells) demonstrated effective therapeutic impact of the final conjugate for both chemotherapy and radiation therapy by comparing free DOX and AuNP-PMAA independently. Moreover, cell imaging study was also an evidence that AuNP-PMAA-Cys-DOX could be a beneficial candidate as a diagnostic agent.

Numerical algorithms for finite element computations on concurrent processors

NASA Technical Reports Server (NTRS)

Ortega, J. M.

1986-01-01

The work of several graduate students which relate to the NASA grant is briefly summarized. One student has worked on a detailed analysis of the so-called ijk forms of Gaussian elemination and Cholesky factorization on concurrent processors. Another student has worked on the vectorization of the incomplete Cholesky conjugate method on the CYBER 205. Two more students implemented various versions of Gaussian elimination and Cholesky factorization on the FLEX/32.

Time Periodic Control of a Multi-Blade Helicopter.

DTIC Science & Technology

1988-05-01

part of an element of p X rotor inflow ratio; Langrangian multiplier; Poincare exponent H rotor inflow ratio with respect to the hub *P plane A...and a $ complex conjugate pair in the right- half plane resulting from ( the longitudinal velocity and pitch coupling. Without a horizontal tail, the ... Poincare Exponents . . .. 182 VI. Controller Gains ...... ................ 184 viii I ’Q List of Symbols Listed below are the principal symbols used in this

Rephasing invariants of the Cabibbo-Kobayashi- Maskawa matrix

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

Pérez R, H.; Kielanowski, P., E-mail: kiel@fis.cinvestav.mx; Juárez W, S. R., E-mail: rebeca@esfm.ipn.mx

2016-03-15

The paper is motivated by the importance of the rephasing invariance of the CKM (Cabibbo-Kobayashi-Maskawa) matrix observables. These observables appear in the discussion of the CP violation in the standard model (Jarlskog invariant) and also in the renormalization group equations for the quark Yukawa couplings. Our discussion is based on the general phase invariant monomials built out of the CKM matrix elements and their conjugates. We show that there exist 30 fundamental phase invariant monomials and 18 of them are a product of 4 CKM matrix elements and 12 are a product of 6 CKM matrix elements. In the mainmore » theorem we show that a general rephasing invariant monomial can be expressed as a product of at most five factors: four of them are fundamental phase invariant monomials and the fifth factor consists of powers of squares of absolute values of the CKM matrix elements. We also show that the imaginary part of any rephasing invariant monomial is proportional to the Jarlskog’s invariant J or is 0.« less

Multiple methods integration for structural mechanics analysis and design

NASA Technical Reports Server (NTRS)

Housner, J. M.; Aminpour, M. A.

1991-01-01

A new research area of multiple methods integration is proposed for joining diverse methods of structural mechanics analysis which interact with one another. Three categories of multiple methods are defined: those in which a physical interface are well defined; those in which a physical interface is not well-defined, but selected; and those in which the interface is a mathematical transformation. Two fundamental integration procedures are presented that can be extended to integrate various methods (e.g., finite elements, Rayleigh Ritz, Galerkin, and integral methods) with one another. Since the finite element method will likely be the major method to be integrated, its enhanced robustness under element distortion is also examined and a new robust shell element is demonstrated.

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes.

PubMed

Gufford, Brandon T; Robarge, Jason D; Eadon, Michael T; Gao, Hongyu; Lin, Hai; Liu, Yunlong; Desta, Zeruesenay; Skaar, Todd C

2018-04-01

Rifampin is a pleiotropic inducer of multiple drug metabolizing enzymes and transporters. This work utilized a global approach to evaluate rifampin effects on conjugating enzyme gene expression with relevance to human xeno- and endo-biotic metabolism. Primary human hepatocytes from 7 subjects were treated with rifampin (10 μmol/L, 24 hours). Standard methods for RNA-seq library construction, EZBead preparation, and NextGen sequencing were used to measure UDP-glucuronosyl transferase UGT, sulfonyltransferase SULT, N acetyltransferase NAT, and glutathione-S-transferase GST mRNA expression compared to vehicle control (0.01% MeOH). Rifampin-induced (>1.25-fold) mRNA expression of 13 clinically important phase II drug metabolizing genes and repressed (>1.25-fold) the expression of 3 genes ( P  <   .05). Rifampin-induced miRNA expression changes correlated with mRNA changes and miRNAs were identified that may modulate conjugating enzyme expression. NAT2 gene expression was most strongly repressed (1.3-fold) by rifampin while UGT1A4 and UGT1A1 genes were most strongly induced (7.9- and 4.8-fold, respectively). Physiologically based pharmacokinetic modeling (PBPK) was used to simulate the clinical consequences of rifampin induction of CYP3A4- and UGT1A4-mediated midazolam metabolism. Simulations evaluating isolated UGT1A4 induction predicted increased midazolam N-glucuronide exposure (~4-fold) with minimal reductions in parent midazolam exposure (~10%). Simulations accounting for simultaneous induction of both CYP3A4 and UGT1A4 predicted a ~10-fold decrease in parent midazolam exposure with only a ~2-fold decrease in midazolam N-glucuronide metabolite exposure. These data reveal differential effects of rifampin on the human conjugating enzyme transcriptome and potential associations with miRNAs that form the basis for future mechanistic studies to elucidate the interplay of conjugating enzyme regulatory elements.

Momentum-weighted conjugate gradient descent algorithm for gradient coil optimization.

PubMed

Lu, Hanbing; Jesmanowicz, Andrzej; Li, Shi-Jiang; Hyde, James S

2004-01-01

MRI gradient coil design is a type of nonlinear constrained optimization. A practical problem in transverse gradient coil design using the conjugate gradient descent (CGD) method is that wire elements move at different rates along orthogonal directions (r, phi, z), and tend to cross, breaking the constraints. A momentum-weighted conjugate gradient descent (MW-CGD) method is presented to overcome this problem. This method takes advantage of the efficiency of the CGD method combined with momentum weighting, which is also an intrinsic property of the Levenberg-Marquardt algorithm, to adjust step sizes along the three orthogonal directions. A water-cooled, 12.8 cm inner diameter, three axis torque-balanced gradient coil for rat imaging was developed based on this method, with an efficiency of 2.13, 2.08, and 4.12 mT.m(-1).A(-1) along X, Y, and Z, respectively. Experimental data demonstrate that this method can improve efficiency by 40% and field uniformity by 27%. This method has also been applied to the design of a gradient coil for the human brain, employing remote current return paths. The benefits of this design include improved gradient field uniformity and efficiency, with a shorter length than gradient coil designs using coaxial return paths. Copyright 2003 Wiley-Liss, Inc.

Conjugal Transfer of the Pathogenicity Island ROD21 in Salmonella enterica serovar Enteritidis Depends on Environmental Conditions

PubMed Central

Salazar-Echegarai, Francisco J.; Tobar, Hugo E.; Nieto, Pamela A.; Riedel, Claudia A.; Bueno, Susan M.

2014-01-01

Unstable pathogenicity islands are chromosomal elements that can be transferred from one bacterium to another. Salmonella enterica serovar Enteritidis (S. Enteritidis) is a pathogenic bacterium containing such unstable pathogenicity islands. One of them, denominated ROD21, is 26.5 kb in size and capable of excising from the chromosome in certain culture conditions, as well as during bacterial infection of phagocytic cells. In this study we have evaluated whether ROD21 can be effectively transferred from one bacterium to another. We generated a donor and several recipient strains of S. Enteritidis to carry out transfer assays in liquid LB medium. These assays showed that ROD21 is effectively transferred from donor to recipient strains of S. Enteritidis and S. Typhimurium. When Escherichia coli was used as the recipient strain, ROD21 transfer failed to be observed. Subsequently, we showed that a conjugative process was required for the transfer of the island and that changes in temperature and pH increased the transfer frequency between Salmonella strains. Our data indicate that ROD21 is an unstable pathogenicity island that can be transferred by conjugation in a species-specific manner between Salmonellae. Further, ROD21 transfer frequency increases in response to environmental changes, such as pH and temperature. PMID:24705125

Inhibition of HIV Replication by Cyclic and Hairpin PNAs Targeting the HIV-1 TAR RNA Loop

PubMed Central

Upert, Gregory; Di Giorgio, Audrey; Upadhyay, Alok; Manvar, Dinesh; Pandey, Nootan; Pandey, Virendra N.; Patino, Nadia

2012-01-01

Human immunodeficiency virus-1 (HIV-1) replication and gene expression entails specific interaction of the viral protein Tat with its transactivation responsive element (TAR), to form a highly stable stem-bulge-loop structure. Previously, we described triphenylphosphonium (TPP) cation-based vectors that efficiently deliver nucleotide analogs (PNAs) into the cytoplasm of cells. In particular, we showed that the TPP conjugate of a linear 16-mer PNA targeting the apical stem-loop region of TAR impedes Tat-mediated transactivation of the HIV-1 LTR in vitro and also in cell culture systems. In this communication, we conjugated TPP to cyclic and hairpin PNAs targeting the loop region of HIV-1 TAR and evaluated their antiviral efficacy in a cell culture system. We found that TPP-cyclic PNAs containing only 8 residues, showed higher antiviral potency compared to hairpin PNAs of 12 or 16 residues. We further noted that the TPP-conjugates of the 8-mer cyclic PNA as well as the 16-mer linear PNA displayed similar antiviral efficacy. However, cyclic PNAs were shown to be highly specific to their target sequences. This communication emphasizes on the importance of small constrained cyclic PNAs over both linear and hairpin structures for targeting biologically relevant RNA hairpins. PMID:23029603

X-ray computed tomography imaging of a tumor with high sensitivity using gold nanoparticles conjugated to a cancer-specific antibody via polyethylene glycol chains on their surface

NASA Astrophysics Data System (ADS)

Nakagawa, Tomohiko; Gonda, Kohsuke; Kamei, Takashi; Cong, Liman; Hamada, Yoh; Kitamura, Narufumi; Tada, Hiroshi; Ishida, Takanori; Aimiya, Takuji; Furusawa, Naoko; Nakano, Yasushi; Ohuchi, Noriaki

2016-01-01

Contrast agents are often used to enhance the contrast of X-ray computed tomography (CT) imaging of tumors to improve diagnostic accuracy. However, because the iodine-based contrast agents currently used in hospitals are of low molecular weight, the agent is rapidly excreted from the kidney or moves to extravascular tissues through the capillary vessels, depending on its concentration gradient. This leads to nonspecific enhancement of contrast images for tissues. Here, we created gold (Au) nanoparticles as a new contrast agent to specifically image tumors with CT using an enhanced permeability and retention (EPR) effect. Au has a higher X-ray absorption coefficient than does iodine. Au nanoparticles were supported with polyethylene glycol (PEG) chains on their surface to increase the blood retention and were conjugated with a cancer-specific antibody via terminal PEG chains. The developed Au nanoparticles were injected into tumor-bearing mice, and the distribution of Au was examined with CT imaging, transmission electron microscopy, and elemental analysis using inductively coupled plasma optical emission spectrometry. The results show that specific localization of the developed Au nanoparticles in the tumor is affected by a slight difference in particle size and enhanced by the conjugation of a specific antibody against the tumor.

Finite element area and line integral transforms for generalization of aperture function and geometry in Kirchhoff scalar diffraction theory

NASA Astrophysics Data System (ADS)

Kraus, Hal G.

1993-02-01

Two finite element-based methods for calculating Fresnel region and near-field region intensities resulting from diffraction of light by two-dimensional apertures are presented. The first is derived using the Kirchhoff area diffraction integral and the second is derived using a displaced vector potential to achieve a line integral transformation. The specific form of each of these formulations is presented for incident spherical waves and for Gaussian laser beams. The geometry of the two-dimensional diffracting aperture(s) is based on biquadratic isoparametric elements, which are used to define apertures of complex geometry. These elements are also used to build complex amplitude and phase functions across the aperture(s), which may be of continuous or discontinuous form. The finite element transform integrals are accurately and efficiently integrated numerically using Gaussian quadrature. The power of these methods is illustrated in several examples which include secondary obstructions, secondary spider supports, multiple mirror arrays, synthetic aperture arrays, apertures covered by screens, apodization, phase plates, and off-axis apertures. Typically, the finite element line integral transform results in significant gains in computational efficiency over the finite element Kirchhoff transform method, but is also subject to some loss in generality.

Six elements of integrated primary healthcare.

PubMed

Brown, Lynsey J; Oliver-Baxter, Jodie

2016-03-01

Integrated care has the potential to deliver efficiencies and improvements in patient experiences and health outcomes. Efforts towards integrated care, especially at the primary and community health levels, have increasingly been under focus, both nationally and internationally. In Australia, regional integration is a priority, and integration of care is a task for meso-level organisations such as Primary Health Networks (PHNs). This paper seeks to provide a list of elements and questions for consideration by organisations working across primary healthcare settings, looking to enact and improve the delivery of integrated care. Six elements that consistently emerged during the development of a series of rapid reviews on integrated primary healthcare in Australia are presented in this paper. The elements identified are context, governance and leadership, infrastructure, financing, engagement, and communication. They offer a starting point for reflection in the planning and practices of organisations in their drive for continuous improvements in integrated care.

Well-Balanced Ambipolar Conjugated Polymers Featuring Mild Glass Transition Temperatures Toward High-Performance Flexible Field-Effect Transistors.

PubMed

Shi, Keli; Zhang, Weifeng; Gao, Dong; Zhang, Shiying; Lin, Zuzhang; Zou, Ye; Wang, Liping; Yu, Gui

2018-03-01

Conjugated polymers, which can be fabricated by simple processing techniques and possess excellent electrical performance, are key to the fabrication of flexible polymer field-effect transistors (PFETs) and integrated circuits. Herein, two ambipolar conjugated polymers based on (3E,7E)-3,7-bis(2-oxo-1H-pyrrolo[2,3-b]pyridin-3(2H)-ylidene)benzo[1,2-b:4,5-b']difuran-2,6(3H,7H)-dione and dithienylbenzothiadiazole units, namely PNBDOPV-DTBT and PNBDOPV-DTF2BT, are developed. Both copolymers possess almost planar conjugated backbone conformations and suitable highest occupied molecular orbital (HOMO)/lowest unoccupied molecular orbital (LUMO) energy levels (-5.64/-4.38 eV for PNBDOPV-DTBT and -5.79/-4.48 eV for PNBDOPV-DTF2BT). Note that PNBDOPV-DTBT has a glass transition temperature (140 °C) lower than the deformation temperature of polyethylene terephthalate (PET), meaning well-ordered molecular packing can be obtained on PET substrate before its deformation in mild thermal annealing process. Flexible PFETs based on PNBDOPV-DTBT fabricated on PET substrates exhibit high and well-balanced hole/electron mobilities of 4.68/4.72 cm 2 V -1 s -1 under ambient conditions. After the further modification of Au source/drain electrodes with 1-octanethiol self-assembled monolayers, impressively high and well-balanced hole/electron mobilities up to 5.97/7.07 cm 2 V -1 s -1 are achieved in the flexible PFETs. Meanwhile, flexible complementary-like inverters based on PNBDOPV-DTBT on PET substrate also afford a much high gain of 148. The device performances of both the PFETs and inverters are among the highest values for ambipolar conjugated polymers reported to date. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Process development of a New Haemophilus influenzae type b conjugate vaccine and the use of mathematical modeling to identify process optimization possibilities.

PubMed

Hamidi, Ahd; Kreeftenberg, Hans; V D Pol, Leo; Ghimire, Saroj; V D Wielen, Luuk A M; Ottens, Marcel

2016-05-01

Vaccination is one of the most successful public health interventions being a cost-effective tool in preventing deaths among young children. The earliest vaccines were developed following empirical methods, creating vaccines by trial and error. New process development tools, for example mathematical modeling, as well as new regulatory initiatives requiring better understanding of both the product and the process are being applied to well-characterized biopharmaceuticals (for example recombinant proteins). The vaccine industry is still running behind in comparison to these industries. A production process for a new Haemophilus influenzae type b (Hib) conjugate vaccine, including related quality control (QC) tests, was developed and transferred to a number of emerging vaccine manufacturers. This contributed to a sustainable global supply of affordable Hib conjugate vaccines, as illustrated by the market launch of the first Hib vaccine based on this technology in 2007 and concomitant price reduction of Hib vaccines. This paper describes the development approach followed for this Hib conjugate vaccine as well as the mathematical modeling tool applied recently in order to indicate options for further improvements of the initial Hib process. The strategy followed during the process development of this Hib conjugate vaccine was a targeted and integrated approach based on prior knowledge and experience with similar products using multi-disciplinary expertise. Mathematical modeling was used to develop a predictive model for the initial Hib process (the 'baseline' model) as well as an 'optimized' model, by proposing a number of process changes which could lead to further reduction in price. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:568-580, 2016. © 2016 American Institute of Chemical Engineers.

A Novel Polygonal Finite Element Method: Virtual Node Method

NASA Astrophysics Data System (ADS)

Tang, X. H.; Zheng, C.; Zhang, J. H.

2010-05-01

Polygonal finite element method (PFEM), which can construct shape functions on polygonal elements, provides greater flexibility in mesh generation. However, the non-polynomial form of traditional PFEM, such as Wachspress method and Mean Value method, leads to inexact numerical integration. Since the integration technique for non-polynomial functions is immature. To overcome this shortcoming, a great number of integration points have to be used to obtain sufficiently exact results, which increases computational cost. In this paper, a novel polygonal finite element method is proposed and called as virtual node method (VNM). The features of present method can be list as: (1) It is a PFEM with polynomial form. Thereby, Hammer integral and Gauss integral can be naturally used to obtain exact numerical integration; (2) Shape functions of VNM satisfy all the requirements of finite element method. To test the performance of VNM, intensive numerical tests are carried out. It found that, in standard patch test, VNM can achieve significantly better results than Wachspress method and Mean Value method. Moreover, it is observed that VNM can achieve better results than triangular 3-node elements in the accuracy test.

Structural fabrics, mineralization and Lamaride kinematics of the Idaho Springs-Ralston shear zone, Colorado mineral belt and central Front Range uplift

USGS Publications Warehouse

Caine, Jonathan S.; Nelson, E.P.; Beach, S.T.; Layer, P.W.

2006-01-01

The Idaho Springs and Central City mining districts form the central portion of a structurally controlled hydrothermal precious- and base-metal vein system in the Front Range of the northeast-trending Colorado Mineral Belt. Three new 40Ar/39Ar plateau ages on hydrothermal sericite indicate the veins formed during the Laramide orogeny between 65.4??1.5 - 61.9??1.3 Ma. We compile structural geologic data from surface geological maps, subsurface mine maps, and theses for analysis using modern graphical methods and integration into models of formation of economic mineral deposits. Structural data sets, produced in the 1950s and 1960s by the U.S. Geological Survey, are compiled for fabric elements, including metamorphic foliations, fold axial trends, major brittle fault zones, quartz and precious- and base-metal veins and fault veins, Tertiary dikes, and joints. These fabric elements are plotted on equal-area projections and analyzed for mean fabric orientations. Strike-slip fault-vein sets are mostly parallel or sub-parallel, and not conjugate as interpreted by previous work; late-stage, normal-slip fault veins possibly show a pattern indicative of triaxial strain. Fault-slip kinematic analysis was used to model the trend of the Laramide maximum horizontal stress axis, or compression direction, and to determine compatibility of opening and shear motions within a single stress field. The combined-model maximum compression direction for all strike slip fault veins is ???068??, which is consistent with published Laramide compression directions of ???064?? (mean of 23 regional models) and ???072?? for the Front Range uplift. The orientations of fabric elements were analyzed for mechanical and kinematic compatibility with opening, and thus permeability enhancement, in the modeled regional east-northeast, Laramide compression direction. The fabric orientation analysis and paleostress modeling show that structural permeability during mineralization was enhanced along pre-existing metamorphic foliations and fold axial planes. Large orientation dispersion in most fabric elements likely caused myriad potential pathways for permeability. The dominant orientations of opening and shear mode structures are consistent with a sub-parallel network of structures that formed in the Laramide east-northeast compression direction. The results presented demonstrate the importance of using mechanical and kinematic theory integrated with contemporary ideas of permeability structure to better understand the coupled nature of fluid flow, mineral deposition, stress, and strain. Further, the results demonstrate that there is significant internal strain within this basement-cored uplift that was localized by optimally oriented pre-existing structures in a regional stress field.

Spin injection into Pt-polymers with large spin-orbit coupling

NASA Astrophysics Data System (ADS)

Sun, Dali; McLaughlin, Ryan; Siegel, Gene; Tiwari, Ashutosh; Vardeny, Z. Valy

2014-03-01

Organic spintronics has entered a new era of devices that integrate organic light-emitting diodes (OLED) in organic spin valve (OSV) geometry (dubbed bipolar organic spin valve, or spin-OLED), for actively manipulating the device electroluminescence via the spin alignment of two ferromagnetic electrodes (Science 337, 204-209, 2012; Appl. Phys. Lett. 103, 042411, 2013). Organic semiconductors that contain heavy metal elements have been widely used as phosphorescent dopants in white-OLEDs. However such active materials are detrimental for OSV operation due to their large spin-orbit coupling (SOC) that may limit the spin diffusion length and thus spin-OLED based on organics with large SOC is a challenge. We report the successful fabrication of OSVs based on pi-conjugated polymers which contain intrachain Platinum atoms (dubbed Pt-polymers). Spin injection into the Pt-polymers is investigated by the giant magnetoresistance (GMR) effect as a function of bias voltage, temperature and polymer layer thickness. From the GMR bias voltage dependence we infer that the ``impendence mismatch'' between ferromagnetic electrodes and Pt-polymer may be suppressed due to the large SOC. Research sponsored by the NSF (Grant No. DMR-1104495) and NSF-MRSEC (DMR 1121252) at the University of Utah.

GPU-based acceleration of computations in nonlinear finite element deformation analysis.

PubMed

Mafi, Ramin; Sirouspour, Shahin

2014-03-01

The physics of deformation for biological soft-tissue is best described by nonlinear continuum mechanics-based models, which then can be discretized by the FEM for a numerical solution. However, computational complexity of such models have limited their use in applications requiring real-time or fast response. In this work, we propose a graphic processing unit-based implementation of the FEM using implicit time integration for dynamic nonlinear deformation analysis. This is the most general formulation of the deformation analysis. It is valid for large deformations and strains and can account for material nonlinearities. The data-parallel nature and the intense arithmetic computations of nonlinear FEM equations make it particularly suitable for implementation on a parallel computing platform such as graphic processing unit. In this work, we present and compare two different designs based on the matrix-free and conventional preconditioned conjugate gradients algorithms for solving the FEM equations arising in deformation analysis. The speedup achieved with the proposed parallel implementations of the algorithms will be instrumental in the development of advanced surgical simulators and medical image registration methods involving soft-tissue deformation. Copyright © 2013 John Wiley & Sons, Ltd.

A three-dimensional nonlinear Timoshenko beam based on the core-congruential formulation

NASA Technical Reports Server (NTRS)

Crivelli, Luis A.; Felippa, Carlos A.

1992-01-01

A three-dimensional, geometrically nonlinear two-node Timoshenkoo beam element based on the total Larangrian description is derived. The element behavior is assumed to be linear elastic, but no restrictions are placed on magnitude of finite rotations. The resulting element has twelve degrees of freedom: six translational components and six rotational-vector components. The formulation uses the Green-Lagrange strains and second Piola-Kirchhoff stresses as energy-conjugate variables and accounts for the bending-stretching and bending-torsional coupling effects without special provisions. The core-congruential formulation (CCF) is used to derived the discrete equations in a staged manner. Core equations involving the internal force vector and tangent stiffness matrix are developed at the particle level. A sequence of matrix transformations carries these equations to beam cross-sections and finally to the element nodal degrees of freedom. The choice of finite rotation measure is made in the next-to-last transformation stage, and the choice of over-the-element interpolation in the last one. The tangent stiffness matrix is found to retain symmetry if the rotational vector is chosen to measure finite rotations. An extensive set of numerical examples is presented to test and validate the present element.

Signal Processing with Degenrate Four-Wave Mixing.

DTIC Science & Technology

1987-03-17

warth [71 and Au Yueng er al. 1181 in CS, filled fibers. The first authors achieved high-fidelity conjugation with In the weakly guiding case, that...waves with. of course, taneously as its own pump wave. Au Yueng er al. [181 K 12, given by the "overlap integrals." In the absence of used single-mode

Extended depth of field integral imaging using multi-focus fusion

NASA Astrophysics Data System (ADS)

Piao, Yongri; Zhang, Miao; Wang, Xiaohui; Li, Peihua

2018-03-01

In this paper, we propose a new method for depth of field extension in integral imaging by realizing the image fusion method on the multi-focus elemental images. In the proposed method, a camera is translated on a 2D grid to take multi-focus elemental images by sweeping the focus plane across the scene. Simply applying an image fusion method on the elemental images holding rich parallax information does not work effectively because registration accuracy of images is the prerequisite for image fusion. To solve this problem an elemental image generalization method is proposed. The aim of this generalization process is to geometrically align the objects in all elemental images so that the correct regions of multi-focus elemental images can be exacted. The all-in focus elemental images are then generated by fusing the generalized elemental images using the block based fusion method. The experimental results demonstrate that the depth of field of synthetic aperture integral imaging system has been extended by realizing the generation method combined with the image fusion on multi-focus elemental images in synthetic aperture integral imaging system.

Blueprinting macromolecular electronics.

PubMed

Palma, Carlos-Andres; Samorì, Paolo

2011-06-01

Recently, by mastering either top-down or bottom-up approaches, tailor-made macromolecular nano-objects with semiconducting properties have been fabricated. These engineered nanostructures for organic electronics are based on conjugated systems predominantly made up of sp²-hybridized carbon, such as graphene nanoribbons. Here, we describe developments in a selection of these nanofabrication techniques, which include graphene carving, stimulus-induced synthesis of conjugated polymers and surface-assisted synthesis. We also assess their potential to reproduce chemically and spatially precise molecular arrangements, that is, molecular blueprints. In a broad context, the engineering of a molecular blueprint represents the fabrication of an integrated all-organic macromolecular electronic circuit. In this Perspective, we suggest chemical routes, as well as convergent on-surface synthesis and microfabrication approaches, for the ultimate goal of bringing the field closer to technology.

Improved finite element methodology for integrated thermal structural analysis

NASA Technical Reports Server (NTRS)

Dechaumphai, P.; Thornton, E. A.

1982-01-01

An integrated thermal-structural finite element approach for efficient coupling of thermal and structural analysis is presented. New thermal finite elements which yield exact nodal and element temperatures for one dimensional linear steady state heat transfer problems are developed. A nodeless variable formulation is used to establish improved thermal finite elements for one dimensional nonlinear transient and two dimensional linear transient heat transfer problems. The thermal finite elements provide detailed temperature distributions without using additional element nodes and permit a common discretization with lower order congruent structural finite elements. The accuracy of the integrated approach is evaluated by comparisons with analytical solutions and conventional finite element thermal structural analyses for a number of academic and more realistic problems. Results indicate that the approach provides a significant improvement in the accuracy and efficiency of thermal stress analysis for structures with complex temperature distributions.

Iterative algorithms for large sparse linear systems on parallel computers

NASA Technical Reports Server (NTRS)

Adams, L. M.

1982-01-01

Algorithms for assembling in parallel the sparse system of linear equations that result from finite difference or finite element discretizations of elliptic partial differential equations, such as those that arise in structural engineering are developed. Parallel linear stationary iterative algorithms and parallel preconditioned conjugate gradient algorithms are developed for solving these systems. In addition, a model for comparing parallel algorithms on array architectures is developed and results of this model for the algorithms are given.

Single-shot measurement of nonlinear absorption and nonlinear refraction.

PubMed

Jayabalan, J; Singh, Asha; Oak, Shrikant M

2006-06-01

A single-shot method for measurement of nonlinear optical absorption and refraction is described and analyzed. A spatial intensity variation of an elliptical Gaussian beam in conjugation with an array detector is the key element of this method. The advantages of this single-shot technique were demonstrated by measuring the two-photon absorption and free-carrier absorption in GaAs as well as the nonlinear refractive index of CS2 using a modified optical Kerr setup.

A replaceable liposomal aptamer for the ultrasensitive and rapid detection of biotin

NASA Astrophysics Data System (ADS)

Sung, Tzu-Cheng; Chen, Wen-Yih; Shah, Pramod; Chen, Chien-Sheng

2016-02-01

Biotin is an essential vitamin which plays an important role for maintaining normal physiological function. A rapid, sensitive, and simple method is necessary to monitor the biotin level. Here, we reported a replacement assay for the detection of biotin using a replaceable liposomal aptamer. Replacement assay is a competitive assay where a sample analyte replaces the labeled competitor of analyte out of its biorecognition element on a surface. It is user friendly and time-saving because of washing free. We used aptamer as a competitor, not a biorecognition element as tradition. To label aptamers, we used cholesterol-conjugated aptamers to tag signal-amplifying-liposomes. Without the need of conjugation procedure, aptamers can be easily incorporated into the surface of dye-encapsulating liposomes. Two aptamers as competitors of biotin, ST-21 and ST-21M with different affinities to streptavidin, were studied in parallel for the detection of biotin using replacement assays. ST-21 and ST-21M aptamers reached to limits of detection of 1.32 pg/80 μl and 0.47 pg/80 μl, respectively. The dynamic ranges of our assays using ST-21 and ST-21M aptamers were seven and four orders of magnitude, respectively. This assay can be completed in 20 minutes without washing steps. These results were overall better than previous reported assays.

Improved accuracy for finite element structural analysis via an integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, S. N.; Hopkins, D. A.; Aiello, R. A.; Berke, L.

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

A computer program for anisotropic shallow-shell finite elements using symbolic integration

NASA Technical Reports Server (NTRS)

Andersen, C. M.; Bowen, J. T.

1976-01-01

A FORTRAN computer program for anisotropic shallow-shell finite elements with variable curvature is described. A listing of the program is presented together with printed output for a sample case. Computation times and central memory requirements are given for several different elements. The program is based on a stiffness (displacement) finite-element model in which the fundamental unknowns consist of both the displacement and the rotation components of the reference surface of the shell. Two triangular and four quadrilateral elements are implemented in the program. The triangular elements have 6 or 10 nodes, and the quadrilateral elements have 4 or 8 nodes. Two of the quadrilateral elements have internal degrees of freedom associated with displacement modes which vanish along the edges of the elements (bubble modes). The triangular elements and the remaining two quadrilateral elements do not have bubble modes. The output from the program consists of arrays corresponding to the stiffness, the geometric stiffness, the consistent mass, and the consistent load matrices for individual elements. The integrals required for the generation of these arrays are evaluated by using symbolic (or analytic) integration in conjunction with certain group-theoretic techniques. The analytic expressions for the integrals are exact and were developed using the symbolic and algebraic manipulation language.

Covalent Chemical Ligation Strategy for Mono- and Polyclonal Immunoglobulins at Their Nucleotide Binding Sites.

PubMed

Lac, Diana; Feng, Chun; Bhardwaj, Gaurav; Le, Huong; Tran, Jimmy; Xing, Li; Fung, Gabriel; Liu, Ruiwu; Cheng, Holland; Lam, Kit S

2016-01-20

Nonspecific ligation methods have been traditionally used to chemically modify immunoglobulins. Site-specific ligation of compounds (toxins or ligands) to antibodies has become increasingly important in the fields of therapeutic antibody-drug conjugates and bispecific antibodies. In this present study, we took advantage of the reported nucleotide-binding pocket (NBP) in the Fab arms of immunoglobulins by developing indole-based, 5-fluoro-2,4-dinitrobenzene-derivatized OBOC peptide libraries for the identification of affinity elements that can be used as site-specific derivatization agents against both mono- and polyclonal antibodies. Ligation can occur at any one of the few lysine residues located at the NBP. Immunoconjugates resulting from such affinity elements can be used as therapeutics against cancer or infectious agents.

Microscopy with multimode fibers

NASA Astrophysics Data System (ADS)

Moser, Christophe; Papadopoulos, Ioannis; Farahi, Salma; Psaltis, Demetri

2013-04-01

Microscopes are usually thought of comprising imaging elements such as objectives and eye-piece lenses. A different type of microscope, used for endoscopy, consists of waveguiding elements such as fiber bundles, where each fiber in the bundle transports the light corresponding to one pixel in the image. Recently a new type of microscope has emerged that exploits the large number of propagating modes in a single multimode fiber. We have successfully produced fluorescence images of neural cells with sub-micrometer resolution via a 200 micrometer core multimode fiber. The method for achieving imaging consists of using digital phase conjugation to reproduce a focal spot at the tip of the multimode fiber. The image is formed by scanning the focal spot digitally and collecting the fluorescence point by point.

Proposal for a prototype of portable μXRF spectrometer

NASA Astrophysics Data System (ADS)

Polese, C.; Dabagov, S. B.; Esposito, A.; Liedl, A.; Hampai, D.; Bartùli, C.; Ferretti, M.

2015-07-01

μXRF is a powerful instrument for non-destructive characterization of materials of cultural interest. At the XLab Frascati Laboratory this technique is already well performed thanks to the polyCO set equipment allowing simultaneous μXRF 2D mapping. However, due to the strict demand for in situ analysis in this particular field, a new portable μXRF spectrometer equipped with a full polycapillary lens conjugated with a transmission anode X-ray tube is proposed. Many cultural objects are characterized by elements (Ag, Sn, etc.) with high energy fluorescence K-lines. Thus, the capability of a full lens to deliver a high energy fraction of X-ray spectrum, in order to excite the fluorescence K-lines of such elements, is tested.

Biology of Three ICE Families: SXT/R391, ICEBs1, and ICESt1/ICESt3.

PubMed

Carraro, Nicolas; Burrus, Vincent

2014-12-01

Integrative and Conjugative Elements (ICEs) are bacterial mobile genetic elements that play a key role in bacterial genomes dynamics and evolution. ICEs are widely distributed among virtually all bacterial genera. Recent extensive studies have unraveled their high diversity and complexity. The present review depicts the general conserved features of ICEs and describes more precisely three major families of ICEs that have been extensively studied in the past decade for their biology, their evolution and their impact on genomes dynamics. First, the large SXT/R391 family of ICEs disseminates antibiotic resistance genes and drives the exchange of mobilizable genomic islands (MGIs) between many enteric pathogens such as Vibrio cholerae. Second, ICEBs1 of Bacillus subtilis is the most well understood ICE of Gram-positive bacteria, notably regarding the regulation of its dissemination and its initially unforeseen extrachromosomal replication, which could be a common feature of ICEs of both Gram-positive and Gram-negative bacteria. Finally, ICESt1 and ICESt3 of Streptococcus thermophilus are the prototypes of a large family of ICEs widely distributed among various streptococci. These ICEs carry an original regulation module that associates regulators related to those of both SXT/R391 and ICEBs1. Study of ICESt1 and ICESt3 uncovered the cis-mobilization of related genomic islands (CIMEs) by a mechanism called accretion-mobilization, which likely represents a paradigm for the evolution of many ICEs and genomic islands. These three major families of ICEs give a glimpse about ICEs dynamics and their high impact on bacterial adaptation.

Silicon-nanomembrane-based photonic crystal nanostructures for chip-integrated open sensor systems

NASA Astrophysics Data System (ADS)

Chakravarty, Swapnajit; Lai, Wei-Cheng; Zou, Yi; Lin, Cheyun; Wang, Xiaolong; Chen, Ray T.

2011-11-01

We experimentally demonstrate two devices on the photonic crystal platform for chip-integrated optical absorption spectroscopy and chip-integrated biomolecular microarray assays. Infrared optical absorption spectroscopy and biomolecular assays based on conjugate-specific binding principles represent two dominant sensing mechanisms for a wide spectrum of applications in environmental pollution sensing in air and water, chem-bio agents and explosives detection for national security, microbial contamination sensing in food and beverages to name a few. The easy scalability of photonic crystal devices to any wavelength ensures that the sensing principles hold across a wide electromagnetic spectrum. Silicon, the workhorse of the electronics industry, is an ideal platform for the above optical sensing applications.

Genetic engineering in Actinoplanes sp. SE50/110 - development of an intergeneric conjugation system for the introduction of actinophage-based integrative vectors.

PubMed

Gren, Tetiana; Ortseifen, Vera; Wibberg, Daniel; Schneiker-Bekel, Susanne; Bednarz, Hanna; Niehaus, Karsten; Zemke, Till; Persicke, Marcus; Pühler, Alfred; Kalinowski, Jörn

2016-08-20

The α-glucosidase inhibitor acarbose is used for treatment of diabetes mellitus type II, and is manufactured industrially with overproducing derivatives of Actinoplanes sp. SE50/110, reportedly obtained by conventional mutagenesis. Despite of high industrial significance, only limited information exists regarding acarbose metabolism, function and regulation of these processes, due to the absence of proper genetic engineering methods and tools developed for this strain. Here, a basic toolkit for genetic engineering of Actinoplanes sp. SE50/110 was developed, comprising a standardized protocol for a DNA transfer through Escherichia coli-Actinoplanes intergeneric conjugation and applied for the transfer of ϕC31, ϕBT1 and VWB actinophage-based integrative vectors. Integration sites, occurring once per genome for all vectors, were sequenced and characterized for the first time in Actinoplanes sp. SE50/110. Notably, in case of ϕC31 based vector pSET152, the integration site is highly conserved, while for ϕBT1 and the VWB based vectors pRT801 and pSOK804, respectively, no sequence similarities to those in other bacteria were detected. The studied plasmids were proven to be stable and neutral with respect to strain morphology and acarbose production, enabling future use for genetic manipulations of Actinoplanes sp. SE50/110. To further broaden the spectrum of available tools, a GUS reporter system, based on the pSET152 derived vector, was also established in Actinoplanes sp. SE50/110. Copyright © 2016 Elsevier B.V. All rights reserved.

Translating the Elements of Health Governance for Integrated Care from Theory to Practice: A Case Study Approach.

PubMed

Nicholson, Caroline; Hepworth, Julie; Burridge, Letitia; Marley, John; Jackson, Claire

2018-01-31

Against a paucity of evidence, a model describing elements of health governance best suited to achieving integrated care internationally was developed. The aim of this study was to explore how health meso-level organisations used, or planned to use, the governance elements. A case study design was used to offer two contrasting contexts of health governance. Semi-structured interviews were conducted with participants who held senior governance roles. Data were thematically analysed to identify if the elements of health governance were being used, or intended to be in the future. While all participants agreed that the ten elements were essential to developing future integrated care, most were not used. Three major themes were identified: (1) organisational versus system focus, (2) leadership and culture, and, (3) community (dis)engagement. Several barriers and enablers to the use of the elements were identified and would require addressing in order to make evidence-based changes. Despite a clear international policy direction in support of integrated care this study identified a number of significant barriers to its implementation. The study reconfirmed that a focus on all ten elements of health governance is essential to achieve integrated care.

Conjugate Heat Transfer and Thermo-Structural Analysis of the Actively Cooled Multi-Stage Conical Nozzle and Hypersonic Low-Reynolds Diffuser of the New Arc-Heated Wind Tunnel (AWHT-II) of the University of Texas at Arlington

NASA Astrophysics Data System (ADS)

Campbell, David R.

Arc-heated wind tunnels are the primary test facility for screening and qualification of candidate materials for hypersonic thermal protection systems (TPS). Via an electric arc that largely augments the enthalpy (by tens of MJ/kg) of the working fluid (Air, Nitrogen, CO2 in case of Mars-entry studies) passed through a converging-diverging nozzle at specific stagnation conditions, different regimes encountered in entry and re-entry hypersonic aerothermodynamics can be simulated. Because of the high-enthalpies (and associated temperatures that generally exceed the limits required by the thermo-structural integrity of the facility) the active cooling of the arc-heated wind tunnel's parts exposed to the working gas is critical. This criticality is particularly severe in these facilities due to the time scales associated with their continuous operation capabilities (order of minutes). This research focuses on the design and the conjugate heat transfer and resultant thermo-structural analysis of a multi-segment nozzle and low-Reynolds, hypersonic diffuser for the new arc-heated wind tunnel (AHWT-II) of the University of Texas at Arlington. Nozzles and hypersonic diffusers are critical components that experience highly complex flows (non-equilibrium aerothermochemistry) and high (local and distributed) heat-flux loads which significantly augment the complexity of the problems associated with their thermal management. The proper design and thermo-mechanical analysis of these components are crucial elements for the operability of the new facility. This work is centered on the design considerations, methodologies and the detailed analysis of the aforementioned components which resulted in the definition of final parts and assemblies that are under manufacturing at this writing. The project is jointly sponsored by the Office of Naval Research (ONR) and the Defense Advanced Research Project Agency (DARPA).

Comparative Study of Coherent, Non-Coherent, and Semi-Coherent Integration Schemes for GNSS Receivers (Preprint)

DTIC Science & Technology

2007-04-01

input signal with the conjugate of a delayed copy of itself, i.e., )exp(2* kjAzz knn ϕ=− , has a phase argument independent of n. As a result, the...Signal Processing (Elseivier), 2005. S.M. Kay, “A Fast and Accurate Single Frequency Estimator,” IEEE Trans. Acous. Speech Signal Proc., 37(12), 1987

Non-covalent attachment of silver nanoclusters onto single-walled carbon nanotubes with human serum albumin as linking molecule

NASA Astrophysics Data System (ADS)

Rodríguez-Galván, Andrés; Heredia, Alejandro; Amelines-Sarria, Oscar; Rivera, Margarita; Medina, Luis A.; Basiuk, Vladimir A.

2015-03-01

The attachment of silver nanoclusters (AgNCs) onto single-walled carbon nanotubes (SWNTs) for the formation of integrated fluorescence sites has attracted much attention due their potential applications as biological probes and nanovectors in theragnosis. Here, we report the preparation through assembly of fluorescent quasi 1-D nanomaterial based on SWNTs and silver nanoclusters (AgNCs) non-covalently attached to human serum albumin as biological linker. The fluorescent SWNT-AgNCs-HSA conjugates were characterized by atomic force microscopy, high-resolution transmission electron microscopy (HRTEM), high angle annular dark field scanning TEM (HAADF-STEM), fluorescent and UV-vis spectroscopy. The above techniques confirmed that AgNCs were non-covalently attached onto the external surface of SWNTs. In addition, it was observed that the modification did not affect the optical properties of the synthesized AgNCs since the absorption spectra and fluorescence under UV irradiation (λ = 365 nm) remain the same. The effect of the functionalized systems was tested on mammal red blood cells (RBCs) and it was found that their structural integrity was compromised by the conjugates, limiting their biological and medical applications.

Solution conformation and flexibility of capsular polysaccharides from Neisseria meningitidis and glycoconjugates with the tetanus toxoid protein

NASA Astrophysics Data System (ADS)

Abdelhameed, Ali Saber; Morris, Gordon A.; Almutairi, Fahad; Adams, Gary G.; Duvivier, Pierre; Conrath, Karel; Harding, Stephen E.

2016-10-01

The structural integrity of meningococcal native, micro-fluidized and activated capsular polysaccharides and their glycoconjugates - in the form most relevant to their potential use as vaccines (dilute solution) - have been investigated with respect to their homogeneity, conformation and flexibility. Sedimentation velocity analysis showed that the polysaccharide size distributions were generally bimodal with some evidence for higher molar mass forms at higher concentration. Weight average molar masses Mw where lower for activated polysaccharides. Conjugation with tetanus toxoid protein however greatly increased the molar mass and polydispersity of the final conjugates. Glycoconjugates had an approximately unimodal log-normal but broad and large molar mass profiles, confirmed by sedimentation equilibrium “SEDFIT MSTAR” analysis. Conformation analysis using HYDFIT (which globally combines sedimentation and viscosity data), “Conformation Zoning” and Wales-van Holde approaches showed a high degree of flexibility - at least as great as the unconjugated polysaccharides, and very different from the tetanus toxoid (TT) protein used for the conjugation. As with the recently published finding for Hib-TT complexes, it is the carbohydrate component that dictates the solution behaviour of these glycoconjugates, although the lower intrinsic viscosities suggest some degree of compaction of the carbohydrate chains around the protein.

Solution conformation and flexibility of capsular polysaccharides from Neisseria meningitidis and glycoconjugates with the tetanus toxoid protein.

PubMed

Abdelhameed, Ali Saber; Morris, Gordon A; Almutairi, Fahad; Adams, Gary G; Duvivier, Pierre; Conrath, Karel; Harding, Stephen E

2016-10-26

The structural integrity of meningococcal native, micro-fluidized and activated capsular polysaccharides and their glycoconjugates - in the form most relevant to their potential use as vaccines (dilute solution) - have been investigated with respect to their homogeneity, conformation and flexibility. Sedimentation velocity analysis showed that the polysaccharide size distributions were generally bimodal with some evidence for higher molar mass forms at higher concentration. Weight average molar masses M w where lower for activated polysaccharides. Conjugation with tetanus toxoid protein however greatly increased the molar mass and polydispersity of the final conjugates. Glycoconjugates had an approximately unimodal log-normal but broad and large molar mass profiles, confirmed by sedimentation equilibrium "SEDFIT MSTAR" analysis. Conformation analysis using HYDFIT (which globally combines sedimentation and viscosity data), "Conformation Zoning" and Wales-van Holde approaches showed a high degree of flexibility - at least as great as the unconjugated polysaccharides, and very different from the tetanus toxoid (TT) protein used for the conjugation. As with the recently published finding for Hib-TT complexes, it is the carbohydrate component that dictates the solution behaviour of these glycoconjugates, although the lower intrinsic viscosities suggest some degree of compaction of the carbohydrate chains around the protein.

Charge carrier mobility in conjugated organic polymers: simulation of an electron mobility in a carbazole-benzothiadiazole-based polymer

NASA Astrophysics Data System (ADS)

Li, Yaping; Lagowski, Jolanta B.

2011-08-01

Inorganic (mostly silicon based) solar cells are important devices that are used to solve the world energy and environmental needs. Now days, organic solar cells are attracting considerable attention in the field of photovoltaic cells because of their low cost and processing flexibility. Often conjugated polymers are used in the construction of the organic solar cells. We study the conjugated polymers' charge transport using computational approach that involves the use of the density functional theory (DFT), semiempirical (ZINDO), and Monte Carlo (MC) theoretical methods in order to determine their transfer integrals, reorganization energies, transfer rates (with the use of Marcus-Hush equation) and mobilities. We employ the experimentally determined three dimensional (3D) structure of poly(9,9'-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) to estimate the electron mobility in a similar co-alternating polymer consisting of carbazole and benzothiadiazole units (C8BT). In agreement with our previous work, we found that including an orientational disorder in the crystal reduces the electron mobility in C8BT. We hope that the proposed computational approach can be used to predict charge mobility in organic materials that are used in solar cells.

Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12.

PubMed

Kingston, Anthony W; Roussel-Rossin, Chloé; Dupont, Claire; Raleigh, Elisabeth A

2015-01-01

In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F'-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10(-12) CFU/recipient per hour.

The implementation of integrated care: the empirical validation of the Development Model for Integrated Care

PubMed Central

2011-01-01

Background Integrated care is considered as a strategy to improve the delivery, efficiency, client outcomes and satisfaction rates of health care. To integrate the care from multiple providers into a coherent client-focused service, a large number of activities and agreements have to be implemented like streamlining information flows and patient transfers. The Development Model for Integrated care (DMIC) describes nine clusters containing in total 89 elements that contribute to the integration of care. We have empirically validated this model in practice by assessing the relevance, implementation and plans of the elements in three integrated care service settings in The Netherlands: stroke, acute myocardial infarct (AMI), and dementia. Methods Based on the DMIC, a survey was developed for integrated care coordinators. We invited all Dutch stroke and AMI-services, as well as the dementia care networks to participate, of which 84 did (response rate 83%). Data were collected on relevance, presence, and year of implementation of the 89 elements. The data analysis was done by means of descriptive statistics, Chi Square, ANOVA and Kruskal-Wallis H tests. Results The results indicate that the integrated care practice organizations in all three care settings rated the nine clusters and 89 elements of the DMIC as highly relevant. The average number of elements implemented was 50 ± 18, 42 ± 13, and 45 ± 22 for stroke, acute myocardial infarction, and dementia care services, respectively. Although the dementia networks were significantly younger, their numbers of implemented elements were comparable to those of the other services. The analyses of the implementation timelines showed that the older integrated care services had fewer plans for further implementation than the younger ones. Integrated care coordinators stated that the DMIC helped them to assess their integrated care development in practice and supported them in obtaining ideas for expanding their integrated care activities. Conclusions Although the patient composites and the characteristics of the 84 participating integrated care services differed considerably, the results confirm that the clusters and the vast majority of DMIC elements are relevant to all three groups. Therefore, the DMIC can serve as a general quality management tool for integrated care. Applying the model in practice can help in steering further implementations as well as the development of new integrated care practices. PMID:21801428

The implementation of integrated care: the empirical validation of the Development Model for Integrated care.

PubMed

Minkman, Mirella M N; Vermeulen, Robbert P; Ahaus, Kees T B; Huijsman, Robbert

2011-07-30

Integrated care is considered as a strategy to improve the delivery, efficiency, client outcomes and satisfaction rates of health care. To integrate the care from multiple providers into a coherent client-focused service, a large number of activities and agreements have to be implemented like streamlining information flows and patient transfers. The Development Model for Integrated care (DMIC) describes nine clusters containing in total 89 elements that contribute to the integration of care. We have empirically validated this model in practice by assessing the relevance, implementation and plans of the elements in three integrated care service settings in The Netherlands: stroke, acute myocardial infarct (AMI), and dementia. Based on the DMIC, a survey was developed for integrated care coordinators. We invited all Dutch stroke and AMI-services, as well as the dementia care networks to participate, of which 84 did (response rate 83%). Data were collected on relevance, presence, and year of implementation of the 89 elements. The data analysis was done by means of descriptive statistics, Chi Square, ANOVA and Kruskal-Wallis H tests. The results indicate that the integrated care practice organizations in all three care settings rated the nine clusters and 89 elements of the DMIC as highly relevant. The average number of elements implemented was 50 ± 18, 42 ± 13, and 45 ± 22 for stroke, acute myocardial infarction, and dementia care services, respectively. Although the dementia networks were significantly younger, their numbers of implemented elements were comparable to those of the other services. The analyses of the implementation timelines showed that the older integrated care services had fewer plans for further implementation than the younger ones. Integrated care coordinators stated that the DMIC helped them to assess their integrated care development in practice and supported them in obtaining ideas for expanding their integrated care activities. Although the patient composites and the characteristics of the 84 participating integrated care services differed considerably, the results confirm that the clusters and the vast majority of DMIC elements are relevant to all three groups. Therefore, the DMIC can serve as a general quality management tool for integrated care. Applying the model in practice can help in steering further implementations as well as the development of new integrated care practices.

Workshop on the Integration of Finite Element Modeling with Geometric Modeling

NASA Technical Reports Server (NTRS)

Wozny, Michael J.

1987-01-01

The workshop on the Integration of Finite Element Modeling with Geometric Modeling was held on 12 May 1987. It was held to discuss the geometric modeling requirements of the finite element modeling process and to better understand the technical aspects of the integration of these two areas. The 11 papers are presented except for one for which only the abstract is given.

Mapping the Conjugate Gradient Algorithm onto High Performance Heterogeneous Computers

DTIC Science & Technology

2014-05-01

Matrix Storage Formats According to J . Dongarra (Dongerra 2000), the efficiency of most iterative methods, such as CG, can be attributed to the...valh = aij) ⇒ (colh = j ). The ptr integer vector is of length n + 1 and contains the index in val where each matrix row starts. For example, the...first nonzero element of matrix rowm is found at index ptrm of val. By convention, ptrn+1 ≡ nz + 1. Notice that (aij) ⇒ (ptri ≤ j < ptri+1) for all i. An

Programmable Iterative Optical Image And Data Processing

NASA Technical Reports Server (NTRS)

Jackson, Deborah J.

1995-01-01

Proposed method of iterative optical image and data processing overcomes limitations imposed by loss of optical power after repeated passes through many optical elements - especially, beam splitters. Involves selective, timed combination of optical wavefront phase conjugation and amplification to regenerate images in real time to compensate for losses in optical iteration loops; timing such that amplification turned on to regenerate desired image, then turned off so as not to regenerate other, undesired images or spurious light propagating through loops from unwanted reflections.

CPDES3: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in three dimensions

NASA Astrophysics Data System (ADS)

Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

1988-11-01

Many physical problems require the solution of coupled partial differential equations on three-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES3 allows each spatial operator to have 7, 15, 19, or 27 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect induces which is vectorizable on some of the newer scientific computers.

CPDES2: A preconditioned conjugate gradient solver for linear asymmetric matrix equations arising from coupled partial differential equations in two dimensions

NASA Astrophysics Data System (ADS)

Anderson, D. V.; Koniges, A. E.; Shumaker, D. E.

1988-11-01

Many physical problems require the solution of coupled partial differential equations on two-dimensional domains. When the time scales of interest dictate an implicit discretization of the equations a rather complicated global matrix system needs solution. The exact form of the matrix depends on the choice of spatial grids and on the finite element or finite difference approximations employed. CPDES2 allows each spatial operator to have 5 or 9 point stencils and allows for general couplings between all of the component PDE's and it automatically generates the matrix structures needed to perform the algorithm. The resulting sparse matrix equation is solved by either the preconditioned conjugate gradient (CG) method or by the preconditioned biconjugate gradient (BCG) algorithm. An arbitrary number of component equations are permitted only limited by available memory. In the sub-band representation used, we generate an algorithm that is written compactly in terms of indirect indices which is vectorizable on some of the newer scientific computers.

Modulating nanoparticle superlattice structure using proteins with tunable bond distributions

DOE PAGES

McMillan, Janet R.; Brodin, Jeffrey D.; Millan, Jaime A.; ...

2017-01-25

Here, we investigate the use of proteins with tunable DNA modification distributions to modulate nanoparticle superlattice structure. Using Beta-galactosidase (βgal) as a model system, we have employed the orthogonal chemical reactivities of surface amines and thiols to synthesize protein-DNA conjugates with 36 evenly distributed or 8 specifically positioned oligonucleotides. When assembled into crystalline superlattices with AuNPs, we find that the distribution of DNA modifications modulates the favored structure: βgal with uniformly distributed DNA bonding elements results in body-centered cubic crystals, whereas DNA functionalization of cysteines results in AB 2 packing. We probe the role of protein oligonucleotide number and conjugatemore » size on this observation, which revealed the importance of oligonucleotide distribution and number in this observed assembly behavior. These results indicate that proteins with defined DNA-modification patterns are powerful tools to control the nanoparticle superlattices architecture, and establish the importance of oligonucleotide distribution in the assembly behavior of protein-DNA conjugates.« less

Observation of laser formation inside a laser cavity containing a phase conjugate mirror

NASA Astrophysics Data System (ADS)

Wu, Frank F.

2012-03-01

Adaptive optics (AO) systems are used to compensate atmospheric perturbations on a propagating laser beam. However, AO needs a beacon to obtain the phase information. This paper presents a possible formation of beacon in target-in-theloop (TIL) geometry which is analog to a laser cavity. The TIL laser cavity is formed with a high reflectivity mirror on one end and an optical phase conjugate mirror as the second mirror. The TIL laser is initialized by a single frequency 10 ns Q-switched laser pulse. This is very similar to how an injection seeding or regenerative amplifier scheme starts a laser oscillation. With a cavity length of around 11 meters and an initial laser pulse of 10 ns, we have been able to isolate laser field images related to each round-trip pulse. Furthermore, by replacing the first mirror with a rough-surface target to simulate an uncooperative target and adding phase distortion elements to simulate atmospheric effects, we can observe the image status under such conditions.

Novel Brassinosteroid-Modified Polyethylene Glycol Micelles for Controlled Release of Agrochemicals.

PubMed

Pérez Quiñones, Javier; Brüggemann, Oliver; Kjems, Jørgen; Shahavi, Mohammad Hassan; Peniche Covas, Carlos

2018-02-21

Two synthetic analogues of brassinosteroids (DI31 and S7) exhibit good plant growth enhancer activity. However, their hydrophobicity and quick metabolism in plants have limited their application and benefits in agriculture. Our objective was to prepare novel brassinosteroid-modified polyethylene glycol (PEG) micelles to achieve controlled release with extended stability while retaining agrochemical activity. Spectroscopic studies confirmed quantitative disubstitution of studied PEGs with the brassinosteroids, while elemental analysis assessed purity of the synthesized conjugates. Conjugates were also characterized by X-ray diffraction and thermal analysis. Dynamic and static light scattering showed stable and homogeneous approximately spherical micelles with average hydrodynamic diameters of 22-120 nm and almost neutral ζ potential. Spherical 30-140 nm micelles were observed by electron microscopy. Sustained in vitro releases at pH 5.5 were extended up to 96 h. Prepared PEG micelles showed good agrochemical activity in the radish seed bioassay and no cytotoxicity to the human microvascular endothelial cell line in the MTS test.

A novel strategy for development of glucocorticoids through non-genomic mechanism.

PubMed

Zhou, Jian; Li, Min; Sheng, Chun-Quan; Liu, Lei; Li, Zhen; Wang, Yan; Zhou, Jiang-Rui; Jing, Zai-Ping; Chen, Yi-Zhang; Jiang, Chun-Lei

2011-04-01

Glucocorticoids (GCs) are routinely believed to take effect through genomic mechanisms, which are also largely responsible for GCs' side effects. Beneficial non-genomic effects of GCs have been reported as being independent of the genomic pathway. Here, we synthesized a new type of GCs, which took effect mainly via non-genomic mechanisms. Hydrocortisone was conjugated with glycine, lysine and phenylalanine to get a bigger molecular structure, which could hardly go through the cell membrane. Evaluation of the anti-inflammatory efficacy showed that hydrocortisone-conjugated glycine (HG) and lysine could inhibit neutrophil degranulation within 15 min. HG could inhibit IgE-mediated histamine release from mast cells via a non-genomic pathway, and rapidly alleviate allergic reaction. Luciferase reporter assay showed that HG would not activate the glucocorticoid response element within 30 min, which verified the rapid effects independent of the genomic pathway. The work proposes a novel insight into the development of novel GCs, and provides new tools for experimental study on non-genomic mechanisms.

Improved accuracy for finite element structural analysis via a new integrated force method

NASA Technical Reports Server (NTRS)

Patnaik, Surya N.; Hopkins, Dale A.; Aiello, Robert A.; Berke, Laszlo

1992-01-01

A comparative study was carried out to determine the accuracy of finite element analyses based on the stiffness method, a mixed method, and the new integrated force and dual integrated force methods. The numerical results were obtained with the following software: MSC/NASTRAN and ASKA for the stiffness method; an MHOST implementation method for the mixed method; and GIFT for the integrated force methods. The results indicate that on an overall basis, the stiffness and mixed methods present some limitations. The stiffness method generally requires a large number of elements in the model to achieve acceptable accuracy. The MHOST method tends to achieve a higher degree of accuracy for course models than does the stiffness method implemented by MSC/NASTRAN and ASKA. The two integrated force methods, which bestow simultaneous emphasis on stress equilibrium and strain compatibility, yield accurate solutions with fewer elements in a model. The full potential of these new integrated force methods remains largely unexploited, and they hold the promise of spawning new finite element structural analysis tools.

Mapping the resistance-associated mobilome of a carbapenem-resistant Klebsiella pneumoniae strain reveals insights into factors shaping these regions and facilitates generation of a 'resistance-disarmed' model organism.

PubMed

Bi, Dexi; Jiang, Xiaofei; Sheng, Zi-Ke; Ngmenterebo, David; Tai, Cui; Wang, Minggui; Deng, Zixin; Rajakumar, Kumar; Ou, Hong-Yu

2015-10-01

This study aims to investigate the landscape of the mobile genome, with a focus on antibiotic resistance-associated factors in carbapenem-resistant Klebsiella pneumoniae. The mobile genome of the completely sequenced K. pneumoniae HS11286 strain (an ST11, carbapenem-resistant, near-pan-resistant, clinical isolate) was annotated in fine detail. The identified mobile genetic elements were mapped to the genetic contexts of resistance genes. The blaKPC-2 gene and a 26 kb region containing 12 clustered antibiotic resistance genes and one biocide resistance gene were deleted, and the MICs were determined again to ensure that antibiotic resistance had been lost. HS11286 contains six plasmids, 49 ISs, nine transposons, two separate In2-related integron remnants, two integrative and conjugative elements (ICEs) and seven prophages. Sixteen plasmid-borne resistance genes were identified, 14 of which were found to be directly associated with Tn1721-, Tn3-, Tn5393-, In2-, ISCR2- and ISCR3-derived elements. IS26 appears to have actively moulded several of these genetic regions. The deletion of blaKPC-2, followed by the deletion of a 26 kb region containing 12 clustered antibiotic resistance genes, progressively decreased the spectrum and level of resistance exhibited by the resultant mutant strains. This study has reiterated the role of plasmids as bearers of the vast majority of resistance genes in this species and has provided valuable insights into the vital role played by ISs, transposons and integrons in shaping the resistance-coding regions in this important strain. The 'resistance-disarmed' K. pneumoniae ST11 strain generated in this study will offer a more benign and readily genetically modifiable model organism for future extensive functional studies. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Vibrio cholerae O1 epidemic variants in Angola: a retrospective study between 1992 and 2006.

PubMed

Valia, Romy; Taviani, Elisa; Spagnoletti, Matteo; Ceccarelli, Daniela; Cappuccinelli, Piero; Colombo, Mauro M

2013-01-01

Cholera is still a major public health concern in many African countries. In Angola, after a decade of absence, cholera reemerged in 1987, spreading throughout the country until 1996, with outbreaks recurring in a seasonal pattern. In 2006 Angola was hit by one of the most severe outbreaks of the last decade, with ca. 240,000 cases reported. We analyzed 21 clinical strains isolated between 1992 and 2006 from several provinces throughout the country: Benguela, Bengo, Luanda, Cuando Cubango, and Cabinda. We used two multiplex PCR assays to investigate discriminatory mobile genetic elements (MGE) [Integrative Conjugative Elements (ICEs), VSP-II, GI12, GI14, GI15, K, and TLC phages] and we compared the profiles obtained with those of different reference V. cholerae O1 variants (prototypical, altered, and hybrid), responsible for the ongoing 7th pandemic. We also tested the strains for the presence of specific VSP-II variants and for the presence of a genomic island (GI) (WASA-1), correlated with the transmission of seventh pandemic cholera from Africa to South America. Based on the presence/absence of the analyzed genetic elements, five novel profiles were detected in the epidemic strains circulating in the 1990s. The most frequent profiles, F and G, were characterized by the absence of ICEs and the three GIs tested, and the presence of GI WASA-1 and the WASA variant of the VSP-II island. Our results identified unexpected variability within the 1990s epidemic, showing different rearrangements in a dynamic part of the genome not present in the prototypical V. cholerae O1 N16961. Moreover the 2006 strains differed from the current pandemic V. cholerae O1 strain. Taken together, our results highlight the role of horizontal gene transfer (HGT) in diversifying the genetic background of V. cholerae within a single epidemic.

Design and characterization of nanomaterial-biomolecule conjugates

NASA Astrophysics Data System (ADS)

Yim, Tae-Jin

In the field of nanobiotechnology, nanoscale dimensions result in physical properties that differ from more conventional bulk material state. The integration of nanomaterials with biomolecules has begun to be used for unique physical properties, and for biological specific recognition, thereby leading to novel nanomaterial-biomolecule conjugates. The direction of this dissertation is to develop biocatalytic nanomaterial-biomolecule conjugates and to characterize them. For this, biological catalysts are employed to combine with nanomaterials. Two large parts include functional ization of nanomaterials with biomolecules and assembly of nanomaterials using a biological catalyst. First part of this thesis work is the exploration of the biocatalytic properties of nanomaterial-biomolecule conjugates. Si nanocolumns have higher surface area which leads more amount of biocatalytis immobilization than flat Si wafer with the same projected area. The enhanced activity of soybean peroxidase (SBP) immobilized onto Si nanocolumns as novel nanostructured supports is focused. Next, the catalytic activity of immobilized DNAzyme onto multiwalled carbon nanotubes (MWNTs) is compared to that in solution phase, and multiple turnovers are examined. The relationship between hybridization efficiency and activity is investigated as a function of surface density of DNAzyme on MWNTs. Then, cellular delivery of silica nanoparticle-protein conjugates is visually confirmed and therefore the intracellular function of a protein delivered by silica nanoparticle-protein conjugates is proved. For one example of the intracellular function, stable SBP immobilized onto silica nanoparticles to activate a prodrug is demonstrated. Second part of this thesis work is the formation of nanostructured materials through the enzymatic assembly of single-walled carbon nanotubes (SWNTs). Enzymatic polymerization of a phenol compound is applied to the bridging of two or more SWNTs functionalized with phenol monomers. Next, future work based on previous works is proposed; first, the cellular delivery of DNAzyme using SWNTs is proposed to be a promising nonviral nanovehicle for gene silencing. Second, hydrophobic/hydrophilic switchable surface using DNAzyme is suggested to expand its usage to hydrophobically gradient surface. Finally, reversible assembly and disassembly of poly-L-histidine coated MWNTs can be applied to a reversible nanotube patterning on surface. And, the expansion of the works presented in this thesis to "nanomedicine" is suggested.

Finite Element Simulation of Articular Contact Mechanics with Quadratic Tetrahedral Elements

PubMed Central

Maas, Steve A.; Ellis, Benjamin J.; Rawlins, David S.; Weiss, Jeffrey A.

2016-01-01

Although it is easier to generate finite element discretizations with tetrahedral elements, trilinear hexahedral (HEX8) elements are more often used in simulations of articular contact mechanics. This is due to numerical shortcomings of linear tetrahedral (TET4) elements, limited availability of quadratic tetrahedron elements in combination with effective contact algorithms, and the perceived increased computational expense of quadratic finite elements. In this study we implemented both ten-node (TET10) and fifteen-node (TET15) quadratic tetrahedral elements in FEBio (www.febio.org) and compared their accuracy, robustness in terms of convergence behavior and computational cost for simulations relevant to articular contact mechanics. Suitable volume integration and surface integration rules were determined by comparing the results of several benchmark contact problems. The results demonstrated that the surface integration rule used to evaluate the contact integrals for quadratic elements affected both convergence behavior and accuracy of predicted stresses. The computational expense and robustness of both quadratic tetrahedral formulations compared favorably to the HEX8 models. Of note, the TET15 element demonstrated superior convergence behavior and lower computational cost than both the TET10 and HEX8 elements for meshes with similar numbers of degrees of freedom in the contact problems that we examined. Finally, the excellent accuracy and relative efficiency of these quadratic tetrahedral elements was illustrated by comparing their predictions with those for a HEX8 mesh for simulation of articular contact in a fully validated model of the hip. These results demonstrate that TET10 and TET15 elements provide viable alternatives to HEX8 elements for simulation of articular contact mechanics. PMID:26900037

A governance model for integrated primary/secondary care for the health-reforming first world – results of a systematic review

PubMed Central

2013-01-01

Background Internationally, key health care reform elements rely on improved integration of care between the primary and secondary sectors. The objective of this systematic review is to synthesise the existing published literature on elements of current integrated primary/secondary health care. These elements and how they have supported integrated healthcare governance are presented. Methods A systematic review of peer-reviewed literature from PubMed, MEDLINE, CINAHL, the Cochrane Library, Informit Health Collection, the Primary Health Care Research and Information Service, the Canadian Health Services Research Foundation, European Foundation for Primary Care, European Forum for Primary Care, and Europa Sinapse was undertaken for the years 2006–2012. Relevant websites were also searched for grey literature. Papers were assessed by two assessors according to agreed inclusion criteria which were published in English, between 2006–2012, studies describing an integrated primary/secondary care model, and had reported outcomes in care quality, efficiency and/or satisfaction. Results Twenty-one studies met the inclusion criteria. All studies evaluated the process of integrated governance and service delivery structures, rather than the effectiveness of services. They included case reports and qualitative data analyses addressing policy change, business issues and issues of clinical integration. A thematic synthesis approach organising data according to themes identified ten elements needed for integrated primary/secondary health care governance across a regional setting including: joint planning; integrated information communication technology; change management; shared clinical priorities; incentives; population focus; measurement – using data as a quality improvement tool; continuing professional development supporting joint working; patient/community engagement; and, innovation. Conclusions All examples of successful primary/secondary care integration reported in the literature have focused on a combination of some, if not all, of the ten elements described in this paper, and there appears to be agreement that multiple elements are required to ensure successful and sustained integration efforts. Whilst no one model fits all systems these elements provide a focus for setting up integration initiatives which need to be flexible for adapting to local conditions and settings. PMID:24359610

A governance model for integrated primary/secondary care for the health-reforming first world - results of a systematic review.

PubMed

Nicholson, Caroline; Jackson, Claire; Marley, John

2013-12-20

Internationally, key health care reform elements rely on improved integration of care between the primary and secondary sectors. The objective of this systematic review is to synthesise the existing published literature on elements of current integrated primary/secondary health care. These elements and how they have supported integrated healthcare governance are presented. A systematic review of peer-reviewed literature from PubMed, MEDLINE, CINAHL, the Cochrane Library, Informit Health Collection, the Primary Health Care Research and Information Service, the Canadian Health Services Research Foundation, European Foundation for Primary Care, European Forum for Primary Care, and Europa Sinapse was undertaken for the years 2006-2012. Relevant websites were also searched for grey literature. Papers were assessed by two assessors according to agreed inclusion criteria which were published in English, between 2006-2012, studies describing an integrated primary/secondary care model, and had reported outcomes in care quality, efficiency and/or satisfaction. Twenty-one studies met the inclusion criteria. All studies evaluated the process of integrated governance and service delivery structures, rather than the effectiveness of services. They included case reports and qualitative data analyses addressing policy change, business issues and issues of clinical integration. A thematic synthesis approach organising data according to themes identified ten elements needed for integrated primary/secondary health care governance across a regional setting including: joint planning; integrated information communication technology; change management; shared clinical priorities; incentives; population focus; measurement - using data as a quality improvement tool; continuing professional development supporting joint working; patient/community engagement; and, innovation. All examples of successful primary/secondary care integration reported in the literature have focused on a combination of some, if not all, of the ten elements described in this paper, and there appears to be agreement that multiple elements are required to ensure successful and sustained integration efforts. Whilst no one model fits all systems these elements provide a focus for setting up integration initiatives which need to be flexible for adapting to local conditions and settings.

A computer code for calculations in the algebraic collective model of the atomic nucleus

NASA Astrophysics Data System (ADS)

Welsh, T. A.; Rowe, D. J.

2016-03-01

A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.

49 CFR 192.911 - What are the elements of an integrity management program?

Code of Federal Regulations, 2012 CFR

2012-10-01

...? An operator's initial integrity management program begins with a framework (see § 192.907) and...), by electronic or other means, a copy of the operator's risk analysis or integrity management program... 49 Transportation 3 2012-10-01 2012-10-01 false What are the elements of an integrity management...

49 CFR 192.911 - What are the elements of an integrity management program?

Code of Federal Regulations, 2014 CFR

2014-10-01

...? An operator's initial integrity management program begins with a framework (see § 192.907) and...), by electronic or other means, a copy of the operator's risk analysis or integrity management program... 49 Transportation 3 2014-10-01 2014-10-01 false What are the elements of an integrity management...

49 CFR 192.911 - What are the elements of an integrity management program?

Code of Federal Regulations, 2013 CFR

2013-10-01

...? An operator's initial integrity management program begins with a framework (see § 192.907) and...), by electronic or other means, a copy of the operator's risk analysis or integrity management program... 49 Transportation 3 2013-10-01 2013-10-01 false What are the elements of an integrity management...

49 CFR 192.911 - What are the elements of an integrity management program?

Code of Federal Regulations, 2011 CFR

2011-10-01

...? An operator's initial integrity management program begins with a framework (see § 192.907) and...), by electronic or other means, a copy of the operator's risk analysis or integrity management program... 49 Transportation 3 2011-10-01 2011-10-01 false What are the elements of an integrity management...

Inventory of available data elements for the San Bernardino, California region

NASA Technical Reports Server (NTRS)

Christenson, J.; Michel, R.

1981-01-01

Elements of data sets that are available to be integrated for the San Bernardino vertical data integration project are given. Each of the data sets has specified for it the ownership, validity, accuracy and technical requirements for integration.

Translating the Elements of Health Governance for Integrated Care from Theory to Practice: A Case Study Approach

PubMed Central

Hepworth, Julie; Burridge, Letitia; Marley, John; Jackson, Claire

2018-01-01

Introduction: Against a paucity of evidence, a model describing elements of health governance best suited to achieving integrated care internationally was developed. The aim of this study was to explore how health meso-level organisations used, or planned to use, the governance elements. Methods: A case study design was used to offer two contrasting contexts of health governance. Semi-structured interviews were conducted with participants who held senior governance roles. Data were thematically analysed to identify if the elements of health governance were being used, or intended to be in the future. Results: While all participants agreed that the ten elements were essential to developing future integrated care, most were not used. Three major themes were identified: (1) organisational versus system focus, (2) leadership and culture, and, (3) community (dis)engagement. Discussion: Several barriers and enablers to the use of the elements were identified and would require addressing in order to make evidence-based changes. Conclusion: Despite a clear international policy direction in support of integrated care this study identified a number of significant barriers to its implementation. The study reconfirmed that a focus on all ten elements of health governance is essential to achieve integrated care. PMID:29588645

The tapered slot antenna - A new integrated element for millimeter-wave applications

NASA Technical Reports Server (NTRS)

Yngvesson, K. Sigfrid; Kim, Young-Sik; Korzeniowski, T. L.; Kollberg, Erik L.; Johansson, Joakim F.

1989-01-01

Tapered slot antennas (TSAs) with a number of potential applications as single elements and focal-plane arrays are discussed. TSAs are fabricated with photolithographic techniques and integrated in either hybrid or MMIC circuits with receiver or transmitter components. They offer considerably narrower beams than other integrated antenna elements and have high aperture efficiency and packing density as array elements. Both the circuit and radiation properties of TSAs are reviewed. Topics covered include: antenna beamwidth, directivity, and gain of single-element TSAs; their beam shape and the effect of different taper shapes; and the input impedance and the effects of using thick dielectrics. These characteristics are also given for TSA arrays, as are the circuit properties of the array elements. Different array structures and their applications are also described.

Simultaneous analysis and design

NASA Technical Reports Server (NTRS)

Haftka, R. T.

1984-01-01

Optimization techniques are increasingly being used for performing nonlinear structural analysis. The development of element by element (EBE) preconditioned conjugate gradient (CG) techniques is expected to extend this trend to linear analysis. Under these circumstances the structural design problem can be viewed as a nested optimization problem. There are computational benefits to treating this nested problem as a large single optimization problem. The response variables (such as displacements) and the structural parameters are all treated as design variables in a unified formulation which performs simultaneously the design and analysis. Two examples are used for demonstration. A seventy-two bar truss is optimized subject to linear stress constraints and a wing box structure is optimized subject to nonlinear collapse constraints. Both examples show substantial computational savings with the unified approach as compared to the traditional nested approach.

Conference Proceedings: 7th Annual Review of Progress in Applied Computational Electromagnetics at the Naval Postgraduate School, Monterey, California, March 18-22, 1991

DTIC Science & Technology

1991-03-01

34Volume integral Equations and Conjugate Gradient Methods in Electromagnetic Non destructive Evaluation’ by Dr. Harold P.. Sabbagh, Sabbagh Associates...8217 Experimental Demonstrations far teaching Electroamgnetic Folods and Energy’ M. Zathn, J. Mectrer...8217-....................................... . ...................................................... 329 ’PoalarimetrIc Scattering and Control at Radar Crass Section of Chirat Targets at Simple

Preclinical Evaluation to Specifically Target Ovarian Cancer with Folic Acid-Conjugated Nanoceria

DTIC Science & Technology

2014-08-01

cancer . Our experimental nanoparticle is Nanoceria (NCe), a cerium oxide nanoparticle . Nanotechnology -based tools and techniques are rapidly... cancer we proposed the present work, where we are integrating the field of nanotechnology with ovarian cancer cell’s unique property of...overexpressing folic acid receptor alpha (FR-a) to specifically target ovarian cancer . A cerium oxide nanoparticle , called Nanoceria (NCe), that has the ability

Protein quality control at the inner nuclear membrane

PubMed Central

Khmelinskii, Anton; Blaszczak, Ewa; Pantazopoulou, Marina; Fischer, Bernd; Omnus, Deike J.; Le Dez, Gaëlle; Brossard, Audrey; Gunnarsson, Alexander; Barry, Joseph D.; Meurer, Matthias; Kirrmaier, Daniel; Boone, Charles; Huber, Wolfgang; Rabut, Gwenaël; Ljungdahl, Per O.; Knop, Michael

2015-01-01

The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression1. The outer nuclear membrane is continuous with the endoplasmic reticulum (ER) and is the site of membrane protein synthesis. Protein homeostasis in this compartment is ensured by ER-associated protein degradation (ERAD) pathways that in yeast involve the integral membrane E3 ubiquitin ligases Hrd1 and Doa10 operating with the E2 ubiquitin-conjugating enzymes Ubc6 and Ubc72,3. However, little is known regarding protein quality control at the INM. Here we describe a protein degradation pathway at the INM mediated by the Asi complex consisting of the RING domain proteins Asi1 and Asi34. We report that the As complex functions together with the ubiquitin conjugating enzymes Ubc6andUbc7to degrade soluble and integral membrane proteins. Genetic evidence suggest that the Asi ubiquitin ligase defines a pathway distinct from but complementary to ERAD. Using unbiased screening with a novel genome-wide yeast library based on a tandem fluorescent protein timer (tFT)5, we identify more than 50 substrates of the Asi, Hrd1 and Doa10 E3 ubiquity ligases. We show that the Asi ubiquitin ligase is involved in degradation of mislocalised integral membrane proteins, thus acting to maintain and safeguard the identity of the INM. PMID:25519137

Capture of dengue viruses using antibody-integrated graphite-encapsulated magnetic beads produced using gas plasma technology

PubMed Central

SAKUDO, AKIKAZU; VISWAN, ANCHU; CHOU, HAN; SASAKI, TADAHIRO; IKUTA, KAZUYOSHI; NAGATSU, MASAAKI

2016-01-01

Despite significant advances in medicine, global health is threatened by emerging infectious diseases caused by a number of viruses. Dengue virus (DENV) is a mosquito-borne virus, which can be transmitted to humans via mosquito vectors. Previously, the Ministry of Health, Labour and Welfare in Japan reported the country's first domestically acquired case of dengue fever for almost 70 years. To address this issue, it is important to develop novel technologies for the sensitive detection of DENV. The present study reported on the development of plasma-functionalized, graphite-encapsulated magnetic nanoparticles (GrMNPs) conjugated with anti-DENV antibody for DENV capture. Radiofrequency wave-excited inductively-coupled Ar and ammonia gas plasmas were used to introduce amino groups onto the surface of the GrMNPs. The GrMNPs were then conjugated with an antibody against DENV, and the antibody-integrated magnetic beads were assessed for their ability to capture DENV. Beads incubated in a cell culture medium of DENV-infected mosquito cells were separated from the supernatant by applying a magnetic field and were then washed. The adsorption of DENV serotypes 1–4 onto the beads was confirmed using reverse transcription-polymerase chain reaction, which detected the presence of DENV genomic RNA on the GrMNPs. The methodology described in the present study, which employed the plasma-functionalization of GrMNPs to enable antibody-integration, represents a significant improvement in the detection of DENV. PMID:27221214

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

Ochiai, Yoshihiro

Heat-conduction analysis under steady state without heat generation can easily be treated by the boundary element method. However, in the case with heat conduction with heat generation can approximately be solved without a domain integral by an improved multiple-reciprocity boundary element method. The convention multiple-reciprocity boundary element method is not suitable for complicated heat generation. In the improved multiple-reciprocity boundary element method, on the other hand, the domain integral in each step is divided into point, line, and area integrals. In order to solve the problem, the contour lines of heat generation, which approximate the actual heat generation, are used.

Strip biosensor for amplified detection of nerve growth factor-beta based on a molecular translator and catalytic DNA circuit.

PubMed

Liu, Jun; Lai, Ting; Mu, Kejie; Zhou, Zheng

2014-10-07

We have demonstrated a new visual detection approach based on a molecular translator and a catalytic DNA circuit for the detection of nerve growth factor-beta (NGF-β). In this assay, a molecular translator based on the binding-induced DNA strand-displacement reaction was employed to convert the input protein to an output DNA signal. The molecular translator is composed of a target recognition element and a signal output element. Target recognition is achieved by the binding of the anti-NGF-β antibody to the target protein. Polyclonal anti-NGF-β antibody is conjugated to DNA1 and DNA2. The antibody conjugated DNA1 is initially hybridized to DNA3 to form a stable DNA1/DNA3 duplex. In the presence of NGF-β, the binding of the same target protein brings DNA1 and DNA2 into close proximity, resulting in an increase in their local effective concentration. This process triggers the strand-displacement reaction between DNA2 and DNA3 and releases the output DNA3. The released DNA3 is further amplified by a catalytic DNA circuit. The product of the catalytic DNA circuit is detected by a strip biosensor. This proposed assay has high sensitivity and selectivity with a dynamic response ranging from 10 fM to 10 pM, and its detection limit is 10 fM of NGF-β. This work provides a sensitive, enzyme-free, and universal strategy for the detection of other proteins.

Finite element simulation of articular contact mechanics with quadratic tetrahedral elements.

PubMed

Maas, Steve A; Ellis, Benjamin J; Rawlins, David S; Weiss, Jeffrey A

2016-03-21

Although it is easier to generate finite element discretizations with tetrahedral elements, trilinear hexahedral (HEX8) elements are more often used in simulations of articular contact mechanics. This is due to numerical shortcomings of linear tetrahedral (TET4) elements, limited availability of quadratic tetrahedron elements in combination with effective contact algorithms, and the perceived increased computational expense of quadratic finite elements. In this study we implemented both ten-node (TET10) and fifteen-node (TET15) quadratic tetrahedral elements in FEBio (www.febio.org) and compared their accuracy, robustness in terms of convergence behavior and computational cost for simulations relevant to articular contact mechanics. Suitable volume integration and surface integration rules were determined by comparing the results of several benchmark contact problems. The results demonstrated that the surface integration rule used to evaluate the contact integrals for quadratic elements affected both convergence behavior and accuracy of predicted stresses. The computational expense and robustness of both quadratic tetrahedral formulations compared favorably to the HEX8 models. Of note, the TET15 element demonstrated superior convergence behavior and lower computational cost than both the TET10 and HEX8 elements for meshes with similar numbers of degrees of freedom in the contact problems that we examined. Finally, the excellent accuracy and relative efficiency of these quadratic tetrahedral elements was illustrated by comparing their predictions with those for a HEX8 mesh for simulation of articular contact in a fully validated model of the hip. These results demonstrate that TET10 and TET15 elements provide viable alternatives to HEX8 elements for simulation of articular contact mechanics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Site-specific chemical conjugation of human Fas ligand extracellular domain using trans-cyclooctene - methyltetrazine reactions.

PubMed

Muraki, Michiro; Hirota, Kiyonori

2017-07-03

Fas ligand plays a key role in the human immune system as a major cell death inducing protein. The extracellular domain of human Fas ligand (hFasLECD) triggers apoptosis of malignant cells, and therefore is expected to have substantial potentials in medical biotechnology. However, the current application of this protein to clinical medicine is hampered by a shortage of the benefits relative to the drawbacks including the side-effects in systemic administration. Effective procedures for the engineering of the protein by attaching useful additional functions are required to overcome the problem. A procedure for the site-specific chemical conjugation of hFasLECD with a fluorochrome and functional proteins was devised using an inverse-electron-demand Diels-Alder reaction between trans-cyclooctene group and methyltetrazine group. The conjugations in the present study were attained by using much less molar excess amounts of the compounds to be attached as compared with the conventional chemical modification reactions using maleimide derivatives in the previous study. The isolated conjugates of hFasLECD with sulfo-Cy3, avidin and rabbit IgG Fab' domain presented the functional and the structural integrities of the attached molecules without impairing the specific binding activity toward human Fas receptor extracellular domain. The present study provided a new fundamental strategy for the production of the engineered hFasLECDs with additional beneficial functions, which will lead to the developments of the improved diagnostic systems and the effective treatment methods of serious diseases by using this protein as a component of novel molecular tools.

Multivalent ligands control stem cell behaviour in vitro and in vivo

NASA Astrophysics Data System (ADS)

Conway, Anthony; Vazin, Tandis; Spelke, Dawn P.; Rode, Nikhil A.; Healy, Kevin E.; Kane, Ravi S.; Schaffer, David V.

2013-11-01

There is broad interest in designing nanostructured materials that can interact with cells and regulate key downstream functions. In particular, materials with nanoscale features may enable control over multivalent interactions, which involve the simultaneous binding of multiple ligands on one entity to multiple receptors on another and are ubiquitous throughout biology. Cellular signal transduction of growth factor and morphogen cues (which have critical roles in regulating cell function and fate) often begins with such multivalent binding of ligands, either secreted or cell-surface-tethered to target cell receptors, leading to receptor clustering. Cellular mechanisms that orchestrate ligand-receptor oligomerization are complex, however, so the capacity to control multivalent interactions and thereby modulate key signalling events within living systems is currently very limited. Here, we demonstrate the design of potent multivalent conjugates that can organize stem cell receptors into nanoscale clusters and control stem cell behaviour in vitro and in vivo. The ectodomain of ephrin-B2, normally an integral membrane protein ligand, was conjugated to a soluble biopolymer to yield multivalent nanoscale conjugates that potently induce signalling in neural stem cells and promote their neuronal differentiation both in culture and within the brain. Super-resolution microscopy analysis yielded insights into the organization of the receptor-ligand clusters at the nanoscale. We also found that synthetic multivalent conjugates of ephrin-B1 strongly enhance human embryonic and induced pluripotent stem cell differentiation into functional dopaminergic neurons. Multivalent bioconjugates are therefore powerful tools and potential nanoscale therapeutics for controlling the behaviour of target stem cells in vitro and in vivo.

Dynamic coding of vertical facilitated vergence by premotor saccadic burst neurons.

PubMed

Van Horn, Marion R; Cullen, Kathleen E

2008-10-01

To redirect our gaze in three-dimensional space we frequently combine saccades and vergence. These eye movements, known as disconjugate saccades, are characterized by eyes rotating by different amounts, with markedly different dynamics, and occur whenever gaze is shifted between near and far objects. How the brain ensures the precise control of binocular positioning remains controversial. It has been proposed that the traditionally assumed "conjugate" saccadic premotor pathway does not encode conjugate commands but rather encodes monocular commands for the right or left eye during saccades. Here, we directly test this proposal by recording from the premotor neurons of the horizontal saccade generator during a dissociation task that required a vergence but no horizontal conjugate saccadic command. Specifically, saccadic burst neurons (SBNs) in the paramedian pontine reticular formation were recorded while rhesus monkeys made vertical saccades made between near and far targets. During this task, we first show that peak vergence velocities were enhanced to saccade-like speeds (e.g., >150 vs. <100 degrees/s during saccade-free movements for comparable changes in vergence angle). We then quantified the discharge dynamics of SBNs during these movements and found that the majority of the neurons preferentially encode the velocity of the ipsilateral eye. Notably, a given neuron typically encoded the movement of the same eye during horizontal saccades that were made in depth. Taken together, our findings demonstrate that the brain stem saccadic burst generator encodes integrated conjugate and vergence commands, thus providing strong evidence for the proposal that the classic saccadic premotor pathway controls gaze in three-dimensional space.

Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances

PubMed Central

Flórez, Ana B.; Mayo, Baltasar

2017-01-01

The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability. PMID:29312272

Multi-viewer tracking integral imaging system and its viewing zone analysis.

PubMed

Park, Gilbae; Jung, Jae-Hyun; Hong, Keehoon; Kim, Yunhee; Kim, Young-Hoon; Min, Sung-Wook; Lee, Byoungho

2009-09-28

We propose a multi-viewer tracking integral imaging system for viewing angle and viewing zone improvement. In the tracking integral imaging system, the pickup angles in each elemental lens in the lens array are decided by the positions of viewers, which means the elemental image can be made for each viewer to provide wider viewing angle and larger viewing zone. Our tracking integral imaging system is implemented with an infrared camera and infrared light emitting diodes which can track the viewers' exact positions robustly. For multiple viewers to watch integrated three-dimensional images in the tracking integral imaging system, it is needed to formulate the relationship between the multiple viewers' positions and the elemental images. We analyzed the relationship and the conditions for the multiple viewers, and verified them by the implementation of two-viewer tracking integral imaging system.

49 CFR 192.911 - What are the elements of an integrity management program?

Code of Federal Regulations, 2010 CFR

2010-10-01

...) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) PIPELINE SAFETY TRANSPORTATION OF NATURAL AND OTHER GAS BY PIPELINE: MINIMUM FEDERAL SAFETY STANDARDS Gas Transmission Pipeline Integrity Management § 192.911 What are the elements of an integrity management program...

A distinct and divergent lineage of genomic island-associated Type IV Secretion Systems in Legionella.

PubMed

Wee, Bryan A; Woolfit, Megan; Beatson, Scott A; Petty, Nicola K

2013-01-01

Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches.

A Distinct and Divergent Lineage of Genomic Island-Associated Type IV Secretion Systems in Legionella

PubMed Central

Wee, Bryan A.; Woolfit, Megan; Beatson, Scott A.; Petty, Nicola K.

2013-01-01

Legionella encodes multiple classes of Type IV Secretion Systems (T4SSs), including the Dot/Icm protein secretion system that is essential for intracellular multiplication in amoebal and human hosts. Other T4SSs not essential for virulence are thought to facilitate the acquisition of niche-specific adaptation genes including the numerous effector genes that are a hallmark of this genus. Previously, we identified two novel gene clusters in the draft genome of Legionella pneumophila strain 130b that encode homologues of a subtype of T4SS, the genomic island-associated T4SS (GI-T4SS), usually associated with integrative and conjugative elements (ICE). In this study, we performed genomic analyses of 14 homologous GI-T4SS clusters found in eight publicly available Legionella genomes and show that this cluster is unusually well conserved in a region of high plasticity. Phylogenetic analyses show that Legionella GI-T4SSs are substantially divergent from other members of this subtype of T4SS and represent a novel clade of GI-T4SSs only found in this genus. The GI-T4SS was found to be under purifying selection, suggesting it is functional and may play an important role in the evolution and adaptation of Legionella. Like other GI-T4SSs, the Legionella clusters are also associated with ICEs, but lack the typical integration and replication modules of related ICEs. The absence of complete replication and DNA pre-processing modules, together with the presence of Legionella-specific regulatory elements, suggest the Legionella GI-T4SS-associated ICE is unique and may employ novel mechanisms of regulation, maintenance and excision. The Legionella GI-T4SS cluster was found to be associated with several cargo genes, including numerous antibiotic resistance and virulence factors, which may confer a fitness benefit to the organism. The in-silico characterisation of this new T4SS furthers our understanding of the diversity of secretion systems involved in the frequent horizontal gene transfers that allow Legionella to adapt to and exploit diverse environmental niches. PMID:24358157

Designer diatom episomes delivered by bacterial conjugation

DOE PAGES

Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.; ...

2015-04-21

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify amore » yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.« less

Designer diatom episomes delivered by bacterial conjugation

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

Karas, Bogumil J.; Diner, Rachel E.; Lefebvre, Stephane C.

Eukaryotic microalgae hold great promise for the bioproduction of fuels and higher value chemicals. However, compared with model genetic organisms such as Escherichia coli and Saccharomyces cerevisiae, characterization of the complex biology and biochemistry of algae and strain improvement has been hampered by the inefficient genetic tools. To date, many algal species are transformable only via particle bombardment, and the introduced DNA is integrated randomly into the nuclear genome. Here we describe the first nuclear episomal vector for diatoms and a plasmid delivery method via conjugation from Escherichia coli to the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. We identify amore » yeast-derived sequence that enables stable episome replication in these diatoms even in the absence of antibiotic selection and show that episomes are maintained as closed circles at copy number equivalent to native chromosomes. This highly efficient genetic system facilitates high-throughput functional characterization of algal genes and accelerates molecular phytoplankton research.« less

Recombinant Clone Heterogeneity in ESCHERICHIA COLI Conjunction: Effect of Ph and Partially Replicated Recipient Deoxyribonucleic Acid

PubMed Central

Ou, Jonathan T.

1975-01-01

At pH 6.8, a substantial fraction of recombinant colonies obtained from conjugation with an HfrH donor contained multiple recombinant classes in a single colony (polygenotypic colony). In contrast, when the conjugation was performed at pH 7.6, the number of polygenotypic colonies was drastically reduced, and the recombinant colonies were predominantly monogenotypic or digenotypic. Genetic analysis revealed that the digenotypic recombinants differ in those donor markers near the origin of DNA replication but share those donor markers near the terminus. This integration pattern suggests that the formation of digenotypic recombinants involves recombination of a single copy of the exogenome with a partially replicated recipient DNA molecule. This suggestion was supported by examination of the genotype of recombinant colonies recovered from crosses with an HfrKL96 donor which was derived from HfrH but transfers its chromosome in the reverse direction. PMID:8360

Excessive Labeling Technique Provides a Highly Sensitive Fluorescent Probe for Real-time Monitoring of Biodegradation of Biopolymer Pharmaceuticals in vivo.

PubMed

Terekhov, S S; Smirnov, I V; Shamborant, O G; Zenkova, M A; Chernolovskaya, E L; Gladkikh, D V; Murashev, A N; Dyachenko, I A; Knorre, V D; Belogurov, A A; Ponomarenko, N A; Deyev, S M; Vlasov, V V; Gabibov, A G

2014-10-01

Recombinant proteins represent a large sector of the biopharma market. Determination of the main elimination pathways raises the opportunities to significantly increase their half-lives in vivo. However, evaluation of biodegradation of pharmaceutical biopolymers performed in the course of pre-clinical studies is frequently complicated. Noninvasive pharmacokinetic and biodistribution studies in living organism are possible using proteins conjugated with near-infrared dyes. In the present study we designed a highly efficient probe based on fluorescent dye self-quenching for monitoring of in vivo biodegradation of recombinant human butyrylcholinesterase. The maximum enhancement of integral fluorescence in response to degradation of an intravenously administered enzyme was observed 6 h after injection. Importantly, excessive butyrylcholinesterase labeling with fluorescent dye results in significant changes in the pharmacokinetic properties of the obtained conjugate. This fact must be taken into consideration during future pharmacokinetic studies using in vivo bioimaging.

Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone.

PubMed

Villa, Laura; Feudi, Claudia; Fortini, Daniela; Brisse, Sylvain; Passet, Virginie; Bonura, Celestino; Endimiani, Andrea; Mammina, Caterina; Ocampo, Ana Maria; Jimenez, Judy Natalia; Doumith, Michel; Woodford, Neil; Hopkins, Katie; Carattoli, Alessandra

2017-04-01

The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and the human host. Sequence analysis revealed novel plasmid-located virulence factors, including a cluster for glycogen synthesis. Glycogen production is considered to be one of the possible adaptive responses to long-term survival and growth in environments outside the host. Chromosomally-encoded virulence traits in the clone comprised fimbriae, an integrative conjugative element carrying the yersiniabactin siderophore, and two different capsular loci. Compared with the ST258 clone, capsulated ST307 isolates showed higher resistance to complement-mediated killing. The acquired genetic features identified in the genome of this new emerging clone may contribute to increased persistence of ST307 in the hospital environment and shed light on its potential epidemiological success.

Heterologous Expression of Spinosyn Biosynthetic Gene Cluster in Streptomyces Species Is Dependent on the Expression of Rhamnose Biosynthesis Genes.

PubMed

Zhao, Chen; Huang, Ying; Guo, Chao; Yang, Bolei; Zhang, Yan; Lan, Zhou; Guan, Xiong; Song, Yuan; Zhang, Xiaolin

2017-01-01

Spinosyns are a group of macrolide insecticides produced by Saccharopolyspora spinosa. Although S. spinosa can be used for industrial-scale production of spinosyns, this might suffer from several limitations, mainly related to its long growth cycle, low fermentation biomass, and inefficient utilization of starch. It is crucial to generate a robust strain for further spinosyn production and the development of spinosyn derivatives. A BAC vector, containing the whole biosynthetic gene cluster for spinosyn (74 kb) and the elements required for conjugal transfer and site-specific integration, was introduced into different Streptomyces hosts in order to obtain heterologous spinosyn-producing strains. The exconjugants of different Streptomyces strains did not show spinosyn production unless the rhamnose biosynthesis genes from S. spinosa genomic DNA were present and expressed under the control of a strong constitutive ermE*p promoter. Using this heterologous expression system resulted in yields of 1 μg/mL and 1.5 μg/mL spinosyns in Streptomyces coelicolor and Streptomyces lividans, respectively. This report demonstrates spinosyn production in 2 Streptomyces strains and stresses the essential role of rhamnose in this process. This work also provides a potential alternative route for producing spinosyn analogs by means of genetic manipulation in the heterologous hosts. © 2017 S. Karger AG, Basel.

Integrator element as a promoter of active learning in engineering teaching

NASA Astrophysics Data System (ADS)

Oliveira, Paulo C.; Oliveira, Cristina G.

2014-03-01

In this paper, we present a teaching proposal used in an Introductory Physics course to civil engineering students from Porto's Engineering Institute/Instituto Superior de Engenharia do Porto (ISEP). The proposal was born from the need to change students' perception and motivation for learning physics. It consists in the use of an integrator element, called the physics elevator project. This integrator element allows us to use, in a single project, all the content taught in the course and uses several active learning strategies. In this paper, we analyse this project as: (i) a clarifying element of the contents covered in the course; (ii) a promoter element of motivation and active participation in class and finally and (iii) a link between the contents covered in the course and the 'real world'. The data were collected by a questionnaire and interviews to students. From the data collected, it seems that the integrator element improves students' motivation towards physics and develops several skills that they consider to be important to their professional future. It also acts as a clarifying element and makes the connection between the physics that is taught and the 'real world'.

Ellipsoidal terrain correction based on multi-cylindrical equal-area map projection of the reference ellipsoid

NASA Astrophysics Data System (ADS)

Ardalan, A. A.; Safari, A.

2004-09-01

An operational algorithm for computation of terrain correction (or local gravity field modeling) based on application of closed-form solution of the Newton integral in terms of Cartesian coordinates in multi-cylindrical equal-area map projection of the reference ellipsoid is presented. Multi-cylindrical equal-area map projection of the reference ellipsoid has been derived and is described in detail for the first time. Ellipsoidal mass elements with various sizes on the surface of the reference ellipsoid are selected and the gravitational potential and vector of gravitational intensity (i.e. gravitational acceleration) of the mass elements are computed via numerical solution of the Newton integral in terms of geodetic coordinates {λ,ϕ,h}. Four base- edge points of the ellipsoidal mass elements are transformed into a multi-cylindrical equal-area map projection surface to build Cartesian mass elements by associating the height of the corresponding ellipsoidal mass elements to the transformed area elements. Using the closed-form solution of the Newton integral in terms of Cartesian coordinates, the gravitational potential and vector of gravitational intensity of the transformed Cartesian mass elements are computed and compared with those of the numerical solution of the Newton integral for the ellipsoidal mass elements in terms of geodetic coordinates. Numerical tests indicate that the difference between the two computations, i.e. numerical solution of the Newton integral for ellipsoidal mass elements in terms of geodetic coordinates and closed-form solution of the Newton integral in terms of Cartesian coordinates, in a multi-cylindrical equal-area map projection, is less than 1.6×10-8 m2/s2 for a mass element with a cross section area of 10×10 m and a height of 10,000 m. For a mass element with a cross section area of 1×1 km and a height of 10,000 m the difference is less than 1.5×10-4m2/s2. Since 1.5× 10-4 m2/s2 is equivalent to 1.5×10-5m in the vertical direction, it can be concluded that a method for terrain correction (or local gravity field modeling) based on closed-form solution of the Newton integral in terms of Cartesian coordinates of a multi-cylindrical equal-area map projection of the reference ellipsoid has been developed which has the accuracy of terrain correction (or local gravity field modeling) based on the Newton integral in terms of ellipsoidal coordinates.

Wild eel microbiome reveals that skin mucus of fish could be a natural niche for aquatic mucosal pathogen evolution.

PubMed

Carda-Diéguez, Miguel; Ghai, Rohit; Rodríguez-Valera, Francisco; Amaro, Carmen

2017-12-21

Fish skin mucosal surfaces (SMS) are quite similar in composition and function to some mammalian MS and, in consequence, could constitute an adequate niche for the evolution of mucosal aquatic pathogens in natural environments. We aimed to test this hypothesis by searching for metagenomic and genomic evidences in the SMS-microbiome of a model fish species (Anguilla Anguilla or eel), from different ecosystems (four natural environments of different water salinity and one eel farm) as well as the water microbiome (W-microbiome) surrounding the host. Remarkably, potentially pathogenic Vibrio monopolized wild eel SMS-microbiome from natural ecosystems, Vibrio anguillarum/Vibrio vulnificus and Vibrio cholerae/Vibrio metoecus being the most abundant ones in SMS from estuary and lake, respectively. Functions encoded in the SMS-microbiome differed significantly from those in the W-microbiome and allowed us to predict that successful mucus colonizers should have specific genes for (i) attachment (mainly by forming biofilms), (ii) bacterial competence and communication, and (iii) resistance to mucosal innate immunity, predators (amoeba), and heavy metals/drugs. In addition, we found several mobile genetic elements (mainly integrative conjugative elements) as well as a series of evidences suggesting that bacteria exchange DNA in SMS. Further, we isolated and sequenced a V. metoecus strain from SMS. This isolate shares pathogenicity islands with V. cholerae O1 from intestinal infections that are absent in the rest of sequenced V. metoecus strains, all of them from water and extra-intestinal infections. We have obtained metagenomic and genomic evidence in favor of the hypothesis on the role of fish mucosal surfaces as a specialized habitat selecting microbes capable of colonizing and persisting on other comparable mucosal surfaces, e.g., the human intestine.

Antimicrobials & cholera: are we stranded?

PubMed Central

Ghosh, Amit; Ramamurthy, T.

2011-01-01

Antimicrobial resistance poses a major threat in the treatment of infectious diseases. Though significant progress in the management of diarrhoeal diseases has been achieved by improved hygiene, development of new antimicrobials and vaccines, the burden remains the same, especially in children below 5 yr of age. In the case of cholera, though oral rehydration treatment is the mainstay, antimicrobial therapy is mandatory at times to reduce the volume of stool and shorten the duration of the disease. Though for many pathogens, antimicrobial resistance emerged soon after the introduction of antibiotics, Vibrio cholerae remained sensitive to most of the antibiotics for quite a long period. However, the scenario changed over the years and today, V. cholerae strains isolated world over are resistant to multiple antibiotics. A myriad number of mechanisms underlie this phenomenon. These include production of extended-spectrum beta-lactamases, enhanced multi-drug efflux pump activity, plasmid-mediated quinolone and fluoroquinolone resistance, and chromosomal mutations. Horizontal transfer of resistance determinants with mobile genetic elements like integrons and the integrating conjugative elements (ICEs), SXTs help in the dissemination of drug resistance. Though all strains isolated are not resistant to all antibiotics and we are not as yet “stranded”, expanding spectrum of drug resistance is a definite cause for concern. Pipelines of discovery of new antibiotics are drying up as major pharmaceutical companies are losing interest in investing money in this endeavour, mainly due to the short shelf-life of the antibiotics and also due to the fast emergence of drug resistance. To address this issue, attempts are now being made to discover drugs which are pathogen specific and target their “virulence mechanisms”. It is expected that development of resistance against such antibiotics would take much longer. This review briefly focuses on all these issues. PMID:21415499

Antimicrobials & cholera: are we stranded?

PubMed

Ghosh, Amit; Ramamurthy, T

2011-02-01

Antimicrobial resistance poses a major threat in the treatment of infectious diseases. Though significant progress in the management of diarrhoeal diseases has been achieved by improved hygiene, development of new antimicrobials and vaccines, the burden remains the same, especially in children below 5 yr of age. In the case of cholera, though oral rehydration treatment is the mainstay, antimicrobial therapy is mandatory at times to reduce the volume of stool and shorten the duration of the disease. Though for many pathogens, antimicrobial resistance emerged soon after the introduction of antibiotics, Vibrio cholerae remained sensitive to most of the antibiotics for quite a long period. However, the scenario changed over the years and today, V. cholerae strains isolated world over are resistant to multiple antibiotics. A myriad number of mechanisms underlie this phenomenon. These include production of extended-spectrum beta-lactamases, enhanced multi-drug efflux pump activity, plasmid-mediated quinolone and fluoroquinolone resistance, and chromosomal mutations. Horizontal transfer of resistance determinants with mobile genetic elements like integrons and the integrating conjugative elements (ICEs), SXTs help in the dissemination of drug resistance. Though all strains isolated are not resistant to all antibiotics and we are not as yet "stranded", expanding spectrum of drug resistance is a definite cause for concern. Pipelines of discovery of new antibiotics are drying up as major pharmaceutical companies are losing interest in investing money in this endeavour, mainly due to the short shelf-life of the antibiotics and also due to the fast emergence of drug resistance. To address this issue, attempts are now being made to discover drugs which are pathogen specific and target their "virulence mechanisms". It is expected that development of resistance against such antibiotics would take much longer. This review briefly focuses on all these issues.

Comparative genomics of Enterococcus spp. isolated from bovine feces.

PubMed

Beukers, Alicia G; Zaheer, Rahat; Goji, Noriko; Amoako, Kingsley K; Chaves, Alexandre V; Ward, Michael P; McAllister, Tim A

2017-03-08

Enterococcus is ubiquitous in nature and is a commensal of both the bovine and human gastrointestinal (GI) tract. It is also associated with clinical infections in humans. Subtherapeutic administration of antibiotics to cattle selects for antibiotic resistant enterococci in the bovine GI tract. Antibiotic resistance genes (ARGs) may be present in enterococci following antibiotic use in cattle. If located on mobile genetic elements (MGEs) their dissemination between Enterococcus species and to pathogenic bacteria may be promoted, reducing the efficacy of antibiotics. We present a comparative genomic analysis of twenty-one Enterococcus spp. isolated from bovine feces including Enterococcus hirae (n = 10), Enterococcus faecium (n = 3), Enterococcus villorum (n = 2), Enterococcus casseliflavus (n = 2), Enterococcus faecalis (n = 1), Enterococcus durans (n = 1), Enterococcus gallinarum (n = 1) and Enterococcus thailandicus (n = 1). The analysis revealed E. faecium and E. faecalis from bovine feces share features with human clinical isolates, including virulence factors. The Tn917 transposon conferring macrolide-lincosamide-streptogramin B resistance was identified in both E. faecium and E. hirae, suggesting dissemination of ARGs on MGEs may occur in the bovine GI tract. An E. faecium isolate was also identified with two integrative conjugative elements (ICEs) belonging to the Tn916 family of ICE, Tn916 and Tn5801, both conferring tetracycline resistance. This study confirms the presence of enterococci in the bovine GI tract possessing ARGs on MGEs, but the predominant species in cattle, E. hirae is not commonly associated with infections in humans. Analysis using additional complete genomes of E. faecium from the NCBI database demonstrated differential clustering of commensal and clinical isolates, suggesting that these strains may be specifically adapted to their respective environments.

A simple 96 well microfluidic chip combined with visual and densitometry detection for resource-poor point of care testing

PubMed Central

Yang, Minghui; Sun, Steven; Kostov, Yordan

2010-01-01

There is a well-recognized need for low cost biodetection technologies for resource-poor settings with minimal medical infrastructure. Lab-on-a-chip (LOC) technology has the ability to perform biological assays in such settings. The aim of this work is to develop a low cost, high-throughput detection system for the analysis of 96 samples simultaneously outside the laboratory setting. To achieve this aim, several biosensing elements were combined: a syringe operated ELISA lab-on-a-chip (ELISA-LOC) which integrates fluid delivery system into a miniature 96-well plate; a simplified non-enzymatic reporter and detection approach using a gold nanoparticle-antibody conjugate as a secondary antibody and silver enhancement of the visual signal; and Carbon nanotubes (CNT) to increase primary antibody immobilization and improve assay sensitivity. Combined, these elements obviate the need for an ELISA washer, electrical power for operation and a sophisticated detector. We demonstrate the use of the device for detection of Staphylococcal enterotoxin B, a major foodborne toxin using three modes of detection, visual detection, CCD camera and document scanner. With visual detection or using a document scanner to measure the signal, the limit of detection (LOD) was 0.5ng/ml. In addition to visual detection, for precise quantitation of signal using densitometry and a CCD camera, the LOD was 0.1ng/ml for the CCD analysis and 0.5 ng/ml for the document scanner. The observed sensitivity is in the same range as laboratory-based ELISA testing. The point of care device can analyze 96 samples simultaneously, permitting high throughput diagnostics in the field and in resource poor areas without ready access to laboratory facilities or electricity. PMID:21503269

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.

PubMed

Ramsay, Joshua P; Tester, Laura G L; Major, Anthony S; Sullivan, John T; Edgar, Christina D; Kleffmann, Torsten; Patterson-House, Jackson R; Hall, Drew A; Tate, Warren P; Hynes, Michael F; Ronson, Clive W

2015-03-31

Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym(R7A) is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSym(R7A), suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSym(R7A)-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSym(R7A) excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSym(R7A) transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSym(R7A) transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels.

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element

PubMed Central

Ramsay, Joshua P.; Tester, Laura G. L.; Major, Anthony S.; Sullivan, John T.; Edgar, Christina D.; Kleffmann, Torsten; Patterson-House, Jackson R.; Hall, Drew A.; Tate, Warren P.; Hynes, Michael F.; Ronson, Clive W.

2015-01-01

Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSymR7A is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNAphe from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSymR7A, suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSymR7A-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSymR7A excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSymR7A transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSymR7A transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels. PMID:25787256

Concanavalin A conjugated biodegradable nanoparticles for oral insulin delivery

NASA Astrophysics Data System (ADS)

Hurkat, Pooja; Jain, Aviral; Jain, Ashish; Shilpi, Satish; Gulbake, Arvind; Jain, Sanjay K.

2012-11-01

Major research issues in oral protein delivery include the stabilization of protein in delivery devices which could increase its oral bioavailability. The study deals with development of oral insulin delivery system utilizing biodegradable poly(lactic-co-glycolic acid) (PLGA) nanoparticles and modifying its surface with Concanavalin A to increase lymphatic uptake. Surface-modified PLGA nanoparticles were characterized for conjugation efficiency of ligand, shape and surface morphology, particle size, zeta potential, polydispersity index, entrapment efficiency, and in vitro drug release. Stability of insulin in the developed formulation was confirmed by SDS-PAGE, and integrity of entrapped insulin was assessed using circular dichroism spectrum. Ex vivo study was performed on Wistar rats, which exhibited the higher intestinal uptake of Con A conjugated nanoparticles. In vivo study performed on streptozotocin-induced diabetic rats which indicate that a surface-modified nanoparticle reduces blood glucose level effectively within 4 h of its oral administration. In conclusion, the present work resulted in successful production of Con A NPs bearing insulin with sustained release profile, and better absorption and stability. The Con A NPs showed high insulin uptake, due to its relative high affinity for non-reducing carbohydrate residues i.e., fucose present on M cells and have the potential for oral insulin delivery in effective management of Type 1 diabetes condition.

Quaternion regularization in celestial mechanics, astrodynamics, and trajectory motion control. III

NASA Astrophysics Data System (ADS)

Chelnokov, Yu. N.

2015-09-01

The present paper1 analyzes the basic problems arising in the solution of problems of the optimum control of spacecraft (SC) trajectory motion (including the Lyapunov instability of solutions of conjugate equations) using the principle of the maximum. The use of quaternion models of astrodynamics is shown to allow: (1) the elimination of singular points in the differential phase and conjugate equations and in their partial analytical solutions; (2) construction of the first integrals of the new quaternion; (3) a considerable decrease of the dimensions of systems of differential equations of boundary value optimization problems with their simultaneous simplification by using the new quaternion variables related with quaternion constants of motion by rotation transformations; (4) construction of general solutions of differential equations for phase and conjugate variables on the sections of SC passive motion in the simplest and most convenient form, which is important for the solution of optimum pulse SC transfers; (5) the extension of the possibilities of the analytical investigation of differential equations of boundary value problems with the purpose of identifying the basic laws of optimum control and motion of SC; (6) improvement of the computational stability of the solution of boundary value problems; (7) a decrease in the required volume of computation.

UUCD: a family-based database of ubiquitin and ubiquitin-like conjugation.

PubMed

Gao, Tianshun; Liu, Zexian; Wang, Yongbo; Cheng, Han; Yang, Qing; Guo, Anyuan; Ren, Jian; Xue, Yu

2013-01-01

In this work, we developed a family-based database of UUCD (http://uucd.biocuckoo.org) for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. Although extensive experimental efforts have been taken, an integrative data resource is still not available. From the scientific literature, 26 E1s, 105 E2s, 1003 E3s and 148 deubiquitination enzymes (DUBs) were collected and classified into 1, 3, 19 and 7 families, respectively. To computationally characterize potential enzymes in eukaryotes, we constructed 1, 1, 15 and 6 hidden Markov model (HMM) profiles for E1s, E2s, E3s and DUBs at the family level, separately. Moreover, the ortholog searches were conducted for E3 and DUB families without HMM profiles. Then the UUCD database was developed with 738 E1s, 2937 E2s, 46 631 E3s and 6647 DUBs of 70 eukaryotic species. The detailed annotations and classifications were also provided. The online service of UUCD was implemented in PHP + MySQL + JavaScript + Perl.

A finite element boundary integral formulation for radiation and scattering by cavity antennas using tetrahedral elements

NASA Technical Reports Server (NTRS)

Gong, J.; Volakis, J. L.; Chatterjee, A.; Jin, J. M.

1992-01-01

A hybrid finite element boundary integral formulation is developed using tetrahedral and/or triangular elements for discretizing the cavity and/or aperture of microstrip antenna arrays. The tetrahedral elements with edge based linear expansion functions are chosen for modeling the volume region and triangular elements are used for discretizing the aperture. The edge based expansion functions are divergenceless thus removing the requirement to introduce a penalty term and the tetrahedral elements permit greater geometrical adaptability than the rectangular bricks. The underlying theory and resulting expressions are discussed in detail together with some numerical scattering examples for comparison and demonstration.

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

Mohanty, Subhasish; Majumdar, Saurindranath

Irradiation creep plays a major role in the structural integrity of the graphite components in high temperature gas cooled reactors. Finite element procedures combined with a suitable irradiation creep model can be used to simulate the time-integrated structural integrity of complex shapes, such as the reactor core graphite reflector and fuel bricks. In the present work a comparative study was undertaken to understand the effect of linear and nonlinear irradiation creep on results of finite element based stress analysis. Numerical results were generated through finite element simulations of a typical graphite reflector.

Induced structural changes of humic acid by exposure of polystyrene microplastics: A spectroscopic insight.

PubMed

Chen, Wei; Ouyang, Zhen-Yu; Qian, Chen; Yu, Han-Qing

2018-02-01

The occurrence of microplastics (MPs) as emerging contaminants in the environment may cause changes in water or sediment characteristics, and further affect their biogeochemical cycles. Thus, insights into the interactions between dissolved organic matter (DOM) and MPs are essential for the assessment of environmental impacts of MPs in ecosystems. Integrating spectroscopic methods with chemometric analyses, this work explored the chemical and microstructural changes of DOM-MP complex to reveal the mechanism of DOM-MP interaction at a molecular level. MPs were found to interact with the aromatic structure of DOM via π-π conjugation, then be entrapped in the DOM polymers by the carboxyl groups and C=O bonds, constituting a highly conjugated co-polymer with increased electron density. This induced the fluorescence intensity increase in DOM. The interaction affinity of DOM-MP was highly dependent on the MP size and solution pH. This work offers a new insight into the impact of MP discharge on environment and may provide an analytical framework for evaluating MP hetero-aggregation and the roles of MPs in the transportation of other contaminants. Furthermore, the integrated methods used in this work exhibit potential applications in exploring the fragmentation processes of MPs and formation of secondary MPs under natural conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Northeastern Brazilian margin: Regional tectonic evolution based on integrated analysis of seismic reflection and potential field data and modelling

NASA Astrophysics Data System (ADS)

Blaich, Olav A.; Tsikalas, Filippos; Faleide, Jan Inge

2008-10-01

Integration of regional seismic reflection and potential field data along the northeastern Brazilian margin, complemented by crustal-scale gravity modelling, is used to reveal and illustrate onshore-offshore crustal structure correlation, the character of the continent-ocean boundary, and the relationship of crustal structure to regional variation of potential field anomalies. The study reveals distinct along-margin structural and magmatic changes that are spatially related to a number of conjugate Brazil-West Africa transfer systems, governing the margin segmentation and evolution. Several conceptual tectonic models are invoked to explain the structural evolution of the different margin segments in a conjugate margin context. Furthermore, the constructed transects, the observed and modelled Moho relief, and the potential field anomalies indicate that the Recôncavo, Tucano and Jatobá rift system may reflect a polyphase deformation rifting-mode associated with a complex time-dependent thermal structure of the lithosphere. The constructed transects and available seismic reflection profiles, indicate that the northern part of the study area lacks major breakup-related magmatic activity, suggesting a rifted non-volcanic margin affinity. In contrast, the southern part of the study area is characterized by abrupt crustal thinning and evidence for breakup magmatic activity, suggesting that this region evolved, partially, with a rifted volcanic margin affinity and character.

GFSSP Training Course Lectures

NASA Technical Reports Server (NTRS)

Majumdar, Alok K.

2008-01-01

GFSSP has been extended to model conjugate heat transfer Fluid Solid Network Elements include: a) Fluid nodes and Flow Branches; b) Solid Nodes and Ambient Nodes; c) Conductors connecting Fluid-Solid, Solid-Solid and Solid-Ambient Nodes. Heat Conduction Equations are solved simultaneously with Fluid Conservation Equations for Mass, Momentum, Energy and Equation of State. The extended code was verified by comparing with analytical solution for simple conduction-convection problem The code was applied to model: a) Pressurization of Cryogenic Tank; b) Freezing and Thawing of Metal; c) Chilldown of Cryogenic Transfer Line; d) Boil-off from Cryogenic Tank.

Periodate oxidation of nanoscaled magnetic dextran composites

NASA Astrophysics Data System (ADS)

Hong, Xia; Guo, Wei; Yuan, Hang; Li, Jun; Liu, Yanmei; Ma, Lan; Bai, Yubai; Li, Tiejin

2004-02-01

Highly hydrophilic, uniform and nontoxic magnetic fluids consisting of magnetite (Fe 3O 4) and dextran were prepared. A periodate oxidation method was used to further activate the magnetic dextran, forming magnetic polyaldehyde-dextran, which could be conjugated to biomolecules such as proteins or antibodies. Oxidated Magnetic dextran composites were characterized by TEM, XRD and SQUID magnetometry. Moreover, a flexible, rapid and simple method to detect aldehydes was introduced to the magnetic composite system by utilizing 2,4-dinitrophenylhydrazine reagent. The result of the quantitative analysis of aldehyde was given by thermogravimetric analysis and elemental analysis.

Transplantation of Devitalized Muscle Scaffolds is Insufficient for Appreciable De Novo Muscle Fiber Regeneration After Volumetric Muscle Loss Injury

DTIC Science & Technology

2014-10-10

extremities, and are projected to rank third in disability-adjusted life years (DALYs) lost in 2020 (Vos et al. 2012). Although primarily from high...5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Garg K., Ward C., Rathbone C. R., Corona B. T., 5d. PROJECT NUMBER...TBST and 5 % milk containing peroxidase-conjugated goat anti- rabbit secondary antibody diluted 1:2000. Membranes were rinsed 6 times in TBST before

A new sulfonamide resistance gene (sul3) in Escherichia coli is widespread in the pig population of Switzerland.

PubMed

Perreten, Vincent; Boerlin, Patrick

2003-03-01

A new gene, sul3, which specifies a 263-amino-acid protein similar to a dihydropteroate synthase encoded by the 54-kb conjugative plasmid pVP440 from Escherichia coli was characterized. Expression of the cloned sul3 gene conferred resistance to sulfamethoxazole on E. coli. Two copies of the insertion element IS15Delta/26 flanked the region containing sul3. The sul3 gene was detected in one-third of the sulfonamide-resistant pathogenic E. coli isolates from pigs in Switzerland.

A New Sulfonamide Resistance Gene (sul3) in Escherichia coli Is Widespread in the Pig Population of Switzerland

PubMed Central

Perreten, Vincent; Boerlin, Patrick

2003-01-01

A new gene, sul3, which specifies a 263-amino-acid protein similar to a dihydropteroate synthase encoded by the 54-kb conjugative plasmid pVP440 from Escherichia coli was characterized. Expression of the cloned sul3 gene conferred resistance to sulfamethoxazole on E. coli. Two copies of the insertion element IS15Δ/26 flanked the region containing sul3. The sul3 gene was detected in one-third of the sulfonamide-resistant pathogenic E. coli isolates from pigs in Switzerland. PMID:12604565

Irreversible, direct bonding of nanoporous polymer membranes to PDMS or glass microdevices.

PubMed

Aran, Kiana; Sasso, Lawrence A; Kamdar, Neal; Zahn, Jeffrey D

2010-03-07

A method for integrating porous polymer membranes such as polycarbonate, polyethersulfone and polyethylene terephthalate to microfluidic devices is described. The use of 3-aminopropyltriethoxysilane as a chemical crosslinking agent was extended to integrate membranes with PDMS and glass microfluidic channels. A strong, irreversible bond between the membranes and microfluidic structure was achieved. The bonding strength in the APTES treated devices was significantly greater than in devices fabricated using either a PDMS "glue" or two-part epoxy bonding method. Evaluation of a filtering microdevice and the pore structure via SEM indicates the APTES conjugation does not significantly alter the membrane transport function and pore morphology.

Ambipolar nature of dimethyl benzo difuran (DMBDF) molecule: A charge transport study

NASA Astrophysics Data System (ADS)

Sahoo, Smruti Ranjan; Sahu, Sridhar

2017-05-01

We describe a theoretical study of the charge transport properties of the organic dimethyl benzo difuran (DMBDF) molecule based on density functional theory (DFT). Reorganization energy, ionization potential (IP), electron affinity (EA), energy gaps, transfer integral (t) and charge mobility (μ) has been studied to depict the transport properties in the conjugated organic molecules. We computed, large homo transfer integral and IP value leading to high hole mobility (4.46 cm2/V sec). However, the electron reorganization energy (0.34 eV) and the electron mobility of 1.62 cm2/V sec, infers that the DMBDF organic molecule bears an ambipolar character.

Social integration and health insurance status among African American men and women.

PubMed

Williams, Beverly Rosa; Wang, Min Qi; Holt, Cheryl L; Schulz, Emily; Clark, Eddie M

2015-01-01

Using 2010 national data, we investigate the relationship between social integration and health insurance for African American adults. During the previous year 21.6% of men and 19.8% of women lacked continuous health insurance. The effect of marital status, income, and employment on insurance coverage differed by age and gender. Additionally, frequency of church attendance was positively associated with continuous health insurance for women aged 51-64. Spiritual/religious identity was marginally associated with insurance status for men aged 36-50. As provisions of the Affordable Care Act take effect, implementation programs should expand enrollment efforts to include the conjugal unit and the church.

Carbon nanotube-enzyme conjugates for the fabrication of diagnostic biosensors

NASA Astrophysics Data System (ADS)

Karunwi, Olukayode Adedamola

The fabrication of multi-analyte biotransducers continues to be a major technical challenge when the length scales of the individual transducer elements are on the order of microns Generation-3 (Gen-3) biosensors and advanced enzyme biofuel cells will benefit from direct electron transfer to oxidoreductases facilitated by single-walled carbon nanotubes (SWNTs). Direct electron transfer helps to mitigate errors from the instability in oxygen tension, eliminate use of a mediator and produce a device with low operating potential close to the redox potential of the enzymes. Supramolecular conjugates of SWNT-glucose oxidase (GOx-SWNT) may be produced via ultrasonic processing. Using a Plackett-Burman experimental design to investigate the process of tip ultrasonication, conjugate formation was investigated as a function of ultrasonication times and functionalized SWNTs of various tube lengths. Supramolecular conjugates formed from shorter, -OH functionalized SWNTs using longer sonication times gave the most favored combination for forming bioactive conjugates. There has also been growing interest in the fabrication of CNT-enzyme supramolecular constructs that control the placement of SWNTs within tunneling distance of co-factors for enhanced electron transfer efficiency in generation 3 biosensors and advanced biofuel cells. These conjugate systems raise a series of questions such as: Which peptide sequences within the enzymes have high affinity for the SWNTs? And, are these high affinity sequences likely to be in the vicinity of the redox-active co-factor to allow for direct electron transfer? Phage display has recently been used to identify specific peptide sequences that have high affinity for SWNTs. Molecular dynamics simulations were performed to study the interactions of five discrete peptides with (16,0) SWNT in explicit water as well as with graphene. The end residues appear to dominate the progression of adsorption regardless of character. Sequences identified by phage display share some homology with key enzymes (GOx, lactate oxidase and laccase) used in biosensors and enzyme-based biofuel cells. Furthermore, the role of pyrrole electropolymerization as an additive technique for the biofabrication of side-by-side biotransducers for glucose and lactate with minimum cross-talk was investigated along with an electrodeposited layer of Fe/Ni hexacyanoferrate to serve as peroxide mediator, decorated with the electropolymerized PPy-Enzyme biorecognition layer, characterized in vitro, and implanted into the trapezius muscle of a piglet ( Sus scrofa) hemorrhage model. Internal calibration, response under controlled hemorrhage conditions, and post-resection re-characterization were used to evaluate biotransducer performance.

Mechanical properties of conjugate faults in the Makran accretionary prism estimated from InSAR observations of coseismic deformation due to the 2013 Baluchistan (Mw 7.7) earthquake

NASA Astrophysics Data System (ADS)

Dutta, R.; Harrington, J.; Wang, T.; Feng, G.; Vasyura-Bathke, H.; Jonsson, S.

2017-12-01

Interferometric Synthetic Aperture Radar (InSAR) measurements allow us to study various mechanical and rheological properties around faults. For example, strain localizations along faults induced by nearby earthquakes observed by InSAR have been explained by the elastic response of compliant fault zones (CFZ) where the elastic moduli is reduced with respect to that of the surrounding rock. We observed similar strain localizations (up to 1-3 cm displacements in the line-of-sight direction of InSAR) along several conjugate faults near the rupture of the 2013 Mw7.7 Baluchistan (Pakistan) earthquake in the accretionary prism of the Makran subduction zone. These conjugate compliant faults, which have strikes of N30°E and N45°W, are located 15-30 km from the mainshock fault rupture in a N-S compressional stress regime. The long-term geologic slip direction of these faults is left-lateral for the N30°E striking faults and right-lateral for the N45°W striking faults. The 2013 Baluchistan earthquake caused WSW-ENE extensional coseismic stress changes across the conjugate fault system and the observed strain localizations shows opposite sense of motion to that of the geologic long-term slip. We use 3D Finite Element modeling (FEM) to study the effects extensional coseismic stresses have on the conjugate CFZs that is otherwise loaded in a compressional regional stress. We use coseismic static displacements due to the earthquake along the FEM domain boundaries to simulate the extensional coseismic stress change acting across the fault system. Around 0.5-2 km wide CFZs with reduction in shear modulus by a factor of 3 to 4 can explain the observed InSAR strain localizations and the opposite sense of motion. The InSAR measurements were also used to constrain the ranges of the length, width and rigidity variations of the CFZs. The FEM solution shows that the N45°W striking faults localize mostly extensional strain and a small amount of left-lateral shear (opposite sense to the geologic motion), whereas the N30°E striking faults localize mostly right-lateral shear (opposite sense) and a small amount of extensional strain. Similar results were found for CFZs near the 1992 Landers and the 1999 Hector Mine earthquakes in California, although here the strain localizations occur on a more complex conjugate sets of faults.

Goat anti-rabbit IgG conjugated fluorescent dye-doped silica nanoparticles for human breast carcinoma cell recognition.

PubMed

Chen, Min-Yan; Chen, Ze-Zhong; Wu, Ling-Ling; Tang, Hong-Wu; Pang, Dai-Wen

2013-11-12

We report an indirect method for cancer cell recognition using photostable fluorescent silica nanoprobes as biological labels. The dye-doped fluorescent silica nanoparticles were synthesized using the water-in-oil (W/O) reverse microemulsion method. The silica matrix was produced by the controlled hydrolysis of tetraethylorthosilicate (TEOS) in water nanodroplets with the initiation of ammonia (NH3·H2O). Fluorescein isothiocyanate (FITC) or rhodamine B isothiocyanate conjugated with dextran (RBITC-Dextran) was doped in silica nanoparticles (NPs) with a size of 60 ± 5 nm as a fluorescent signal element by covalent bonding and steric hindrance, respectively. The secondary antibody, goat anti-rabbit IgG, was conjugated on the surface of the PEG-terminated modified FITC-doped or RBITC-Dextran-doped silica nanoparticles (PFSiNPs or PBSiNPs) by covalent binding to the PEG linkers using the cyanogen bromide method. The concentrations of goat anti-rabbit IgG covering the nanoprobes were quantified via the Bradford method. In the proof-of-concept experiment, an epithelial cell adhesion molecule (EpCAM) on the human breast cancer SK-Br-3 cell surface was used as the tumor marker, and the nanoparticle functionalized with rabbit anti-EpCAM antibody was employed as the nanoprobe for cancer cell recognition. Compared with fluorescent dye labeled IgG (FITC-IgG and RBITC-IgG), the designed nanoprobes display dramatically increased stability of fluorescence as well as photostability under continuous irradiation.

A Phase-Conjugate-Mirror Inspired Approach for Building Cloaking Structures with Left-handed Materials

PubMed Central

Zheng, Guoan; Heng, Xin; Yang, Changhuei

2009-01-01

A phase conjugate mirror (PCM) has a remarkable property of cancellation the back-scattering wave of the lossless scatterers. The similarity of a phase conjugate mirror to the interface of a matched RHM (right-handed material) and a LHM (left-handed material) prompts us to explore the potentials of using the RHM-LHM structure to achieve the anti-scattering property of the PCM. In this paper, we present two such structures. The first one is a RHM-LHM cloaking structure with a lossless arbitrary-shape scatterer imbedded in the RHM and its left-handed duplicate imbedded in the matched LHM. It is shown that such a structure is transparent to the incident electromagnetic (EM) field. As a special case of this structure, we proposed an EM tunnel that allows EM waves to spatially transport to another location in space without significant distortion and reflection. The second one is an RHM-PEC (perfect electric conductor)-LHM cloaking structure, which is composed of a symmetric conducting shell embedded in the interface junction of an RHM and the matched LHM layer. Such a structure presents an anomalously small scattering cross-section to an incident propagating EM field, and the interior of the shell can be used to shield small objects (size comparable to the wavelength) from interrogation. We report the results of 2D finite-element-method (FEM) simulations that were performed to verify our idea, and discuss the unique properties of the proposed structures as well as their limitations. PMID:20126415

Combining ray tracing and CFD in the thermal analysis of a parabolic dish tubular cavity receiver

NASA Astrophysics Data System (ADS)

Craig, Ken J.; Marsberg, Justin; Meyer, Josua P.

2016-05-01

This paper describes the numerical evaluation of a tubular receiver used in a dish Brayton cycle. In previous work considering the use of Computational Fluid Dynamics (CFD) to perform the calculation of the absorbed radiation from the parabolic dish into the cavity as well as the resulting conjugate heat transfer, it was shown that an axi-symmetric model of the dish and receiver absorbing surfaces was useful in reducing the computational cost required for a full 3-D discrete ordinates solution, but concerns remained about its accuracy. To increase the accuracy, the Monte Carlo ray tracer SolTrace is used to perform the calculation of the absorbed radiation profile to be used in the conjugate heat transfer CFD simulation. The paper describes an approach for incorporating a complex geometry like a tubular receiver generated using CFD software into SolTrace. The results illustrate the variation of CFD mesh density that translates into the number of elements in SolTrace as well as the number of rays used in the Monte Carlo approach and their effect on obtaining a resolution-independent solution. The conjugate heat transfer CFD simulation illustrates the effect of applying the SolTrace surface heat flux profile solution as a volumetric heat source to heat up the air inside the tube. Heat losses due to convection and thermal re-radiation are also determined as a function of different tube absorptivities.

Multi-color incomplete Cholesky conjugate gradient methods for vector computers

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

Poole, E.L.

1986-01-01

This research is concerned with the solution on vector computers of linear systems of equations. Ax = b, where A is a large, sparse symmetric positive definite matrix with non-zero elements lying only along a few diagonals of the matrix. The system is solved using the incomplete Cholesky conjugate gradient method (ICCG). Multi-color orderings are used of the unknowns in the linear system to obtain p-color matrices for which a no-fill block ICCG method is implemented on the CYBER 205 with O(N/p) length vector operations in both the decomposition of A and, more importantly, in the forward and back solvesmore » necessary at each iteration of the method. (N is the number of unknowns and p is a small constant). A p-colored matrix is a matrix that can be partitioned into a p x p block matrix where the diagonal blocks are diagonal matrices. The matrix is stored by diagonals and matrix multiplication by diagonals is used to carry out the decomposition of A and the forward and back solves. Additionally, if the vectors across adjacent blocks line up, then some of the overhead associated with vector startups can be eliminated in the matrix vector multiplication necessary at each conjugate gradient iteration. Necessary and sufficient conditions are given to determine which multi-color orderings of the unknowns correspond to p-color matrices, and a process is indicated for choosing multi-color orderings.« less

Dynamic surface electronic reconstruction as symmetry-protected topological orders in topological insulator Bi2Se3

NASA Astrophysics Data System (ADS)

Shu, G. J.; Liou, S. C.; Karna, S. K.; Sankar, R.; Hayashi, M.; Chou, F. C.

2018-04-01

The layered narrow-band-gap semiconductor Bi2Se3 is composed of heavy elements with strong spin-orbital coupling, which has been identified both as a good candidate for a thermoelectric material with high thermoelectric figure of merit (Z T ) and as a topological insulator of the Z2 type with a gapless surface band in a Dirac-cone shape. The existence of a conjugated π -bond system on the surface of each Bi2Se3 quintuple layer is proposed based on an extended valence bond model with valence electrons distributed in the hybridized orbitals. Supporting experimental evidence of a two-dimensional (2D) conjugated π -bond system on each quintuple layer of Bi2Se3 is provided using electron energy-loss spectroscopy and electron density mapping through inverse Fourier transform of x-ray diffraction data. Quantum chemistry calculations support the π -bond existence between partially filled 4 pz orbitals of Se via side-to-side orbital overlap positively. The conjugated π -bond system on the surface of each quintuple Bi2Se3 layer is proposed to be similar to that found in graphite (graphene) and responsible for the unique 2D conduction mechanism. The van der Waals (vdW) attractive force between quintuple layers is interpreted to be coming from the antiferroelectrically ordered effective electric dipoles, which are constructed with π -bond trimer pairs on Se layers across the vdW gap of minimized Coulomb repulsion.

Monolithic optical integrated control circuitry for GaAs MMIC-based phased arrays

NASA Technical Reports Server (NTRS)

Bhasin, K. B.; Ponchak, G. E.; Kascak, T. J.

1985-01-01

Gallium arsenide (GaAs) monolithic microwave integrated circuits (MMIC's) show promise in phased-array antenna applications for future space communications systems. Their efficient usage will depend on the control of amplitude and phase signals for each MMIC element in the phased array and in the low-loss radiofrequency feed. For a phased array contining several MMIC elements a complex system is required to control and feed each element. The characteristics of GaAs MMIC's for 20/30-GHz phased-array systems are discussed. The optical/MMIC interface and the desired characteristics of optical integrated circuits (OIC's) for such an interface are described. Anticipated fabrication considerations for eventual full monolithic integration of optical integrated circuits with MMIC's on a GaAs substrate are presented.

Why farming with high tech methods should integrate elements of organic agriculture.

PubMed

Ammann, Klaus

2009-09-01

In the previous article [Ammann, K. (2008) Feature: integrated farming: why organic farmers should use transgenic crops. New Biotechnol. 25, 101-107], in a plea for the introduction of transgenic crops into organic and integrated farming, it was announced that the complementary topic, namely that high tech farmers should integrate elements of organic agriculture, will be a follow up. Some selected arguments for such a view are summarised here. Basically, they comprise a differentiated view on agro-biodiversity outside the field of production; landscape management methods to enhance biodiversity levels. Both elements are compatible with basic ideas of organic farming. First, Precision Farming is given as one example of the many ways to support agricultural production through high technology, with the aim of reducing energy input, maintaining excellent soil conditions and enhancing yield. It is clear from this analysis that modern agriculture and certain elements of organic-integrated agriculture are compatible. There are sectors of high tech farming, such as the introduction of a better recycling scheme and also a better focus on socio-economic aspects, which need to be taken up seriously from organic-integrated farming, a system which puts a lot of emphasis on those elements and for which important research data are available. In the final part a new concept of dynamic sustainability is presented.

A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation

PubMed Central

2011-01-01

Background One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this family has also been associated with human disease such as multiple sclerosis (MS) and schizophrenia. It is not known whether this broad expression of HERV-W elements represents transcriptional leakage or specific transcription initiated from the retroviral promoter in the long terminal repeat (LTR) region. Therefore, potential influences of genomic context, structure and orientation on the expression levels of individual HERV-W elements in normal human tissues were systematically investigated. Results Whereas intronic HERV-W elements with a pseudogene structure exhibited a strong anti-sense orientation bias, intronic elements with a proviral structure and solo LTRs did not. Although a highly variable expression across tissues and elements was observed, systematic effects of context, structure and orientation were also observed. Elements located in intronic regions appeared to be expressed at higher levels than elements located in intergenic regions. Intronic elements with proviral structures were expressed at higher levels than those elements bearing hallmarks of processed pseudogenes or solo LTRs. Relative to their corresponding genes, intronic elements integrated on the sense strand appeared to be transcribed at higher levels than those integrated on the anti-sense strand. Moreover, the expression of proviral elements appeared to be independent from that of their corresponding genes. Conclusions Intronic HERV-W provirus integrations on the sense strand appear to have elicited a weaker negative selection than pseudogene integrations of transcripts from such elements. Our current findings suggest that the previously observed diversified and tissue-specific expression of elements in the HERV-W family is the result of both directed transcription (involving both the LTR and internal sequence) and leaky transcription of HERV-W elements in normal human tissues. PMID:21226900

Status of the JWST Integrated Science Instrument Module

NASA Astrophysics Data System (ADS)

Greenhouse, Matthew A.; Dunn, Jamie; Kimble, Randy A.; Lambros, Scott; Lundquist, Ray; Rauscher, Bernard J.; Van Campen, Julie

2015-01-01

The James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM) is the science instrument payload of the JWST. It is one of three system elements that comprise the JWST space vehicle. It consists of four science sensors, a fine guidance sensor, and nine other subsystems that support them. At 1.4 metric tons, it comprises approximately 20% of the JWST mass. The ISIM is currently at 100% integration and has completed 2 of 3 planned element-level space simulation tests. The ISIM is on schedule to be delivered for integration with the Optical Telescope Element during 2015. In this poster, we present an overview of the ISIM and its status.

A finite element-boundary integral method for cavities in a circular cylinder

NASA Technical Reports Server (NTRS)

Kempel, Leo C.; Volakis, John L.

1992-01-01

Conformal antenna arrays offer many cost and weight advantages over conventional antenna systems. However, due to a lack of rigorous mathematical models for conformal antenna arrays, antenna designers resort to measurement and planar antenna concepts for designing non-planar conformal antennas. Recently, we have found the finite element-boundary integral method to be very successful in modeling large planar arrays of arbitrary composition in a metallic plane. We extend this formulation to conformal arrays on large metallic cylinders. In this report, we develop the mathematical formulation. In particular, we discuss the shape functions, the resulting finite elements and the boundary integral equations, and the solution of the conformal finite element-boundary integral system. Some validation results are presented and we further show how this formulation can be applied with minimal computational and memory resources.

Boundary element method for normal non-adhesive and adhesive contacts of power-law graded elastic materials

NASA Astrophysics Data System (ADS)

Li, Qiang; Popov, Valentin L.

2018-03-01

Recently proposed formulation of the boundary element method for adhesive contacts has been generalized for contacts of power-law graded materials with and without adhesion. Proceeding from the fundamental solution for single force acting on the surface of an elastic half space, first the influence matrix is obtained for a rectangular grid. The inverse problem for the calculation of required stress in the contact area from a known surface displacement is solved using the conjugate-gradient technique. For the transformation between the stresses and displacements, the Fast Fourier Transformation is used. For the adhesive contact of graded material, the detachment criterion based on the energy balance is proposed. The method is validated by comparison with known exact analytical solutions as well as by proving the independence of the mesh size and the grid orientation.

Large-scale computation of incompressible viscous flow by least-squares finite element method

NASA Technical Reports Server (NTRS)

Jiang, Bo-Nan; Lin, T. L.; Povinelli, Louis A.

1993-01-01

The least-squares finite element method (LSFEM) based on the velocity-pressure-vorticity formulation is applied to large-scale/three-dimensional steady incompressible Navier-Stokes problems. This method can accommodate equal-order interpolations and results in symmetric, positive definite algebraic system which can be solved effectively by simple iterative methods. The first-order velocity-Bernoulli function-vorticity formulation for incompressible viscous flows is also tested. For three-dimensional cases, an additional compatibility equation, i.e., the divergence of the vorticity vector should be zero, is included to make the first-order system elliptic. The simple substitution of the Newton's method is employed to linearize the partial differential equations, the LSFEM is used to obtain discretized equations, and the system of algebraic equations is solved using the Jacobi preconditioned conjugate gradient method which avoids formation of either element or global matrices (matrix-free) to achieve high efficiency. To show the validity of this scheme for large-scale computation, we give numerical results for 2D driven cavity problem at Re = 10000 with 408 x 400 bilinear elements. The flow in a 3D cavity is calculated at Re = 100, 400, and 1,000 with 50 x 50 x 50 trilinear elements. The Taylor-Goertler-like vortices are observed for Re = 1,000.

Terrain Correction on the moving equal area cylindrical map projection of the surface of a reference ellipsoid

NASA Astrophysics Data System (ADS)

Ardalan, A.; Safari, A.; Grafarend, E.

2003-04-01

An operational algorithm for computing the ellipsoidal terrain correction based on application of closed form solution of the Newton integral in terms of Cartesian coordinates in the cylindrical equal area map projected surface of a reference ellipsoid has been developed. As the first step the mapping of the points on the surface of a reference ellipsoid onto the cylindrical equal area map projection of a cylinder tangent to a point on the surface of reference ellipsoid closely studied and the map projection formulas are computed. Ellipsoidal mass elements with various sizes on the surface of the reference ellipsoid is considered and the gravitational potential and the vector of gravitational intensity of these mass elements has been computed via the solution of Newton integral in terms of ellipsoidal coordinates. The geographical cross section areas of the selected ellipsoidal mass elements are transferred into cylindrical equal area map projection and based on the transformed area elements Cartesian mass elements with the same height as that of the ellipsoidal mass elements are constructed. Using the close form solution of the Newton integral in terms of Cartesian coordinates the potential of the Cartesian mass elements are computed and compared with the same results based on the application of the ellipsoidal Newton integral over the ellipsoidal mass elements. The results of the numerical computations show that difference between computed gravitational potential of the ellipsoidal mass elements and Cartesian mass element in the cylindrical equal area map projection is of the order of 1.6 × 10-8m^2/s^2 for a mass element with the cross section size of 10 km × 10 km and the height of 1000 m. For a 1 km × 1 km mass element with the same height, this difference is less than 1.5 × 10-4 m^2}/s^2. The results of the numerical computations indicate that a new method for computing the terrain correction based on the closed form solution of the Newton integral in terms of Cartesian coordinates and with accuracy of ellipsoidal terrain correction has been achieved! In this way one can enjoy the simplicity of the solution of the Newton integral in terms of Cartesian coordinates and at the same time the accuracy of the ellipsoidal terrain correction, which is needed for the modern theory of geoid computations.

An equivalent domain integral method in the two-dimensional analysis of mixed mode crack problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Shivakumar, K. N.

1990-01-01

An equivalent domain integral (EDI) method for calculating J-integrals for two-dimensional cracked elastic bodies is presented. The details of the method and its implementation are presented for isoparametric elements. The EDI method gave accurate values of the J-integrals for two mode I and two mixed mode problems. Numerical studies showed that domains consisting of one layer of elements are sufficient to obtain accurate J-integral values. Two procedures for separating the individual modes from the domain integrals are presented.

Conjugate Analysis of Two-Dimensional Ablation and Pyrolysis in Rocket Nozzles

NASA Astrophysics Data System (ADS)

Cross, Peter G.

The development of a methodology and computational framework for performing conjugate analyses of transient, two-dimensional ablation of pyrolyzing materials in rocket nozzle applications is presented. This new engineering methodology comprehensively incorporates fluid-thermal-chemical processes relevant to nozzles and other high temperature components, making it possible, for the first time, to rigorously capture the strong interactions and interdependencies that exist between the reacting flowfield and the ablating material. By basing thermal protection system engineering more firmly on first principles, improved analysis accuracy can be achieved. The computational framework developed in this work couples a multi-species, reacting flow solver to a two-dimensional material response solver. New capabilities are added to the flow solver in order to be able to model unique aspects of the flow through solid rocket nozzles. The material response solver is also enhanced with new features that enable full modeling of pyrolyzing, anisotropic materials with a true two-dimensional treatment of the porous flow of the pyrolysis gases. Verification and validation studies demonstrating correct implementation of these new models in the flow and material response solvers are also presented. Five different treatments of the surface energy balance at the ablating wall, with increasing levels of fidelity, are investigated. The Integrated Equilibrium Surface Chemistry (IESC) treatment computes the surface energy balance and recession rate directly from the diffusive fluxes at the ablating wall, without making transport coefficient or unity Lewis number assumptions, or requiring pre-computed surface thermochemistry tables. This method provides the highest level of fidelity, and can inherently account for the effects that recession, wall temperature, blowing, and the presence of ablation product species in the boundary layer have on the flowfield and ablation response. Multiple decoupled and conjugate ablation analysis studies for the HIPPO nozzle test case are presented. Results from decoupled simulations show sensitivity to the wall temperature profile used within the flow solver, indicating the need for conjugate analyses. Conjugate simulations show that the thermal response of the nozzle is relatively insensitive to the choice of the surface energy balance treatment. However, the surface energy balance treatment is found to strongly affect the surface recession predictions. Out of all the methods considered, the IESC treatment produces surface recession predictions with the best agreement to experimental data. These results show that the increased fidelity provided by the proposed conjugate ablation modeling methodology produces improved analysis accuracy, as desired.

Nanoparticle-allergen interactions mediate human allergic responses: protein corona characterization and cellular responses.

PubMed

Radauer-Preiml, Isabella; Andosch, Ancuela; Hawranek, Thomas; Luetz-Meindl, Ursula; Wiederstein, Markus; Horejs-Hoeck, Jutta; Himly, Martin; Boyles, Matthew; Duschl, Albert

2016-01-16

Engineered nanomaterials (ENMs) interact with different biomolecules as soon as they are in contact, resulting in the formation of a biomolecule 'corona'. Hence, the 'corona' defines the biological identity of the ENMs and could affect the response of the immune system to ENM exposure. With up to 40 % of the world population suffering from type I allergy, a possible modulation of allergen effects by binding to ENMs is highly relevant with respect to work place and consumer safety. Therefore, the aim of this present study was to gain an insight into the interactions of gold nanoparticles with different seasonally and perennially occurring outdoor and indoor allergens. Gold nanoparticles (AuNPs) were conjugated with the major allergens of birch pollen (Bet v 1), timothy grass pollen (Phl p 5) and house dust mite (Der p 1). The AuNP-allergen conjugates were characterized by means of TEM negative staining, dynamic light scattering (DLS), z-potential measurements and hyperspectral imaging. Furthermore, 3D models were constructed, based on the characterization data, to visualize the interaction between the allergens and the AuNPs surface. Differences in the activation of human basophil cells derived from birch/grass pollen- and house dust mite-allergic patients in response to free allergen and AuNP-allergen conjugates were determined using the basophil activation assay (BAT). Potential allergen corona replacement during BAT was controlled for using Western blotting. The protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was assessed, by an enzymatic activity assay and a cellular assay pertaining to lung type II alveolar epithelial cell tight junction integrity. The formation of a stable corona was found for all three allergens used. Our data suggest, that depending on the allergen, different effects are observed after binding to ENMs, including enhanced allergic responses against Der p 1 and also, for some patients, against Bet v 1. Moreover elevated protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was found. In summary, this study presents that conjugation of allergens to ENMs can modulate the human allergic response, and that protease activity can be increased. Graphical Abstract Cross-linking of IgE receptors and degranulation of human basophils due to epitope alignment of nanoparticle-coated allergens.

The Health Economic Impact of Universal Infant Vaccination with the 10-Valent Pneumococcal Nontypeable Haemophilus influenzae Protein D Conjugate Vaccine as Compared with 13-Valent Pneumococcal Conjugate Vaccine in Hong Kong.

PubMed

Lee, Kenneth K C; Chia Wu, David Bin; Topachevskyi, Oleksandr; Delgleize, Emmanuelle; DeAntonio, Rodrigo

2013-05-01

Pneumococcal universal vaccination in Hong Kong was introduced in 2009. We assessed the health and economic impact of the 10-valent pneumococcal nontypeable Haemophilus influenzae protein D conjugate vaccine (PCV-10) compared with the current 13-valent pneumococcal conjugate vaccine (PCV-13) recommended for Hong Kong in 2011, providing new elements to be considered by public health authorities in the future decision-making process for pneumococcal vaccines in this country. An analytical model was used to estimate the annual economic and health outcomes of invasive pneumococcal disease (IPD), community-acquired pneumonia, and acute otitis media (AOM), including nontypeable H. influenzae-related AOM, for a birth cohort in Hong Kong from the payer perspective with a 10-year horizon. Clinical impact including morbidity-mortality, quality-adjusted life-years (QALYs), incremental costs, and cost-effectiveness comparing PCV-10 and PCV-13 were estimated. Probabilistic sensitivity analyses by using alternate scenarios were performed. Model projections indicate that PCV-13 and PCV-10 have approximately equivalent impact on the prevention of deaths caused by IPD and pneumonia. PCV-13 is projected to prevent 6 additional cases of IPD, whereas PCV-10 is projected to prevent 13,229 additional AOM cases and 101 additional QALYs. For the base case, PCV-10 vaccination is estimated to save 44.6 million Hong Kong dollars (34.1 million Hong Kong dollars discounted). Sensitivity analysis indicated that PCV-10 would generate more QALYs and save costs as compared with PCV-13. Universal infant vaccination with new available pneumococcal vaccines is expected to generate a significant additional impact on reducing the burden of pneumococcal diseases in Hong Kong. PCV-10 vaccination would be potentially a cost-saving strategy compared with PCV-13 vaccination, generating better cost offsets and higher QALY gains. Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Space charge limited current measurements on conjugated polymer films using conductive atomic force microscopy.

PubMed

Reid, Obadiah G; Munechika, Keiko; Ginger, David S

2008-06-01

We describe local (~150 nm resolution), quantitative measurements of charge carrier mobility in conjugated polymer films that are commonly used in thin-film transistors and nanostructured solar cells. We measure space charge limited currents (SCLC) through these films using conductive atomic force microscopy (c-AFM) and in macroscopic diodes. The current densities we measure with c-AFM are substantially higher than those observed in planar devices at the same bias. This leads to an overestimation of carrier mobility by up to 3 orders of magnitude when using the standard Mott-Gurney law to fit the c-AFM data. We reconcile this apparent discrepancy between c-AFM and planar device measurements by accounting for the proper tip-sample geometry using finite element simulations of tip-sample currents. We show that a semiempirical scaling factor based on the ratio of the tip contact area diameter to the sample thickness can be used to correct c-AFM current-voltage curves and thus extract mobilities that are in good agreement with values measured in the conventional planar device geometry.

Virtuality Distributions and γγ * -> π 0 Transition at Handbag Level

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

Radyushkin, Anatoly V.

2015-09-01

We outline a new approach to transverse momentum dependence in hard processes using as an example the exclusive transitionmore » $${\\gamma^{*}\\gamma \\to \\pi^{0}}$$ at the handbag level. We start with the coordinate representation for a matrix element $${\\langle p |{\\cal O}(0,z) |0 \\rangle}$$ of a bilocal operator $${{\\cal O} (0,z)}$$ describing a hadron with momentum p. Treated as a function of (pz) and z$$^{2}$$, it is parametrized through virtuality distribution amplitude (VDA) Φ (x, σ), with x being Fourier-conjugate to (pz) and σ Laplace-conjugate to z$$^{2}$$. For intervals with z$$^{+}$$ = 0, we introduce the transverse momentum distribution amplitude (TMDA) $${\\Ψ (x,k_{\\perp})}$$ , and write it in terms of VDA Φ (x, σ). The results of covariant calculations, written in terms of Φ (x, σ) are converted into expressions involving $${\\Ψ (x,k_{\\perp})}$$ . We propose simple models for soft VDAs/TMDAs, and use them for comparison of handbag results with experimental (BaBar and BELLE) data on the pion transition form factor.« less

New 1H-Benzo[f]indazole-4,9-diones Conjugated with C-Protected Amino Acids and Other Derivatives: Synthesis and in Vitro Antiproliferative Evaluation.

PubMed

Molinari, Aurora; Oliva, Alfonso; Arismendi-Macuer, Marlene; Guzmán, Leda; Fuentealba, Mauricio; Knox, Marcela; Vinet, Raúl; San Feliciano, Arturo

2015-12-08

1H-Benzo[f]indazole-4,9-dione derivatives conjugated with C-protected amino acids (glycine, l-alanine, l-phenylalanine and l-glutamic acid) 6a-l were prepared by chemically modifying the prenyl substituent of 3-methyl-7-(4-methylpent-3-enyl)-1H-benzo[f]indazole-4,9-dione 2 through epoxidation, degradative oxidation, oxidation and N-acyl condensation reactions. The chemical structures of the synthesized compounds were elucidated by analyzing their IR, ¹H-NMR and (13)C-NMR spectral data together with elemental analysis for carbon, hydrogen and nitrogen. The preliminary in vitro antiproliferative activity of the synthesized derivatives was evaluated on KATO-III and MCF-7 cell lines using a cell proliferation assay. The majority of the derivatives exhibited significant antiproliferative activity with IC50 values ranging from 25.5 to 432.5 μM. These results suggest that 1H-benzo[f]indazole-4,9-dione derivatives are promising molecules to be researched for developing new anticancer agents.

Deflection monitoring for a box girder based on a modified conjugate beam method

NASA Astrophysics Data System (ADS)

Chen, Shi-Zhi; Wu, Gang; Xing, Tuo

2017-08-01

After several years of operation, a box girder bridge would commonly experience excessive deflection, which endangers the bridge’s life span as well as the safety of vehicles travelling on it. In order to avoid potential risks, it is essential to constantly monitor the defection of box girders. However, currently, the direct deflection monitoring methods are limited by the complicated environments beneath the bridges, such as rivers or other traffic lanes, which severely impede the layouts of the sensors. The other indirect deflection monitoring methods mostly do not thoroughly consider the inherent shear lag effect and shear deformation in the box girder, resulting in a rather large error. Under these circumstances, a deflection monitoring method suiting box girders is proposed in this article, based on the conjugate beam method and distributed long-gauge fibre Bragg grating (FBG) sensor. A lab experiment was conducted to verify the reliability and feasibility of this method under practical application. Further, the serviceability under different span-depth ratios and web thicknesses was examined through a finite element model.

Synthesis, Characterization, and Antimicrobial Efficacy of Photomicrobicidal Cellulose Paper.

PubMed

Carpenter, Bradley L; Scholle, Frank; Sadeghifar, Hasan; Francis, Aaron J; Boltersdorf, Jonathan; Weare, Walter W; Argyropoulos, Dimitris S; Maggard, Paul A; Ghiladi, Reza A

2015-08-10

Toward our goal of scalable, antimicrobial materials based on photodynamic inactivation, paper sheets comprised of photosensitizer-conjugated cellulose fibers were prepared using porphyrin and BODIPY photosensitizers, and characterized by spectroscopic (infrared, UV-vis diffuse reflectance, inductively coupled plasma optical emission) and physical (gel permeation chromatography, elemental, and thermal gravimetric analyses) methods. Antibacterial efficacy was evaluated against Staphylococcus aureus (ATCC-2913), vancomycin-resistant Enterococcus faecium (ATCC-2320), Acinetobacter baumannii (ATCC-19606), Pseudomonas aeruginosa (ATCC-9027), and Klebsiella pneumoniae (ATCC-2146). Our best results were achieved with a cationic porphyrin-paper conjugate, Por((+))-paper, with inactivation upon illumination (30 min, 65 ± 5 mW/cm(2), 400-700 nm) of all bacterial strains studied by 99.99+% (4 log units), regardless of taxonomic classification. Por((+))-paper also inactivated dengue-1 virus (>99.995%), influenza A (∼ 99.5%), and human adenovirus-5 (∼ 99%). These results demonstrate the potential of cellulose materials to serve as scalable scaffolds for anti-infective or self-sterilizing materials against both bacteria and viruses when employing a photodynamic inactivation mode of action.

Synthesis, kinetic studies and pharmacological evaluation of mutual azo prodrug of 5-aminosalicylic acid with D-phenylalanine for colon specific drug delivery in inflammatory bowel disease.

PubMed

Dhaneshwar, Suneela S; Gairola, Neha; Kandpal, Mini; Bhatt, Lokesh; Vadnerkar, Gaurav; Kadam, S S

2007-04-01

Mutual azo prodrug of 5-aminosalicylic acid with d-phenylalanine was synthesized by coupling D-phenylalanine with salicylic acid, for targeted drug delivery to the inflamed gut tissue in inflammatory bowel disease. The structure of synthesized prodrug was confirmed by elemental analysis, IR and NMR spectroscopy. In vitro kinetic studies in HCl buffer (pH 1.2) showed negligible release of 5-aminosalicylic acid, whereas in phosphate buffer (pH 7.4) only 15% release was observed over a period of 7h. In rat fecal matter the release of 5-aminosalicylic acid was almost complete (85%), with a half-life of 160.1 min, following first order kinetics. The azo conjugate was evaluated for its ulcerogenic potential by Rainsford's cold stress method. Therapeutic efficacy of the carrier system and the mitigating effect of the azo conjugate were evaluated in trinitrobenzenesulfonic acid-induced experimental colitis model. The synthesized prodrug was found to be equally effective in mitigating the colitis in rats as that of sulfasalazine without the ulcerogenicity of 5-aminosalicylic acid.

Linear phase conjugation for atmospheric aberration compensation

NASA Astrophysics Data System (ADS)

Grasso, Robert J.; Stappaerts, Eddy A.

1998-01-01

Atmospheric induced aberrations can seriously degrade laser performance, greatly affecting the beam that finally reaches the target. Lasers propagated over any distance in the atmosphere suffer from a significant decrease in fluence at the target due to these aberrations. This is especially so for propagation over long distances. It is due primarily to fluctuations in the atmosphere over the propagation path, and from platform motion relative to the intended aimpoint. Also, delivery of high fluence to the target typically requires low beam divergence, thus, atmospheric turbulence, platform motion, or both results in a lack of fine aimpoint control to keep the beam directed at the target. To improve both the beam quality and amount of laser energy delivered to the target, Northrop Grumman has developed the Active Tracking System (ATS); a novel linear phase conjugation aberration compensation technique. Utilizing a silicon spatial light modulator (SLM) as a dynamic wavefront reversing element, ATS undoes aberrations induced by the atmosphere, platform motion or both. ATS continually tracks the target as well as compensates for atmospheric and platform motion induced aberrations. This results in a high fidelity, near-diffraction limited beam delivered to the target.

Conformational Analysis of Retinoic Acids: Effects of Steric Interactions on Nonplanar Conjugated Polyenes

PubMed Central

Cox, Bryan D.; Muccio, Donald D.; Hamilton, Tracy P.

2013-01-01

Retinoic acids and other vitamin A analogs contain a trimethylcyclohexenyl ring in conjugation with a polyene chain joined at carbon-6 (C6) and carbon-7 (C7). A MP2-SCS/cc-pVDZ// B3LYP/6-31G(d) 2-D potential energy surface was computed for all-trans retinoic acid, which had 6 minima (3 enantiomeric pairs). The global minima were distorted s-gauche enantiomers (6–7 = 53°) with half-chair conformations of the ring. Distorted s-gauche enantiomers (6–7 = 55°) with inverted half-chair ring conformations were 1.7 kJ/mol above the global minima. The s-trans enantiomers (6–7 = 164°) were 11.3 kJ/mol above the global minima. Steric energies were computed by the method of Guo and Karplus to identify key structural elements in retinoic acids which determines their conformation. Small molecule crystal structures in the CCDC database with trimethylcyclohexenyl ring and exocyclic double bonds have ring-chain geometries near to one of the 6 energy minima of retinoic acids, except for retinaldehyde iminium cations. PMID:25798372

Conformational Analysis of Retinoic Acids: Effects of Steric Interactions on Nonplanar Conjugated Polyenes.

PubMed

Cox, Bryan D; Muccio, Donald D; Hamilton, Tracy P

2013-05-01

Retinoic acids and other vitamin A analogs contain a trimethylcyclohexenyl ring in conjugation with a polyene chain joined at carbon-6 (C6) and carbon-7 (C7). A MP2-SCS/cc-pVDZ// B3LYP/6-31G(d) 2-D potential energy surface was computed for all- trans retinoic acid, which had 6 minima (3 enantiomeric pairs). The global minima were distorted s-gauche enantiomers ( 6-7 = 53°) with half-chair conformations of the ring. Distorted s-gauche enantiomers ( 6-7 = 55°) with inverted half-chair ring conformations were 1.7 kJ/mol above the global minima. The s-trans enantiomers ( 6-7 = 164°) were 11.3 kJ/mol above the global minima. Steric energies were computed by the method of Guo and Karplus to identify key structural elements in retinoic acids which determines their conformation. Small molecule crystal structures in the CCDC database with trimethylcyclohexenyl ring and exocyclic double bonds have ring-chain geometries near to one of the 6 energy minima of retinoic acids, except for retinaldehyde iminium cations.

Measuring ITS deployment and integration

DOT National Transportation Integrated Search

1999-01-01

A consistent and simple methodology was developed to assess both the level of deployment of individual ITS elements and the level of integration between these elements. This method is based on the metropolitan ITS infrastructure, a blueprint defined ...

Nonlinear transient analysis by energy minimization: A theoretical basis for the ACTION computer code. [predicting the response of a lightweight aircraft during a crash

NASA Technical Reports Server (NTRS)

Kamat, M. P.

1980-01-01

The formulation basis for establishing the static or dynamic equilibrium configurations of finite element models of structures which may behave in the nonlinear range are provided. With both geometric and time independent material nonlinearities included, the development is restricted to simple one and two dimensional finite elements which are regarded as being the basic elements for modeling full aircraft-like structures under crash conditions. Representations of a rigid link and an impenetrable contact plane are added to the deformation model so that any number of nodes of the finite element model may be connected by a rigid link or may contact the plane. Equilibrium configurations are derived as the stationary conditions of a potential function of the generalized nodal variables of the model. Minimization of the nonlinear potential function is achieved by using the best current variable metric update formula for use in unconstrained minimization. Powell's conjugate gradient algorithm, which offers very low storage requirements at some slight increase in the total number of calculations, is the other alternative algorithm to be used for extremely large scale problems.

Versatile plasmid-based expression systems for Gram-negative bacteria--General essentials exemplified with the bacterium Ralstonia eutropha H16.

PubMed

Gruber, Steffen; Schwab, Helmut; Koefinger, Petra

2015-12-25

The Gram-negative bacterium Escherichia coli is currently the most efficient and widely used prokaryotic host for recombinant protein and metabolite production. However, due to some limitations and to various interesting features of other Gram-negative bacteria efficient vector systems applicable to a broad range are desired. Basic building blocks for plasmid-based vectors include besides the need for a suitable selection marker in the first line a proper replication and maintenance system. In addition to these basic requirements, further elements are needed for Gram-negative bacteria beyond E. coli, such as Pseudomonas pudita, Ralstonia eutropha, Burkholderia glumae or Acinetobacter sp.. Established building blocks have to be adapted and new building blocks providing the desired functions need to be identified and exploited. This minireview addresses so far described and used genetic elements for broad host range replication, efficient plasmid maintenance, and conjugative plasmid transfer as well as expression elements and protein secretion signals. The industrially important bacterium R. eutropha H16 was chosen as a model organism to provide specific data on the effectivity and utility of building blocks based on such genetic elements. Copyright © 2015 Elsevier B.V. All rights reserved.

Systems Integration Processes for NASA Ares I Crew Launch Vehicle

NASA Technical Reports Server (NTRS)

Taylor, James L.; Reuter, James L.; Sexton, Jeffrey D.

2006-01-01

NASA's Exploration Initiative will require development of many new elements to constitute a robust system of systems. New launch vehicles are needed to place cargo and crew in stable Low Earth Orbit (LEO). This paper examines the systems integration processes NASA is utilizing to ensure integration and control of propulsion and nonpropulsion elements within NASA's Crew Launch Vehicle (CLV), now known as the Ares I. The objective of the Ares I is to provide the transportation capabilities to meet the Constellation Program requirements for delivering a Crew Exploration Vehicle (CEV) or other payload to LEO in support of the lunar and Mars missions. The Ares I must successfully provide this capability within cost and schedule, and with an acceptable risk approach. This paper will describe the systems engineering management processes that will be applied to assure Ares I Project success through complete and efficient technical integration. Discussion of technical review and management processes for requirements development and verification, integrated design and analysis, integrated simulation and testing, and the integration of reliability, maintainability and supportability (RMS) into the design will also be included. The Ares I Project is logically divided into elements by the major hardware groupings, and associated management, system engineering, and integration functions. The processes to be described herein are designed to integrate within these Ares I elements and among the other Constellation projects. Also discussed is launch vehicle stack integration (Ares I to CEV, and Ground and Flight Operations integration) throughout the life cycle, including integrated vehicle performance through orbital insertion, recovery of the first stage, and reentry of the upper stage. The processes for decomposing requirements to the elements and ensuring that requirements have been correctly validated, decomposed, and allocated, and that the verification requirements are properly defined to ensure that the system design meets requirements, will be discussed.

Engineering of dendrimer surfaces to enhance transepithelial transport and reduce cytotoxicity.

PubMed

Jevprasesphant, Rachaneekorn; Penny, Jeffrey; Attwood, David; McKeown, Neil B; D'Emanuele, Antony

2003-10-01

To evaluate the cytotoxicity, permeation, and transport mechanisms of PAMAM dendrimers and surface-modified cationic PAMAM dendrimers using monolayers of the human colon adenocarcinoma cell line, Caco-2. Cytotoxicity was determined using the MTT assay. The effect of dendrimers on monolayer integrity was determined from measurements of transepithelial electrical resistance (TEER) and [14C]mannitol apparent permeability coefficient (Papp). The Papp of dendrimers through monolayers was measured in both the apical (A)-to-basolateral (B) and B --> A directions at 4 degrees C and 37 degrees C and also in the presence and absence of ethylenediamine tetraacetic acid (EDTA) and colchicine. The cytotoxicity and permeation of dendrimers increased with both concentration and generation. The cytotoxicity of cationic dendrimers (G2, G3, G4) was greater than that of anionic dendrimers (G2.5, G3.5) but was reduced by conjugation with lauroyl chloride: the least cytotoxic conjugates were those with six attached lauroyl chains. At 37 degrees C the Papp of cationic dendrimers was higher than that of anionic dendrimers and, in general, increased with the number of attached lipid chains. Cationic dendrimers decreased TEER and significantly increased the Papp of mannitol. Modified dendrimers also reduced TEER and caused a more marked increase in the Papp of mannitol. The Papp values of dendrimers and modified dendrimers were higher in the presence of EDTA, lower in the presence of colchicine, and lower at 4 degrees C than at 37 degrees C. The properties of dendrimers may be significantly modified by surface engineering. Conjugation of cationic PAMAM dendrimers with lauroyl chloride decreased their cytotoxicity and increased their permeation through Caco-2 cell monolayers. Both PAMAM dendrimers and lauroyl-PAMAM dendrimer conjugates can cross epithelial monolayers by paracellular and transcellular pathways.

Magnetic iodixanol - a novel contrast agent and its early characterization.

PubMed

Arokiaraj, M C; Menesson, E; Feltin, N

2018-02-01

Contrast-induced nephropathy is a commonly encountered problem in clinical practice. The purpose of the study was to design and develop a novel contrast agent, which could be used to prevent contrast-induced nephropathy in the future. In total, 20-220nm magnetic nanoparticles were conjugated with iodixanol, and their radio-opacity and magnetic properties were assessed thereafter. Scanning electron microscopy pictures were acquired. Thereafter, the nanoparticles conjugate was tested in cell culture (HUVEC cells), and Quantibody ® assay was studied after cell treatment in 1:5 dilutions for 48h, compared with control. The conjugate preparation had an adequate radio-opacity. A 4mm magnetic bubble was attached to a bar magnet and the properties were studied. The magnetic bubble maintained its structural integrity in all angles including antigravity position. Scanning electron microscopy showed magnetic nanoparticles in all pictures and the particles are of 100-400nm agglomerates with primary particle sizes of roughly 20nm. 1:5 diluted particles had no effect on secretion of IL-1a, IL-1b, IL-4, IL-10, IL-13 and TNFa. Particles increased secretion of IL-8 from 24h and 48h. Secretion of IFNg was also increased when particles were added to the cells as early as 1h. Likewise, IL-6 was strongly secreted by HUVEC treated with particles from 24h incubation time. In contrast, the secretion of MCP-1 was slightly reduced on HUVEC treated with particles. There is potential for a novel iodixanol-magnetic nanoparticle conjugate to be used in cineradiography. Further investigations need to be performed to study its performance in vitro and in vivo. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Activatable iRGD-based peptide monolith: Targeting, internalization, and fluorescence activation for precise tumor imaging.

PubMed

Cho, Hong-Jun; Lee, Sung-Jin; Park, Sung-Jun; Paik, Chang H; Lee, Sang-Myung; Kim, Sehoon; Lee, Yoon-Sik

2016-09-10

A disulfide-bridged cyclic RGD peptide, named iRGD (internalizing RGD, c(CRGDK/RGPD/EC)), is known to facilitate tumor targeting as well as tissue penetration. After the RGD motif-induced targeting on αv integrins expressed near tumor tissue, iRGD encounters proteolytic cleavage to expose the CendR motif that promotes penetration into cancer cells via the interaction with neuropilin-1. Based on these proteolytic cleavage and internalization mechanism, we designed an iRGD-based monolithic imaging probe that integrates multiple functions (cancer-specific targeting, internalization and fluorescence activation) within a small peptide framework. To provide the capability of activatable fluorescence signaling, we conjugated a fluorescent dye to the N-terminal of iRGD, which was linked to the internalizing sequence (CendR motif), and a quencher to the opposite C-terminal. It turned out that fluorescence activation of the dye/quencher-conjugated monolithic peptide probe requires dual (reductive and proteolytic) cleavages on both disulfide and amide bond of iRGD peptide. Furthermore, the cleavage of the iRGD peptide leading to fluorescence recovery was indeed operative depending on the tumor-related angiogenic receptors (αvβ3 integrin and neuropilin-1) in vitro as well as in vivo. Compared to an 'always fluorescent' iRGD control probe without quencher conjugation, the dye/quencher-conjugated activatable monolithic peptide probe visualized tumor regions more precisely with lower background noise after intravenous injection, owing to the multifunctional responses specific to tumor microenvironment. All these results, along with minimal in vitro and in vivo toxicity profiles, suggest potential of the iRGD-based activatable monolithic peptide probe as a promising imaging agent for precise tumor diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.